Incorporating Topic Assignment Constraint and Topic Correlation Limitation into Clinical Goal Discovering for Clinical Pathway Mining

PubMed Central

Xu, Xiao; Wei, Zhijie

2017-01-01

Clinical pathways are widely used around the world for providing quality medical treatment and controlling healthcare cost. However, the expert-designed clinical pathways can hardly deal with the variances among hospitals and patients. It calls for more dynamic and adaptive process, which is derived from various clinical data. Topic-based clinical pathway mining is an effective approach to discover a concise process model. Through this approach, the latent topics found by latent Dirichlet allocation (LDA) represent the clinical goals. And process mining methods are used to extract the temporal relations between these topics. However, the topic quality is usually not desirable due to the low performance of the LDA in clinical data. In this paper, we incorporate topic assignment constraint and topic correlation limitation into the LDA to enhance the ability of discovering high-quality topics. Two real-world datasets are used to evaluate the proposed method. The results show that the topics discovered by our method are with higher coherence, informativeness, and coverage than the original LDA. These quality topics are suitable to represent the clinical goals. Also, we illustrate that our method is effective in generating a comprehensive topic-based clinical pathway model. PMID:29065617

Ubiquitin-proteasome pathway and cellular responses to oxidative stress

USDA-ARS?s Scientific Manuscript database

The ubiquitin-proteasome pathway (UPP) is the primary cytosolic proteolytic machinery for the selective degradation of various forms of damaged proteins. Thus, the UPP is an important protein quality control mechanism. In the canonical UPP, both ubiquitin and the 26S proteasome are involved. Subs...

Design, implementation, and quality control in the Pathways American-Indian multicenter trial

PubMed Central

Stone, Elaine J.; Norman, James E.; Davis, Sally M.; Stewart, Dawn; Clay, Theresa E.; Caballero, Ben; Lohman, Timothy G.; Murray, David M.

2016-01-01

Background Pathways was the first multicenter American-Indian school-based study to test the effectiveness of an obesity prevention program promoting healthy eating and physical activity. Methods Pathways employed a nested cohort design in which 41 schools were randomized to intervention or control conditions and students within these schools were followed as a cohort (1,704 third graders at baseline). The study’s primary endpoint was percent body fat. Secondary endpoints were levels of fat in school lunches; time spent in physical activity; and knowledge, attitudes, and behaviors regarding diet and exercise. Quality control (QC) included design of data management systems which provided standardization and quality assurance of data collection and processing. Data QC procedures at study centers included manuals of operation, training and certification, and monitoring of performance. Process evaluation was conducted to monitor dose and fidelity of the interventions. Registration and tracking systems were used for students and schools. Results No difference in mean percent body fat at fifth grade was found between the intervention and control schools. Percent of calories from fat and saturated fat in school lunches was significantly reduced in the intervention schools as was total energy intake from 24-hour recalls. Significant increases in self-reported physical activity levels and knowledge of healthy behaviors were found for the intervention school students. Conclusions The Pathways study results provide evidence demonstrating the role schools can play in public health promotion. Its study design and QC systems and procedures provide useful models for other similar school based multi- or single-site studies. PMID:14636805

Hospitalist management of vaso-occlusive pain crisis in patients with sickle cell disease using a pathway of care.

PubMed

Allen Liles, Edmund; Kirsch, Jonathan; Gilchrist, Michael; Adem, Mukhtar

2014-04-01

Patients with sickle cell disease (SCD) suffer from intermittent vaso-occlusive pain crises (VOCs). These crises lead to frequent hospitalizations, significant morbidity, and increased mortality risk. Care pathways can enhance efficiency and quality of care. Our study sought to evaluate the development and implementation of a care pathway for patients with SCD experiencing VOCs. The University of North Carolina (UNC) Comprehensive Sickle Cell Program provides all levels of care for a large population of patients with sickle cell anemia. All patients admitted to UNC Hospitals with SCD VOCs from January 2009 through June 2011 were evaluated. During this time period, we also assessed sequential prospective cohorts during progressive phases of developing and implementing a quality improvement and pathway of care program for this patient population in our study. The developed pathway entailed geographic localization for VOC patients, a single group of faculty physicians caring for these patients, and early use of patient-controlled analgesia (PCA) to achieve pain control. Physicians from the UNC Hospital Medicine Program were responsible for the initiatives. Cohorts were compared to a baseline historical control. Outcomes of interest included patient length of stay (LOS) in the hospital, 30-day readmission rate, need for transfusion, incidence of acute chest syndrome, use of naloxone, and use of PCA. Compared with an historical baseline cohort, the development and implementation of a VOC care pathway for patients with SCD led to reduction in average hospital LOS by 1.44 days (P < 0.05) and an increase in use of PCAs (P < 0.05). Patient readmission rates, number of transfusions, incidence of acute chest syndrome, and use of naloxone did not significantly change. Hospitalist-led management of patients with SCD VOCs using a care pathway that emphasizes early, aggressive PCA-based pain control is associated with reduced hospital LOS. The LOS reduction seen in our study is clinically meaningful. Notably, other measures of patient outcomes and quality of care metrics did not change significantly, and some trended towards improvement.

Parkin and PINK1 function in a vesicular trafficking pathway regulating mitochondrial quality control

PubMed Central

McLelland, Gian-Luca; Soubannier, Vincent; Chen, Carol X; McBride, Heidi M; Fon, Edward A

2014-01-01

Mitochondrial dysfunction has long been associated with Parkinson's disease (PD). Parkin and PINK1, two genes associated with familial PD, have been implicated in the degradation of depolarized mitochondria via autophagy (mitophagy). Here, we describe the involvement of parkin and PINK1 in a vesicular pathway regulating mitochondrial quality control. This pathway is distinct from canonical mitophagy and is triggered by the generation of oxidative stress from within mitochondria. Wild-type but not PD-linked mutant parkin supports the biogenesis of a population of mitochondria-derived vesicles (MDVs), which bud off mitochondria and contain a specific repertoire of cargo proteins. These MDVs require PINK1 expression and ultimately target to lysosomes for degradation. We hypothesize that loss of this parkin- and PINK1-dependent trafficking mechanism impairs the ability of mitochondria to selectively degrade oxidized and damaged proteins leading, over time, to the mitochondrial dysfunction noted in PD. PMID:24446486

Total Quality Management Analysis of LAMPS MK 1 Aviation Maintenance Data

DTIC Science & Technology

1992-06-05

Qualit Control? The Japanese Way by Dr. Kaoru Ishikawa translated by David J. Lu offers the Japanese version of Total Quality Management. Dr...causes to an effect or problem. It is called the Ishikawa Diagram after its inventor Kaoru Ishikawa , a pioneer in quality control. The name fishbone...pathways involved. 2) Cause and Effect Diagram (also known as an Ishikawa Diagram or a Fishbone Diagram). This diagram used to identify the causes, and

The loss of SMG1 causes defects in quality control pathways in Physcomitrella patens

PubMed Central

Lang, Daniel; Zimmer, Andreas D; Causier, Barry

2018-01-01

Abstract Nonsense-mediated mRNA decay (NMD) is important for RNA quality control and gene regulation in eukaryotes. NMD targets aberrant transcripts for decay and also directly influences the abundance of non-aberrant transcripts. In animals, the SMG1 kinase plays an essential role in NMD by phosphorylating the core NMD factor UPF1. Despite SMG1 being ubiquitous throughout the plant kingdom, little is known about its function, probably because SMG1 is atypically absent from the genome of the model plant, Arabidopsis thaliana. By combining our previously established SMG1 knockout in moss with transcriptome-wide analysis, we reveal the range of processes involving SMG1 in plants. Machine learning assisted analysis suggests that 32% of multi-isoform genes produce NMD-targeted transcripts and that splice junctions downstream of a stop codon act as the major determinant of NMD targeting. Furthermore, we suggest that SMG1 is involved in other quality control pathways, affecting DNA repair and the unfolded protein response, in addition to its role in mRNA quality control. Consistent with this, smg1 plants have increased susceptibility to DNA damage, but increased tolerance to unfolded protein inducing agents. The potential involvement of SMG1 in RNA, DNA and protein quality control has major implications for the study of these processes in plants. PMID:29596649

Characterization of phenylpropanoid pathway genes within European maize (Zea mays L.) inbreds

PubMed Central

Andersen, Jeppe Reitan; Zein, Imad; Wenzel, Gerhard; Darnhofer, Birte; Eder, Joachim; Ouzunova, Milena; Lübberstedt, Thomas

2008-01-01

Background Forage quality of maize is influenced by both the content and structure of lignins in the cell wall. Biosynthesis of monolignols, constituting the complex structure of lignins, is catalyzed by enzymes in the phenylpropanoid pathway. Results In the present study we have amplified partial genomic fragments of six putative phenylpropanoid pathway genes in a panel of elite European inbred lines of maize (Zea mays L.) contrasting in forage quality traits. Six loci, encoding C4H, 4CL1, 4CL2, C3H, F5H, and CAD, displayed different levels of nucleotide diversity and linkage disequilibrium (LD) possibly reflecting different levels of selection. Associations with forage quality traits were identified for several individual polymorphisms within the 4CL1, C3H, and F5H genomic fragments when controlling for both overall population structure and relative kinship. A 1-bp indel in 4CL1 was associated with in vitro digestibility of organic matter (IVDOM), a non-synonymous SNP in C3H was associated with IVDOM, and an intron SNP in F5H was associated with neutral detergent fiber. However, the C3H and F5H associations did not remain significant when controlling for multiple testing. Conclusion While the number of lines included in this study limit the power of the association analysis, our results imply that genetic variation for forage quality traits can be mined in phenylpropanoid pathway genes of elite breeding lines of maize. PMID:18173847

Role for ribosome-associated complex and stress-seventy subfamily B (RAC-Ssb) in integral membrane protein translation.

PubMed

Acosta-Sampson, Ligia; Döring, Kristina; Lin, Yuping; Yu, Vivian Y; Bukau, Bernd; Kramer, Günter; Cate, Jamie H D

2017-12-01

Targeting of most integral membrane proteins to the endoplasmic reticulum is controlled by the signal recognition particle, which recognizes a hydrophobic signal sequence near the protein N terminus. Proper folding of these proteins is monitored by the unfolded protein response and involves protein degradation pathways to ensure quality control. Here, we identify a new pathway for quality control of major facilitator superfamily transporters that occurs before the first transmembrane helix, the signal sequence recognized by the signal recognition particle, is made by the ribosome. Increased rates of translation elongation of the N-terminal sequence of these integral membrane proteins can divert the nascent protein chains to the ribosome-associated complex and stress-seventy subfamily B chaperones. We also show that quality control of integral membrane proteins by ribosome-associated complex-stress-seventy subfamily B couples translation rate to the unfolded protein response, which has implications for understanding mechanisms underlying human disease and protein production in biotechnology. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

Feasibility of personalised remote long-term follow-up of people with cochlear implants: a randomised controlled trial.

PubMed

Cullington, Helen; Kitterick, Padraig; Weal, Mark; Margol-Gromada, Magdalena

2018-04-20

Substantial resources are required to provide lifelong postoperative care to people with cochlear implants. Most patients visit the clinic annually. We introduced a person-centred remote follow-up pathway, giving patients telemedicine tools to use at home so they would only visit the centre when intervention was required. To assess the feasibility of comparing a remote care pathway with the standard pathway in adults using cochlear implants. Two-arm randomised controlled trial. Randomisation used a minimisation approach, controlling for potential confounding factors. Participant blinding was not possible, but baseline measures occurred before allocation. University of Southampton Auditory Implant Service: provider of National Health Service care. 60 adults who had used cochlear implants for at least 6 months. Control group (n=30) followed usual care pathway.Remote care group (n=30) received care remotely for 6 months incorporating: home hearing in noise test, online support tool and self-adjustment of device (only 10 had compatible equipment). Primary: change in patient activation; measured using the Patient Activation Measure.Secondary: change in hearing and quality of life; qualitative feedback from patients and clinicians. One participant in the remote care group dropped out. The remote care group showed a greater increase in patient activation than the control group. Changes in hearing differed between the groups. The remote care group improved on the Triple Digit Test hearing test; the control group perceived their hearing was worse on the Speech, Spatial and Qualities of Hearing Scale questionnaire. Quality of life remained unchanged in both groups. Patients and clinicians were generally positive about remote care tools and wanted to continue. Adults with cochlear implants were willing to be randomised and complied with the protocol. Personalised remote care for long-term follow-up is feasible and acceptable, leading to more empowered patients. ISRCTN14644286. © Article author(s) (or their employer(s) unless otherwise stated in the text of the article) 2018. All rights reserved. No commercial use is permitted unless otherwise expressly granted.

Feasibility of personalised remote long-term follow-up of people with cochlear implants: a randomised controlled trial

PubMed Central

Kitterick, Padraig; Weal, Mark; Margol-Gromada, Magdalena

2018-01-01

Introduction Substantial resources are required to provide lifelong postoperative care to people with cochlear implants. Most patients visit the clinic annually. We introduced a person-centred remote follow-up pathway, giving patients telemedicine tools to use at home so they would only visit the centre when intervention was required. Objectives To assess the feasibility of comparing a remote care pathway with the standard pathway in adults using cochlear implants. Design Two-arm randomised controlled trial. Randomisation used a minimisation approach, controlling for potential confounding factors. Participant blinding was not possible, but baseline measures occurred before allocation. Setting University of Southampton Auditory Implant Service: provider of National Health Service care. Participants 60 adults who had used cochlear implants for at least 6 months. Interventions Control group (n=30) followed usual care pathway. Remote care group (n=30) received care remotely for 6 months incorporating: home hearing in noise test, online support tool and self-adjustment of device (only 10 had compatible equipment). Main outcome measures Primary: change in patient activation; measured using the Patient Activation Measure. Secondary: change in hearing and quality of life; qualitative feedback from patients and clinicians. Results One participant in the remote care group dropped out. The remote care group showed a greater increase in patient activation than the control group. Changes in hearing differed between the groups. The remote care group improved on the Triple Digit Test hearing test; the control group perceived their hearing was worse on the Speech, Spatial and Qualities of Hearing Scale questionnaire. Quality of life remained unchanged in both groups. Patients and clinicians were generally positive about remote care tools and wanted to continue. Conclusions Adults with cochlear implants were willing to be randomised and complied with the protocol. Personalised remote care for long-term follow-up is feasible and acceptable, leading to more empowered patients. Trial registration number ISRCTN14644286. PMID:29678970

A Six-Year Predictive Test of Adolescent Family Relationship Quality and Effortful Control Pathways to Emerging Adult Social and Emotional Health

PubMed Central

Fosco, Gregory M.; Caruthers, Allison S.; Dishion, Thomas J.

2012-01-01

This longitudinal study examined how a multimethod (youth report, parent report, direct observation) assessment of family relationship quality (cohesion and conflict) in adolescence (age 16 –17) predicted growth and maintenance of effortful control across ages 17, 22, and 23 years old, and, ultimately, subjective well-being, emotional distress, and aggressive behavior in emerging adulthood (23). A diverse sample of 792 youth at age 17 and their families, and youth at ages 22 and 23, were studied to examine family cohesion and conflict and the growth and maintenance of effortful control as predictors of emerging adult social and emotional health. Results indicated that family cohesion and conflict during late adolescence and mean-level effortful control at age 22 each served as unique pathways to emerging adult adjustment. These findings underscore the importance of family functioning during adolescence and the maintenance of effortful control into emerging adulthood for understanding adjustment during the emerging adulthood period. PMID:22709261

The impact of care pathways for exacerbation of Chronic Obstructive Pulmonary Disease: rationale and design of a cluster randomized controlled trial

PubMed Central

2010-01-01

Background Hospital treatment of chronic obstructive pulmonary disease (COPD) frequently does not follow published evidences. This lack of adherence can contribute to the high morbidity, mortality and readmissions rates. The European Quality of Care Pathway (EQCP) study on acute exacerbations of COPD (NTC00962468) is undertaken to determine how care pathways (CP) as complex intervention for hospital treatment of COPD affects care variability, adherence to evidence based key interventions and clinical outcomes. Methods An international cluster Randomized Controlled Trial (cRCT) will be performed in Belgium, Italy, Ireland and Portugal. Based on the power analysis, a sample of 40 hospital teams and 398 patients will be included in the study. In the control arm of the study, usual care will be provided. The experimental teams will implement a CP as complex intervention which will include three active components: a formative evaluation of the quality and organization of care, a set of evidence based key interventions, and support on the development and implementation of the CP. The main outcome will be six-month readmission rate. As a secondary endpoint a set of clinical outcome and performance indicators (including care process evaluation and team functioning indicators) will be measured in both groups. Discussion The EQCP study is the first international cRCT on care pathways. The design of the EQCP project is both a research study and a quality improvement project and will include a realistic evaluation framework including process analysis to further understand why and when CP can really work. Trial Registration number NCT00962468 PMID:21092098

The Arabidopsis endoplasmic reticulum associated degradation pathways are involved in the regulation of heat stress response

DOE Office of Scientific and Technical Information (OSTI.GOV)

Li, Lin-Mao; University of Chinese Academy of Sciences, Beijing; Lü, Shi-You

Abstracts: The Cytosolic Protein Response (CPR) in the cytosol and the Unfolded Protein Response (UPR) and ER-associated degradation (ERAD) in the endoplasmic reticulum are major pathways of the cellular proteostasis network. However, despite years of effort, how these protein quality control systems coordinated in vivo remains largely unknown, particularly in plants. In this study, the roles of two evolutionarily conserved ERAD pathways (DOA10 and HRD1) in heat stress response were investigated through reverse genetic approaches in Arabidopsis. Phenotypic analysis of the mutants showed that the two ERAD pathways additively play negative roles in heat tolerance, which was demonstrated by higher survivalmore » rate and lower electrolyte leakage in the loss of function mutants compared to the wild type plants. Importantly, gene expression analysis revealed that the mutant plants showed elevated transcriptional regulation of several downstream genes, including those encoding CPR and UPR marker genes, under both basal and heat stress conditions. Finally, multiple components of ERAD genes exhibited rapid response to increasing temperature. Taken together, our data not only unravels key insights into the crosstalk between different protein quality control processes, but also provides candidate genes to genetically improve plant heat tolerance in the future. - Highlights: • ERAD pathways cooperatively regulate plant thermotolerance. • ERAD pathways cooperatively regulate UPR and CPR. • ERAD components gene expression are upregulated by heat stress.« less

Mitochondrial quality control and communications with the nucleus are important in maintaining mitochondrial function and cell health☆☆☆

PubMed Central

Kotiadis, Vassilios N.; Duchen, Michael R.; Osellame, Laura D.

2014-01-01

Background The maintenance of cell metabolism and homeostasis is a fundamental characteristic of living organisms. In eukaryotes, mitochondria are the cornerstone of these life supporting processes, playing leading roles in a host of core cellular functions, including energy transduction, metabolic and calcium signalling, and supporting roles in a number of biosynthetic pathways. The possession of a discrete mitochondrial genome dictates that the maintenance of mitochondrial ‘fitness’ requires quality control mechanisms which involve close communication with the nucleus. Scope of review This review explores the synergistic mechanisms that control mitochondrial quality and function and ensure cellular bioenergetic homeostasis. These include antioxidant defence mechanisms that protect against oxidative damage caused by reactive oxygen species, while regulating signals transduced through such free radicals. Protein homeostasis controls import, folding, and degradation of proteins underpinned by mechanisms that regulate bioenergetic capacity through the mitochondrial unfolded protein response. Autophagic machinery is recruited for mitochondrial turnover through the process of mitophagy. Mitochondria also communicate with the nucleus to exact specific transcriptional responses through retrograde signalling pathways. Major conclusions The outcome of mitochondrial quality control is not only reliant on the efficient operation of the core homeostatic mechanisms but also in the effective interaction of mitochondria with other cellular components, namely the nucleus. General significance Understanding mitochondrial quality control and the interactions between the organelle and the nucleus will be crucial in developing therapies for the plethora of diseases in which the pathophysiology is determined by mitochondrial dysfunction. This article is part of a Special Issue entitled Frontiers of Mitochondrial Research. PMID:24211250

The Liverpool Care Pathway for cancer patients dying in hospital medical wards: a before-after cluster phase II trial of outcomes reported by family members.

PubMed

Costantini, Massimo; Pellegrini, Fabio; Di Leo, Silvia; Beccaro, Monica; Rossi, Carla; Flego, Guia; Romoli, Vittoria; Giannotti, Michela; Morone, Paola; Ivaldi, Giovanni P; Cavallo, Laura; Fusco, Flavio; Higginson, Irene J

2014-01-01

Hospital is the most common place of cancer death but concerns regarding the quality of end-of-life care remain. Preliminary assessment of the effectiveness of the Liverpool Care Pathway on the quality of end-of-life care provided to adult cancer patients during their last week of life in hospital. Uncontrolled before-after intervention cluster trial. The trial was performed within four hospital wards participating in the pilot implementation of the Italian version of the Liverpool Care Pathway programme. All cancer patients who died in the hospital wards 2-4 months before and after the implementation of the Italian version of Liverpool Care Pathway were identified. A total of 2 months after the patient's death, bereaved family members were interviewed using the Toolkit After-Death Family Interview (seven 0-100 scales assessing the quality of end-of-life care) and the Italian version of the Views of Informal Carers - Evaluation of Services (VOICES) (three items assessing pain, breathlessness and nausea-vomiting). An interview was obtained for 79 family members, 46 (73.0%) before and 33 (68.8%) after implementation of the Italian version of Liverpool Care Pathway. Following Italian version of Liverpool Care Pathway implementation, there was a significant improvement in the mean scores of four Toolkit scales: respect, kindness and dignity (+16.8; 95% confidence interval = 3.6-30.0; p = 0.015); family emotional support (+20.9; 95% confidence interval = 9.6-32.3; p < 0.001); family self-efficacy (+14.3; 95% confidence interval = 0.3-28.2; p = 0.049) and coordination of care (+14.3; 95% confidence interval = 4.2-24.3; p = 0.007). No significant improvement in symptom' control was observed. These results provide the first robust data collected from family members of a preliminary clinically significant improvement, in some aspects, of quality of care after the implementation of the Italian version of Liverpool Care Pathway programme. The poor effect for symptom control suggests areas for further innovation and development.

Implementation and evaluation of a clinical pathway for TRAM breast reconstruction.

PubMed

Hwang, T G; Wilkins, E G; Lowery, J C; Gentile, J

2000-02-01

Among strategies recently proposed to reduce practice variation, promote quality, and control costs in health care delivery, the concept of the clinical pathway has received considerable attention. Because transverse rectus abdominis musculocutaneous (TRAM) breast reconstruction is a common and often costly intervention, this institution sought to evaluate cost and quality outcomes of a clinical pathways program for this procedure. The TRAM reconstruction clinical pathway was implemented in April of 1996 to standardize postoperative care in this patient population. Outcomes of consecutive pathway cases for the first 14 months of the program were assessed in a retrospective cohort design, by using all nonpathway TRAM cases from the 18 months immediately before pathway implementation as controls. Outcomes assessed included length of hospital stay, postoperative complications, total postoperative charges, and total postoperative costs in relative value units. Data on these dependent variables were collected from hospital charts and billing records. The effects of pathway implementation on the outcomes of interest were analyzed by using analysis of covariance to control for potential confounding by other independent variables, including surgical site (unilateral versus bilateral reconstructions), technique (pedicle versus free TRAMs), timing (immediate versus delayed reconstructions), and patient age. Finally, a comparison of variances in the outcomes of interest between the two groups was analyzed by using an Ftest. For all statistical tests, p values of < or = 0.05 were considered significant. Twenty-nine patients were treated in the TRAM pathway group, whereas the control population included 40 nonpathway patients. After implementation of the TRAM pathway, length of stay decreased from 6.0 to 5.2 days; total postoperative charges were reduced from $8587 to $7744; and total postoperative relative value unit utilization declined from 1686 to 1104. Analysis of covariance showed that the decreases in length of hospital stay and relative value units in the TRAM pathway were statistically significant (p = 0.05 and p = 0.007, respectively). By contrast, no significant increase in complications was observed after pathway implementation. Variability in the TRAM pathway group, as measured by SD, decreased significantly for both length of hospital stay (p = 0.039) and relative value units (p = 0.023). Implementation of the TRAM reconstruction clinical pathway resulted in significant declines in length of hospital stay and total costs. These decreases in resource utilization had no significant effect on postoperative complication rates. Although additional research is needed to further assess the impact of clinical pathways, this approach offers considerable promise for improving the cost-effectiveness of health care.

Metabolic Reprogramming in Leaf Lettuce Grown Under Different Light Quality and Intensity Conditions Using Narrow-Band LEDs.

PubMed

Kitazaki, Kazuyoshi; Fukushima, Atsushi; Nakabayashi, Ryo; Okazaki, Yozo; Kobayashi, Makoto; Mori, Tetsuya; Nishizawa, Tomoko; Reyes-Chin-Wo, Sebastian; Michelmore, Richard W; Saito, Kazuki; Shoji, Kazuhiro; Kusano, Miyako

2018-05-21

Light-emitting diodes (LEDs) are an artificial light source used in closed-type plant factories and provide a promising solution for a year-round supply of green leafy vegetables, such as lettuce (Lactuca sativa L.). Obtaining high-quality seedlings using controlled irradiation from LEDs is critical, as the seedling health affects the growth and yield of leaf lettuce after transplantation. Because key molecular pathways underlying plant responses to a specific light quality and intensity remain poorly characterised, we used a multi-omics-based approach to evaluate the metabolic and transcriptional reprogramming of leaf lettuce seedlings grown under narrow-band LED lighting. Four types of monochromatic LEDs (one blue, two green and one red) and white fluorescent light (control) were used at low and high intensities (100 and 300 μmol·m -2 ·s -1 , respectively). Multi-platform mass spectrometry-based metabolomics and RNA-Seq were used to determine changes in the metabolome and transcriptome of lettuce plants in response to different light qualities and intensities. Metabolic pathway analysis revealed distinct regulatory mechanisms involved in flavonoid and phenylpropanoid biosynthetic pathways under blue and green wavelengths. Taken together, these data suggest that the energy transmitted by green light is effective in creating a balance between biomass production and the production of secondary metabolites involved in plant defence.

Hippo pathway deficiency reverses systolic heart failure after infarction.

PubMed

Leach, John P; Heallen, Todd; Zhang, Min; Rahmani, Mahdis; Morikawa, Yuka; Hill, Matthew C; Segura, Ana; Willerson, James T; Martin, James F

2017-10-12

Mammalian organs vary widely in regenerative capacity. Poorly regenerative organs, such as the heart are particularly vulnerable to organ failure. Once established, heart failure commonly results in mortality. The Hippo pathway, a kinase cascade that prevents adult cardiomyocyte proliferation and regeneration, is upregulated in human heart failure. Here we show that deletion of the Hippo pathway component Salvador (Salv) in mouse hearts with established ischaemic heart failure after myocardial infarction induces a reparative genetic program with increased scar border vascularity, reduced fibrosis, and recovery of pumping function compared with controls. Using translating ribosomal affinity purification, we isolate cardiomyocyte-specific translating messenger RNA. Hippo-deficient cardiomyocytes have increased expression of proliferative genes and stress response genes, such as the mitochondrial quality control gene, Park2. Genetic studies indicate that Park2 is essential for heart repair, suggesting a requirement for mitochondrial quality control in regenerating myocardium. Gene therapy with a virus encoding Salv short hairpin RNA improves heart function when delivered at the time of infarct or after ischaemic heart failure following myocardial infarction was established. Our findings indicate that the failing heart has a previously unrecognized reparative capacity involving more than cardiomyocyte renewal.

Transcriptional profiling of cork oak phellogenic cells isolated by laser microdissection.

PubMed

Teixeira, Rita Teresa; Fortes, Ana Margarida; Bai, Hua; Pinheiro, Carla; Pereira, Helena

2018-02-01

The phenylpropanoid pathway impacts the cork quality development. In cork of bad quality, the flavonoid route is favored, whereas in good quality, cork lignin and suberin production prevails. Cork oaks develop a thick cork tissue as a protective shield that results of the continuous activity of a secondary meristem, the cork cambium, or phellogen. Most studies applied to developmental processes do not consider the cell types from which the samples were extracted. Here, laser microdissection (LM) coupled with transcript profiling using RNA sequencing (454 pyrosequencing) was applied to phellogen cells of trees producing low- and good quality cork. Functional annotation and functional enrichment analyses showed that stress-related genes are enriched in samples extracted from trees producing good quality cork (GQC). This process is under tight transcriptional (transcription factors, kinases) regulation and also hormonal control involving ABA, ethylene, and auxins. The phellogen cells collected from trees producing bad quality cork (BQC) show a consistent up-regulation of genes belonging to the flavonoid pathway as a response to stress. They also display a different modulation of cell wall genes resulting into a thinner cork layer, i.e., less meristematic activity. Based on the analysis of the phenylpropanoid pathway regulating genes, in GQC, the synthesis of lignin and suberin is promoted, whereas in BQC, the same pathway favors the biosynthesis of free phenolic compounds. This study provided new insights of how cell-specific gene expression can determine tissue and organ morphology and physiology and identified robust candidate genes that can be used in breeding programs aiming at improving cork quality.

Preparation and Analysis of RNA Crystals

NASA Technical Reports Server (NTRS)

Todd, Paul

2000-01-01

The crystallization of RiboNucleic Acids (RNA) was studied from the standpoint of mechanisms of crystal growth in three tasks: (1) preparation of high-quality crystals of oligonuclotides for X-ray diffraction, (2) finding pathways to the growth of high-quality crystals for X-ray diffraction and (3) investigation of mechanisms of action of inertial acceleration on crystal growth. In these tasks: (1) RNA crystals were prepared and studied by X-ray diffraction; (2) a pathway to high-quality crystals was discovered and characterized; a combination of kinetic and equilibrium factors could be optimized as described below; and (3) an interplay between purity and gravity was found in a combination of space and ground experiments with nucleic acids and proteins. Most significantly, the rate of concentration of precipitant and RNA can be controlled by membrane-based methods of water removal or by diffusion of multivalent cations across an interface stabilized by a membrane. Oligonucleotide solutions are electrokinetically stabilized colloids, and crystals can form by the controlled addition of multivalent cations.

Retrograde transfer RNA nuclear import provides a new level of tRNA quality control in Saccharomyces cerevisiae.

PubMed

Kramer, Emily B; Hopper, Anita K

2013-12-24

In eukaryotes, transfer RNAs (tRNAs) are transcribed in the nucleus yet function in the cytoplasm; thus, tRNA movement within the cell was believed to be unidirectional--from the nucleus to the cytoplasm. It is now known that mature tRNAs also move in a retrograde direction from the cytoplasm to the nucleus via retrograde tRNA nuclear import, a process that is conserved from yeast to vertebrates. The biological significance of this tRNA nuclear import is not entirely clear. We hypothesized that retrograde tRNA nuclear import might function in proofreading tRNAs to ensure that only proper tRNAs reside in the cytoplasm and interact with the translational machinery. Here we identify two major types of aberrant tRNAs in yeast: a 5', 3' end-extended, spliced tRNA and hypomodified tRNAs. We show that both types of aberrant tRNAs accumulate in mutant cells that are defective in tRNA nuclear traffic, suggesting that they are normally imported into the nucleus and are repaired or degraded. The retrograde pathway functions in parallel with the cytoplasmic rapid tRNA decay pathway previously demonstrated to monitor tRNA quality, and cells are not viable if they lack both pathways. Our data support the hypothesis that the retrograde process provides a newly discovered level of tRNA quality control as a pathway that monitors both end processing of pre-tRNAs and the modification state of mature tRNAs.

Retrograde transfer RNA nuclear import provides a new level of tRNA quality control in Saccharomyces cerevisiae

PubMed Central

Kramer, Emily B.; Hopper, Anita K.

2013-01-01

In eukaryotes, transfer RNAs (tRNAs) are transcribed in the nucleus yet function in the cytoplasm; thus, tRNA movement within the cell was believed to be unidirectional—from the nucleus to the cytoplasm. It is now known that mature tRNAs also move in a retrograde direction from the cytoplasm to the nucleus via retrograde tRNA nuclear import, a process that is conserved from yeast to vertebrates. The biological significance of this tRNA nuclear import is not entirely clear. We hypothesized that retrograde tRNA nuclear import might function in proofreading tRNAs to ensure that only proper tRNAs reside in the cytoplasm and interact with the translational machinery. Here we identify two major types of aberrant tRNAs in yeast: a 5′, 3′ end-extended, spliced tRNA and hypomodified tRNAs. We show that both types of aberrant tRNAs accumulate in mutant cells that are defective in tRNA nuclear traffic, suggesting that they are normally imported into the nucleus and are repaired or degraded. The retrograde pathway functions in parallel with the cytoplasmic rapid tRNA decay pathway previously demonstrated to monitor tRNA quality, and cells are not viable if they lack both pathways. Our data support the hypothesis that the retrograde process provides a newly discovered level of tRNA quality control as a pathway that monitors both end processing of pre-tRNAs and the modification state of mature tRNAs. PMID:24297920

The impact of an empowering Internet-based Breast Cancer Patient Pathway program on breast cancer patients' clinical outcomes: a randomised controlled trial.

PubMed

Ryhänen, Anne M; Rankinen, Sirkku; Siekkinen, Mervi; Saarinen, Maiju; Korvenranta, Heikki; Leino-Kilpi, Helena

2013-04-01

To evaluate the effect of the Breast Cancer Patient Pathway program on breast cancer patient's empowerment process. The results of earlier studies indicate that the use of tailored Internet-based patient education programs increased patient's knowledge level; however, other outcome measures differed. This randomised control trial studied the effect of the Internet-based patient educational program on breast cancer patients' empowerment. In this study, we measured the quality of life, anxiety and managing with treatment-related side effects as the outcomes of breast cancer patients' empowering process. Breast cancer patients who were Internet users in one Finnish university hospital during 2008-2010 were randomised to the control group (n=43) and the intervention group (n=47). Baseline data were collected first in the hospital and the following data seven times during the treatment process, the last time one year after breast cancer diagnosis. There were no statistically significant differences in the quality of life, anxiety or side effects of treatment between the groups. The amount of treatment-related side effects was connected to both physical and psychological well-being. In this study, the Breast Cancer Patient Pathway program did not decrease anxiety level or treatment-related side effects among breast cancer patients or improve subscales of quality of life when compared with controls. There is a need to relieve the side effects caused by patients' care with the help of patient education. Internet-based patient education programs need more focus when developing new patient education methods. © 2013 Blackwell Publishing Ltd.

Reduction of Inpatient Hospital Length of Stay in Lumbar Fusion Patients With Implementation of an Evidence-Based Clinical Care Pathway.

PubMed

Bradywood, Alison; Farrokhi, Farrokh; Williams, Barbara; Kowalczyk, Mark; Blackmore, C Craig

2017-02-01

Quality improvement with before and after evaluation of the intervention. To improve lumbar spine postoperative care and quality outcomes through a series of Lean quality improvement events designed to address root causes of error and variation. Lumbar spine fusion procedures are common, but highly variable in process of care, outcomes, and cost. We implemented a standardized lumbar spine fusion clinical care pathway through a series of Lean quality improvement events. The pathway included an evidence-based electronic order set; a patient visual tool; and multidisciplinary communication, and was designed to delineate expectations for patients, staff, and providers. To evaluate the effectiveness of the intervention, we performed a quality improvement study with before and after evaluation of consecutive patients from January 2012 to September 2014. Outcomes were hospital length of stay and quality measures before and after the April 1, 2013 intervention. Data were analyzed with chi-square and t tests for before and after comparisons, and were explored graphically for temporal trends with statistical process control charts. Our study population was 458 patients (mean 65 years, 65% women). Length of stay decreased from 3.9 to 3.4 days, a difference of 0.5 days (CI 0.3, 0.8, P < 0.001). Discharge disposition also improved with 75% (183/244) being discharged to home postintervention versus 64% (136/214) preintervention (P = 0.002). Urinary catheter removal also improved (P = 0.003). Patient satisfaction scores were not significantly changed. Applying Lean methods to produce standardized clinical pathways is an effective way of improving quality and reducing waste for lumbar spine fusion patients. We believe that quality improvements of this type are valuable for all spine patients, to provide best care outcomes at lowest cost. 4.

Modeling of coupled differential equations for cellular chemical signaling pathways: Implications for assay protocols utilized in cellular engineering.

PubMed

O'Clock, George D

2016-08-01

Cellular engineering involves modification and control of cell properties, and requires an understanding of fundamentals and mechanisms of action for cellular derived product development. One of the keys to success in cellular engineering involves the quality and validity of results obtained from cell chemical signaling pathway assays. The accuracy of the assay data cannot be verified or assured if the effect of positive feedback, nonlinearities, and interrelationships between cell chemical signaling pathway elements are not understood, modeled, and simulated. Nonlinearities and positive feedback in the cell chemical signaling pathway can produce significant aberrations in assay data collection. Simulating the pathway can reveal potential instability problems that will affect assay results. A simulation, using an electrical analog for the coupled differential equations representing each segment of the pathway, provides an excellent tool for assay validation purposes. With this approach, voltages represent pathway enzyme concentrations and operational amplifier feedback resistance and input resistance values determine pathway gain and rate constants. The understanding provided by pathway modeling and simulation is strategically important in order to establish experimental controls for assay protocol structure, time frames specified between assays, and assay concentration variation limits; to ensure accuracy and reproducibility of results.

[A strategy of constructing the technological system for quality control of Chinese medicine based on process control and management].

PubMed

Cheng, Yi-Yu; Qian, Zhong-Zhi; Zhang, Bo-Li

2017-01-01

The current situation, bottleneck problems and severe challenges in quality control technology of Chinese Medicine (CM) are briefly described. It is presented to change the phenomenon related to the post-test as the main means and contempt for process control in drug regulation, reverse the situation of neglecting the development of process control and management technology for pharmaceutical manufacture and reconstruct the technological system for quality control of CM products. The regulation and technology system based on process control and management for controlling CM quality should be established to solve weighty realistic problems of CM industry from the root causes, including backwardness of quality control technology, weakness of quality risk control measures, poor reputation of product quality and so on. By this way, the obstacles from poor controllability of CM product quality could be broken. Concentrating on those difficult problems and weak links in the technical field of CM quality control, it is proposed to build CMC (Chemistry, Manufacturing and Controls) regulation for CM products with Chinese characteristics and promote the regulation international recognition as soon as possible. The CMC technical framework, which is clinical efficacy-oriented, manufacturing manner-centered and process control-focused, was designed. To address the clinical characteristics of traditional Chinese medicine (TCM) and the production feature of CM manufacture, it is suggested to establish quality control engineering for CM manufacturing by integrating pharmaceutical analysis, TCM chemistry, TCM pharmacology, pharmaceutical engineering, control engineering, management engineering and other disciplines. Further, a theoretical model of quality control engineering for CM manufacturing and the methodology of digital pharmaceutical engineering are proposed. A technology pathway for promoting CM standard and realizing the strategic goal of CM internationalization is elaborated. Copyright© by the Chinese Pharmaceutical Association.

The effect of G protein-coupled receptor kinase 2 (GRK2) on lactation and on proliferation of mammary epithelial cells from dairy cows.

PubMed

Hou, Xiaoming; Hu, Hongliu; Lin, Ye; Qu, Bo; Gao, Xuejun; Li, Qingzhang

2016-07-01

Milk protein is an important component of milk and a nutritional source for human consumption. To better understand the molecular events underlying synthesis of milk proteins, the global gene expression patterns in mammary glands of dairy cow with high-quality milk (>3% milk protein; >3.5% milk fat) and low-quality milk (<3% milk protein; <3.5% milk fat) were examined via digital gene expression study. A total of 139 upregulated and 66 downregulated genes were detected in the mammary tissues of lactating cows with high-quality milk compared with the tissues of cows with low-quality milk. A pathway enrichment study of these genes revealed that the top 5 pathways that were differentially affected in the tissues of cows with high- versus low-quality milk involved metabolic pathways, cancer, cytokine-cytokine receptor interactions, regulation of the actin cytoskeleton, and insulin signaling. We also found that the G protein-coupled receptor kinase 2 (GRK2) was one of the most highly upregulated genes in lactating mammary tissue with low-quality milk compared with tissue with high-quality milk. The knockdown of GRK2 in cultured bovine mammary epithelial cells enhanced CSN2 expression and activated signaling molecules related to translation, including protein kinase B, mammalian target of rapamycin, and p70 ribosomal protein S6 kinase 1 (S6K1), whereas overexpression of GRK2 had the opposite effects. However, expression of genes involved in the mitogen-activated protein kinase pathway was positively regulated by GRK2. Therefore, GRK2 seems to act as a negative mediator of milk-protein synthesis via the protein kinase B-mammalian target of rapamycin signaling axis. Furthermore, GRK2 may negatively control milk-protein synthesis by activating the mitogen-activated protein kinase pathway in dairy cow mammary epithelial cells. Copyright © 2016 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Intergenerational volunteering and quality of life: mixed methods evaluation of a randomized control trial involving persons with mild to moderate dementia.

PubMed

George, Daniel R

2011-09-01

This article reports on a mixed methods evaluation of a randomized control trial in Cleveland, Ohio, USA, that assessed whether an intergenerational volunteering intervention could enhance quality of life (QOL) for persons with mild to moderate dementia. Fifteen participants were randomized into intervention and control groups. The intervention group participated in hour-long volunteer sessions with a kindergarten class and an older elementary class in alternating weeks over a 5-month interval. Psychometric data on cognitive functioning, stress, depression, sense of purpose, and sense of usefulness were collected at baseline and at the close of the intervention, and change scores were computed and analyzed for all variables. Ethnography was carried out through the duration of the study, and narrative interviews were held with participants and caregivers. A modified grounded theory approach was used for qualitative analysis. Quantitative analysis demonstrated a significant decrease in stress for the intervention group. Qualitative analysis identified three main pathways through which intergenerational volunteering affected QOL: perceived health benefits, sense of purpose and sense of usefulness, and relationships. Mixed methods evaluation demonstrated that intergenerational volunteering might enhance quality of life through several key pathways, most significantly reduced stress.

A Small RNA-Catalytic Argonaute Pathway Tunes Germline Transcript Levels to Ensure Embryonic Divisions

PubMed Central

Gerson-Gurwitz, Adina; Wang, Shaohe; Sathe, Shashank; Green, Rebecca; Yeo, Gene W.; Oegema, Karen; Desai, Arshad

2016-01-01

SUMMARY Multiple division cycles without growth are a characteristic feature of early embryogenesis. The female germline loads proteins and RNAs into oocytes to support these divisions, which lack many quality control mechanisms operating in somatic cells undergoing growth. Here we describe a small RNA-Argonaute pathway that ensures early embryonic divisions in C. elegans by employing catalytic slicing activity to broadly tune, instead of silence, germline gene expression. Misregulation of one target, a kinesin-13 microtubule depolymerase, underlies a major phenotype associated with pathway loss. Tuning of target transcript levels is guided by density of homologous small RNAs, whose generation must ultimately be related to target sequence. Thus, the tuning action of a small RNA-catalytic Argonaute pathway generates oocytes capable of supporting embryogenesis. We speculate that the specialized nature of germline chromatin led to emergence of small RNA-catalytic Argonaute pathways in the female germline as a post-transcriptional control layer to optimize oocyte composition. PMID:27020753

A probabilistic atlas of human brainstem pathways based on connectome imaging data.

PubMed

Tang, Yuchun; Sun, Wei; Toga, Arthur W; Ringman, John M; Shi, Yonggang

2018-04-01

The brainstem is a critical structure that regulates vital autonomic functions, houses the cranial nerves and their nuclei, relays motor and sensory information between the brain and spinal cord, and modulates cognition, mood, and emotions. As a primary relay center, the fiber pathways of the brainstem include efferent and afferent connections among the cerebral cortex, spinal cord, and cerebellum. While diffusion MRI has been successfully applied to map various brain pathways, its application for the in vivo imaging of the brainstem pathways has been limited due to inadequate resolution and large susceptibility-induced distortion artifacts. With the release of high-resolution data from the Human Connectome Project (HCP), there is increasing interest in mapping human brainstem pathways. Previous works relying on HCP data to study brainstem pathways, however, did not consider the prevalence (>80%) of large distortions in the brainstem even after the application of correction procedures from the HCP-Pipeline. They were also limited in the lack of adequate consideration of subject variability in either fiber pathways or region of interests (ROIs) used for bundle reconstruction. To overcome these limitations, we develop in this work a probabilistic atlas of 23 major brainstem bundles using high-quality HCP data passing rigorous quality control. For the large-scale data from the 500-Subject release of HCP, we conducted extensive quality controls to exclude subjects with severe distortions in the brainstem area. After that, we developed a systematic protocol to manually delineate 1300 ROIs on 20 HCP subjects (10 males; 10 females) for the reconstruction of fiber bundles using tractography techniques. Finally, we leveraged our novel connectome modeling techniques including high order fiber orientation distribution (FOD) reconstruction from multi-shell diffusion imaging and topography-preserving tract filtering algorithms to successfully reconstruct the 23 fiber bundles for each subject, which were then used to calculate the probabilistic atlases in the MNI152 space for public release. In our experimental results, we demonstrate that our method yielded anatomically faithful reconstruction of the brainstem pathways and achieved improved performance in comparison with an existing atlas of cerebellar peduncles based on HCP data. These atlases have been publicly released on NITRIC (https://www.nitrc.org/projects/brainstem_atlas/) and can be readily used by brain imaging researchers interested in studying brainstem pathways. Copyright © 2017 Elsevier Inc. All rights reserved.

Effects of a clinical pathway for video-assisted thoracoscopic surgery (VATS) on quality and cost of care.

PubMed

Schwarzbach, Matthias H M; Ronellenfitsch, Ulrich; Wang, Qian; Rössner, Eric D; Denz, Christof; Post, Stefan; Hohenberger, Peter

2010-04-01

The purpose of this study was to evaluate effects of a clinical pathway (CP) for video-assisted thoracoscopic surgery (VATS) on process quality, outcome quality, and hospital costs. We implemented a CP for VATS and compared 34 patients treated with CP to 77 patients treated without CP. Indicators for process quality were duration of catheter placement, pain intensity, respiratory exercising, and mobilization. Outcome quality was measured through morbidity, mortality, reoperations, and readmissions. Cost of hospital stay was calculated using an imputed daily rate. Foley catheters were removed significantly earlier after CP implementation. All patients on CP were mobilized and received pulmonary exercising on the operation day. Pain levels were low after CP implementation. Median hospital stay significantly reduced by 5 days. Perioperative outcome quality remained unchanged. Costs significantly diminished by 1,510 Euro per stay. CP implementation had positive effects on process quality. Specifically, catheter management was improved and a good pain control achieved. Patients benefited from shortened stay and were treated at lower cost. A clear effect on outcome quality was not found. CPs are a promising tool for quality improvement and cost containment in thoracic surgery.

tRNA biology charges to the front

PubMed Central

Phizicky, Eric M.; Hopper, Anita K.

2010-01-01

tRNA biology has come of age, revealing an unprecedented level of understanding and many unexpected discoveries along the way. This review highlights new findings on the diverse pathways of tRNA maturation, and on the formation and function of a number of modifications. Topics of special focus include the regulation of tRNA biosynthesis, quality control tRNA turnover mechanisms, widespread tRNA cleavage pathways activated in response to stress and other growth conditions, emerging evidence of signaling pathways involving tRNA and cleavage fragments, and the sophisticated intracellular tRNA trafficking that occurs during and after biosynthesis. PMID:20810645

Autophagy modulation as a potential therapeutic target for diverse diseases

PubMed Central

Rubinsztein, David C.; Codogno, Patrice; Levine, Beth

2012-01-01

Autophagy is an essential, conserved lysosomal degradation pathway that controls the quality of the cytoplasm by eliminating protein aggregates and damaged organelles. It begins when double-membraned autophagosomes engulf portions of the cytoplasm, which is followed by fusion of these vesicles with lysosomes and degradation of the autophagic contents. In addition to its vital homeostatic role, this degradation pathway is involved in various human disorders, including metabolic conditions, neurodegenerative diseases, cancers and infectious diseases. This article provides an overview of the mechanisms and regulation of autophagy, the role of this pathway in disease and strategies for therapeutic modulation. PMID:22935804

Biobehavioral Influences on Cancer Progression

PubMed Central

Costanzo, Erin S.; Sood, Anil K.; Lutgendorf, Susan K.

2010-01-01

Synopsis This review focuses on the contributions of stress-related behavioral factors to cancer growth and metastasis and the biobehavioral mechanisms underlying these relationships. We describe behavioral factors that are important in modulation of the stress response and the pivotal role of neuroendocrine regulation in the downstream alteration of physiological pathways relevant to cancer control, including the cellular immune response, inflammation, and tumor angiogenesis, invasion, and cell-signaling pathways. Consequences for cancer progression and metastasis, as well as quality of life, are delineated. Finally, behavioral and pharmacological interventions for cancer patients with the potential to alter these biobehavioral pathways are discussed. PMID:21094927

Role of photoexcited nitrogen dioxide chemistry on ozone formation and emission control strategy over the Pearl River Delta, China

EPA Science Inventory

A new hydroxyl radical formation pathway via photo-excited nitrogen dioxide chemistry is incorporated into a chemistry-only box model as well as a 3D air quality model to examine its potential role on ozone formation and emission control strategy over the Pearl River Delta region...

Smell of Stress: Identification of Induced Biochemical Pathways Affecting the Volatile Composition and Flavor Quality of Crops.

PubMed

Wüst, Matthias

2018-04-11

Recent research has shown that the biosynthesis of several key odorants is controlled by genes whose expression is altered or even induced by biotic or abiotic stress. These new findings provide a roadmap for improvement of flavor quality by the application of moderate, well-controlled stress. This strategy aims at reducing the flavor deficiencies in modern commercial varieties as a "green" alternative to genetic engineering. The workflow for a successful implementation of this approach, from the identification of key odorants by molecular science techniques to the investigation of mechanisms controlling their biosynthesis, is complex and calls for interdisciplinary research.

Prefoldin Promotes Proteasomal Degradation of Cytosolic Proteins with Missense Mutations by Maintaining Substrate Solubility

PubMed Central

Young, Barry P.; Loewen, Christopher J.; Mayor, Thibault

2016-01-01

Misfolded proteins challenge the ability of cells to maintain protein homeostasis and can accumulate into toxic protein aggregates. As a consequence, cells have adopted a number of protein quality control pathways to prevent protein aggregation, promote protein folding, and target terminally misfolded proteins for degradation. In this study, we employed a thermosensitive allele of the yeast Guk1 guanylate kinase as a model misfolded protein to investigate degradative protein quality control pathways. We performed a flow cytometry based screen to identify factors that promote proteasomal degradation of proteins misfolded as the result of missense mutations. In addition to the E3 ubiquitin ligase Ubr1, we identified the prefoldin chaperone subunit Gim3 as an important quality control factor. Whereas the absence of GIM3 did not impair proteasomal function or the ubiquitination of the model substrate, it led to the accumulation of the poorly soluble model substrate in cellular inclusions that was accompanied by delayed degradation. We found that Gim3 interacted with the Guk1 mutant allele and propose that prefoldin promotes the degradation of the unstable model substrate by maintaining the solubility of the misfolded protein. We also demonstrated that in addition to the Guk1 mutant, prefoldin can stabilize other misfolded cytosolic proteins containing missense mutations. PMID:27448207

Does the CONSORT checklist for abstracts improve the quality of reports of randomized controlled trials on clinical pathways?

PubMed

Cui, Qi; Tian, Jinhui; Song, Xuping; Yang, Kehu

2014-12-01

The extension of the Consolidated Standards of Reporting Trials (CONSORT) statement provides reporting guidelines to improve the reporting quality of randomized controlled trials (RCTs). This present study was aim to assess the reporting quality of abstracts of RCTs on clinical pathway. Eight databases were searched from inception to November 2012 to identify RCTs. We extracted basic information and CONSORT items from abstracts. Each abstract was assessed independently by two reviewers. Statistical analyses were performed with SPSS 13.0. Level of significance was set at P < 0.05. 328 abstracts were included. 300 (91.5%) were published in Chinese, of which 292 were published on high impact factor journals. 28 English abstracts were all published on Science Citation Index (SCI) journals. (1) Intervention, objective and outcome were almost fully reported in all abstracts, while recruitment and funding were never reported. (2) There are nine items (P < 0.05) in Chinese that were of low quality compared with in English. There was statistically difference on total score between Chinese and English abstracts (P < 0.00001). (3) There was no difference in any items between high and low impact factor journal in China. (4) In SCI journals, there were significant changes in reporting for three items trial design (P = 0.026), harms (P = 0.039) and trial registration (P = 0.019) in different periods (pre- and post-CONSORT), but only the numbers of randomized (P = 0.003) changed in Chinese abstracts. The reporting quality of abstracts of RCTs on clinical pathway still should be improved. After the publication of CONSORT for abstracts guideline, the RCT abstracts reporting quality were improvement to some extent. The abstracts in Chinese journals showed non-adherence to the CONSORT for abstracts guidelines. © 2014 John Wiley & Sons, Ltd.

Impacts of Lowered Urban Air Temperatures on Precursor Emission and Ozone Air Quality.

PubMed

Taha, Haider; Konopacki, Steven; Akbari, Hashem

1998-09-01

Meteorological, photochemical, building-energy, and power plant simulations were performed to assess the possible precursor emission and ozone air quality impacts of decreased air temperatures that could result from implementing the "cool communities" concept in California's South Coast Air Basin (SoCAB). Two pathways are considered. In the direct pathway, a reduction in cooling energy use translates into reduced demand for generation capacity and, thus, reduced precursor emissions from electric utility power plants. In the indirect pathway, reduced air temperatures can slow the atmospheric production of ozone as well as precursor emission from anthropogenic and biogenic sources. The simulations suggest small impacts on emissions following implementation of cool communities in the SoCAB. In summer, for example, there can be reductions of up to 3% in NO x emissions from in-basin power plants. The photochemical simulations suggest that the air quality impacts of these direct emission reductions are small. However, the indirect atmospheric effects of cool communities can be significant. For example, ozone peak concentrations can decrease by up to 11% in summer and population-weighted exceedance exposure to ozone above the California and National Ambient Air Quality Standards can decrease by up to 11 and 17%, respectively. The modeling suggests that if these strategies are combined with others, such as mobile-source emission control, the improvements in ozone air quality can be substantial.

Associations between Proprioceptive Neural Pathway Structural Connectivity and Balance in People with Multiple Sclerosis

PubMed Central

Fling, Brett W.; Dutta, Geetanjali Gera; Schlueter, Heather; Cameron, Michelle H.; Horak, Fay B.

2014-01-01

Mobility and balance impairments are a hallmark of multiple sclerosis (MS), affecting nearly half of patients at presentation and resulting in decreased activity and participation, falls, injuries, and reduced quality of life. A growing body of work suggests that balance impairments in people with mild MS are primarily the result of deficits in proprioception, the ability to determine body position in space in the absence of vision. A better understanding of the pathophysiology of balance disturbances in MS is needed to develop evidence-based rehabilitation approaches. The purpose of the current study was to (1) map the cortical proprioceptive pathway in vivo using diffusion-weighted imaging and (2) assess associations between proprioceptive pathway white matter microstructural integrity and performance on clinical and behavioral balance tasks. We hypothesized that people with MS (PwMS) would have reduced integrity of cerebral proprioceptive pathways, and that reduced white matter microstructure within these tracts would be strongly related to proprioceptive-based balance deficits. We found poorer balance control on proprioceptive-based tasks and reduced white matter microstructural integrity of the cortical proprioceptive tracts in PwMS compared with age-matched healthy controls (HC). Microstructural integrity of this pathway in the right hemisphere was also strongly associated with proprioceptive-based balance control in PwMS and controls. Conversely, while white matter integrity of the right hemisphere’s proprioceptive pathway was significantly correlated with overall balance performance in HC, there was no such relationship in PwMS. These results augment existing literature suggesting that balance control in PwMS may become more dependent upon (1) cerebellar-regulated proprioceptive control, (2) the vestibular system, and/or (3) the visual system. PMID:25368564

Associations between Proprioceptive Neural Pathway Structural Connectivity and Balance in People with Multiple Sclerosis.

PubMed

Fling, Brett W; Dutta, Geetanjali Gera; Schlueter, Heather; Cameron, Michelle H; Horak, Fay B

2014-01-01

Mobility and balance impairments are a hallmark of multiple sclerosis (MS), affecting nearly half of patients at presentation and resulting in decreased activity and participation, falls, injuries, and reduced quality of life. A growing body of work suggests that balance impairments in people with mild MS are primarily the result of deficits in proprioception, the ability to determine body position in space in the absence of vision. A better understanding of the pathophysiology of balance disturbances in MS is needed to develop evidence-based rehabilitation approaches. The purpose of the current study was to (1) map the cortical proprioceptive pathway in vivo using diffusion-weighted imaging and (2) assess associations between proprioceptive pathway white matter microstructural integrity and performance on clinical and behavioral balance tasks. We hypothesized that people with MS (PwMS) would have reduced integrity of cerebral proprioceptive pathways, and that reduced white matter microstructure within these tracts would be strongly related to proprioceptive-based balance deficits. We found poorer balance control on proprioceptive-based tasks and reduced white matter microstructural integrity of the cortical proprioceptive tracts in PwMS compared with age-matched healthy controls (HC). Microstructural integrity of this pathway in the right hemisphere was also strongly associated with proprioceptive-based balance control in PwMS and controls. Conversely, while white matter integrity of the right hemisphere's proprioceptive pathway was significantly correlated with overall balance performance in HC, there was no such relationship in PwMS. These results augment existing literature suggesting that balance control in PwMS may become more dependent upon (1) cerebellar-regulated proprioceptive control, (2) the vestibular system, and/or (3) the visual system.

In silico Pathway Activation Network Decomposition Analysis (iPANDA) as a method for biomarker development.

PubMed

Ozerov, Ivan V; Lezhnina, Ksenia V; Izumchenko, Evgeny; Artemov, Artem V; Medintsev, Sergey; Vanhaelen, Quentin; Aliper, Alexander; Vijg, Jan; Osipov, Andreyan N; Labat, Ivan; West, Michael D; Buzdin, Anton; Cantor, Charles R; Nikolsky, Yuri; Borisov, Nikolay; Irincheeva, Irina; Khokhlovich, Edward; Sidransky, David; Camargo, Miguel Luiz; Zhavoronkov, Alex

2016-11-16

Signalling pathway activation analysis is a powerful approach for extracting biologically relevant features from large-scale transcriptomic and proteomic data. However, modern pathway-based methods often fail to provide stable pathway signatures of a specific phenotype or reliable disease biomarkers. In the present study, we introduce the in silico Pathway Activation Network Decomposition Analysis (iPANDA) as a scalable robust method for biomarker identification using gene expression data. The iPANDA method combines precalculated gene coexpression data with gene importance factors based on the degree of differential gene expression and pathway topology decomposition for obtaining pathway activation scores. Using Microarray Analysis Quality Control (MAQC) data sets and pretreatment data on Taxol-based neoadjuvant breast cancer therapy from multiple sources, we demonstrate that iPANDA provides significant noise reduction in transcriptomic data and identifies highly robust sets of biologically relevant pathway signatures. We successfully apply iPANDA for stratifying breast cancer patients according to their sensitivity to neoadjuvant therapy.

In silico Pathway Activation Network Decomposition Analysis (iPANDA) as a method for biomarker development

PubMed Central

Ozerov, Ivan V.; Lezhnina, Ksenia V.; Izumchenko, Evgeny; Artemov, Artem V.; Medintsev, Sergey; Vanhaelen, Quentin; Aliper, Alexander; Vijg, Jan; Osipov, Andreyan N.; Labat, Ivan; West, Michael D.; Buzdin, Anton; Cantor, Charles R.; Nikolsky, Yuri; Borisov, Nikolay; Irincheeva, Irina; Khokhlovich, Edward; Sidransky, David; Camargo, Miguel Luiz; Zhavoronkov, Alex

2016-01-01

Signalling pathway activation analysis is a powerful approach for extracting biologically relevant features from large-scale transcriptomic and proteomic data. However, modern pathway-based methods often fail to provide stable pathway signatures of a specific phenotype or reliable disease biomarkers. In the present study, we introduce the in silico Pathway Activation Network Decomposition Analysis (iPANDA) as a scalable robust method for biomarker identification using gene expression data. The iPANDA method combines precalculated gene coexpression data with gene importance factors based on the degree of differential gene expression and pathway topology decomposition for obtaining pathway activation scores. Using Microarray Analysis Quality Control (MAQC) data sets and pretreatment data on Taxol-based neoadjuvant breast cancer therapy from multiple sources, we demonstrate that iPANDA provides significant noise reduction in transcriptomic data and identifies highly robust sets of biologically relevant pathway signatures. We successfully apply iPANDA for stratifying breast cancer patients according to their sensitivity to neoadjuvant therapy. PMID:27848968

Transcriptional profile of breast muscle in heat stressed layers is similar to that of broiler chickens at control temperature.

PubMed

Zahoor, Imran; de Koning, Dirk-Jan; Hocking, Paul M

2017-09-20

In recent years, the commercial importance of changes in muscle function of broiler chickens and of the corresponding effects on meat quality has increased. Furthermore, broilers are more sensitive to heat stress during transport and at high ambient temperatures than smaller egg-laying chickens. We hypothesised that heat stress would amplify muscle damage and expression of genes that are involved in such changes and, thus, lead to the identification of pathways and networks associated with broiler muscle and meat quality traits. Broiler and layer chickens were exposed to control or high ambient temperatures to characterise differences in gene expression between the two genotypes and the two environments. Whole-genome expression studies in breast muscles of broiler and layer chickens were conducted before and after heat stress; 2213 differentially-expressed genes were detected based on a significant (P < 0.05) genotype × treatment interaction. This gene set was analysed with the BioLayout Express 3D and Ingenuity Pathway Analysis software and relevant biological pathways and networks were identified. Genes involved in functions related to inflammatory reactions, cell death, oxidative stress and tissue damage were upregulated in control broilers compared with control and heat-stressed layers. Expression of these genes was further increased in heat-stressed broilers. Differences in gene expression between broiler and layer chickens under control and heat stress conditions suggest that damage of breast muscles in broilers at normal ambient temperatures is similar to that in heat-stressed layers and is amplified when broilers are exposed to heat stress. The patterns of gene expression of the two genotypes under heat stress were almost the polar opposite of each other, which is consistent with the conclusion that broiler chickens were not able to cope with heat stress by dissipating their body heat. The differentially expressed gene networks and pathways were consistent with the pathological changes that are observed in the breast muscle of heat-stressed broilers.

Specific recommendations for accurate and direct use of PET-CT in PET guided radiotherapy for head and neck sites

DOE Office of Scientific and Technical Information (OSTI.GOV)

Thomas, C. M., E-mail: christopher.thomas@gstt.nhs.uk; Convery, D. J.; Greener, A. G.

2014-04-15

Purpose: To provide specific experience-based guidance and recommendations for centers wishing to develop, validate, and implement an accurate and efficient process for directly using positron emission tomography-computed tomography (PET-CT) for the radiotherapy planning of head and neck cancer patients. Methods: A PET-CT system was modified with hard-top couch, external lasers and radiotherapy immobilization and indexing devices and was subject to a commissioning and quality assurance program. PET-CT imaging protocols were developed specifically for radiotherapy planning and the image quality and pathway tested using phantoms and five patients recruited into an in-house study. Security and accuracy of data transfer was testedmore » throughout the whole data pathway. The patient pathway was fully established and tested ready for implementation in a PET-guided dose-escalation trial for head and neck cancer patients. Results: Couch deflection was greater than for departmental CT simulator machines. An area of high attenuation in the couch generated image artifacts and adjustments were made accordingly. Using newly developed protocols CT image quality was suitable to maintain delineation and treatment accuracy. Upon transfer of data to the treatment planning system a half pixel offset between PET and CT was observed and corrected. By taking this into account, PET to CT alignment accuracy was maintained below 1 mm in all systems in the data pathway. Transfer of structures delineated in the PET fusion software to the radiotherapy treatment planning system was validated. Conclusions: A method to perform direct PET-guided radiotherapy planning was successfully validated and specific recommendations were developed to assist other centers. Of major concern is ensuring that the quality of PET and CT data is appropriate for radiotherapy treatment planning and on-treatment verification. Couch movements can be compromised, bore-size can be a limitation for certain immobilization techniques, laser positioning may affect setup accuracy and couch deflection may be greater than scanners dedicated to radiotherapy. The full set of departmental commissioning and routine quality assurance tests applied to radiotherapy CT simulators must be carried out on the PET-CT scanner. CT image quality must be optimized for radiotherapy planning whilst understanding that the appearance will differ between scanners and may affect delineation. PET-CT quality assurance schedules will need to be added to and modified to incorporate radiotherapy quality assurance. Methods of working for radiotherapy and PET staff will change to take into account considerations of both parties. PET to CT alignment must be subject to quality control on a loaded and unloaded couch preferably using a suitable emission phantom, and tested throughout the whole data pathway. Data integrity must be tested throughout the whole pathway and a system included to verify that delineated structures are transferred correctly. Excellent multidisciplinary team communication and working is vital, and key staff members on both sides should be specifically dedicated to the project. Patient pathway should be clearly devised to optimize patient care and the resources of all departments. Recruitment of a cohort of patients into a methodology study is valuable to test the quality assurance methods and pathway.« less

Best strategies to implement clinical pathways in an emergency department setting: study protocol for a cluster randomized controlled trial.

PubMed

Jabbour, Mona; Curran, Janet; Scott, Shannon D; Guttman, Astrid; Rotter, Thomas; Ducharme, Francine M; Lougheed, M Diane; McNaughton-Filion, M Louise; Newton, Amanda; Shafir, Mark; Paprica, Alison; Klassen, Terry; Taljaard, Monica; Grimshaw, Jeremy; Johnson, David W

2013-05-22

The clinical pathway is a tool that operationalizes best evidence recommendations and clinical practice guidelines in an accessible format for 'point of care' management by multidisciplinary health teams in hospital settings. While high-quality, expert-developed clinical pathways have many potential benefits, their impact has been limited by variable implementation strategies and suboptimal research designs. Best strategies for implementing pathways into hospital settings remain unknown. This study will seek to develop and comprehensively evaluate best strategies for effective local implementation of externally developed expert clinical pathways. We will develop a theory-based and knowledge user-informed intervention strategy to implement two pediatric clinical pathways: asthma and gastroenteritis. Using a balanced incomplete block design, we will randomize 16 community emergency departments to receive the intervention for one clinical pathway and serve as control for the alternate clinical pathway, thus conducting two cluster randomized controlled trials to evaluate this implementation intervention. A minimization procedure will be used to randomize sites. Intervention sites will receive a tailored strategy to support full clinical pathway implementation. We will evaluate implementation strategy effectiveness through measurement of relevant process and clinical outcomes. The primary process outcome will be the presence of an appropriately completed clinical pathway on the chart for relevant patients. Primary clinical outcomes for each clinical pathway include the following: Asthma--the proportion of asthmatic patients treated appropriately with corticosteroids in the emergency department and at discharge; and Gastroenteritis--the proportion of relevant patients appropriately treated with oral rehydration therapy. Data sources include chart audits, administrative databases, environmental scans, and qualitative interviews. We will also conduct an overall process evaluation to assess the implementation strategy and an economic analysis to evaluate implementation costs and benefits. This study will contribute to the body of evidence supporting effective strategies for clinical pathway implementation, and ultimately reducing the research to practice gaps by operationalizing best evidence care recommendations through effective use of clinical pathways. ClinicalTrials.gov: NCT01815710.

Recovery after abdominal wall reconstruction.

PubMed

Jensen, Kristian Kiim

2017-03-01

Incisional hernia is a common long-term complication to abdominal surgery, occurring in more than 20% of all patients. Some of these hernias become giant and affect patients in several ways. This patient group often experiences pain, decreased perceived body image, and loss of physical function, which results in a need for surgical repair of the giant hernia, known as abdominal wall reconstruction. In the current thesis, patients with a giant hernia were examined to achieve a better understanding of their physical and psychological function before and after abdominal wall reconstruction. Study I was a systematic review of the existing standardized methods for assessing quality of life after incisional hernia repair. After a systematic search in the electronic databases Embase and PubMed, a total of 26 studies using standardized measures for assessment of quality of life after incisional hernia repair were found. The most commonly used questionnaire was the generic Short-Form 36, which assesses overall health-related quality of life, addressing both physical and mental health. The second-most common questionnaire was the Carolinas Comfort Scale, which is a disease specific questionnaire addressing pain, movement limitation and mesh sensation in relation to a current or previous hernia. In total, eight different questionnaires were used at varying time points in the 26 studies. In conclusion, standardization of timing and method of quality of life assessment after incisional hernia repair was lacking. Study II was a case-control study of the effects of an enhanced recovery after surgery pathway for patients undergoing abdominal wall reconstruction for a giant hernia. Sixteen consecutive patients were included prospectively after the implementation of a new enhanced recovery after surgery pathway at the Digestive Disease Center, Bispebjerg Hospital, and compared to a control group of 16 patients included retrospectively in the period immediately prior to the implementation of the pathway. The enhanced recovery after surgery pathway included preoperative high-dose steroid, daily assessment of revised discharge criteria and an aggressive approach to restore bowel function (chewing gum and enema on postoperative day two). Patients who followed the enhanced recovery after surgery pathway reported low scores of pain, nausea and fatigue, and were discharged significantly faster than patients in the control group. A non-significant increase in postoperative readmissions and reoperations was observed after the introduction of the enhanced recovery after surgery pathway. Study III and IV were prospective studies of patients undergoing abdominal wall reconstruction for giant incisional hernia, who were compared to a control group of patients with an intact abdominal wall undergoing colorectal resection for benign or low-grade malignant disease. Patients were examined within a week preoperatively and again one year postoperatively. In study III, the respiratory function and respiratory quality of life were assessed, and the results showed that patients with a giant incisional hernia had a decreased expiratory lung function (peak expiratory flow and maximal expiratory pressure) compared to the predicted values and also compared to patients in the control group. Both parameters increased significantly after abdominal wall reconstruction, while no other significant changes were found in objective or subjective measures at one-year follow-up in both groups of patients. Lastly, study IV examined the abdominal wall- and extremity function, as well as overall and disease specific quality of life. We found that patients with a giant hernia had a significantly decreased relative function of the abdominal wall compared to patients with an intact abdominal wall, and that this deficit was offset at one-year follow-up. Patients in the control group showed a postoperative decrease in abdominal wall function, while no changes were found in extremity function in either group. Patients reported improved quality of life after abdominal wall reconstruction. In summary, the studies in this thesis concluded that; standardization of patient-reported outcomes after incisional hernia repair is lacking; enhanced recovery after surgery is feasible: after abdominal wall reconstruction and seems to lower the time to discharge; patients with giant incisional hernia have compromised expiratory lung function and abdominal wall function, both of which are restored one year after abdominal wall reconstruction.

Lack of evidence and standardization in care pathway documents for patients with ST-elevated myocardial infarction.

PubMed

Aeyels, Daan; Van Vugt, Stijn; Sinnaeve, Peter R; Panella, Massimiliano; Van Zelm, Ruben; Sermeus, Walter; Vanhaecht, Kris

2016-04-01

Clinical practice variation and the subsequent burden on health care quality has been documented for patients with ST-elevated myocardial infarction (STEMI). Reduction of clinical practice variation is possible by increasing guideline adherence. Care pathway documents can increase guideline adherence by implementing evidence-based key interventions and quality indicators in daily practice. This study aims to examine guideline adherence of care pathway documents for patients with STEMI. Lay-out, size and timeframe of submitted care pathways documents were analysed. Two independent reviewers used a checklist to systematically assess the guideline adherence of care pathway documents. The checklist comprised a set of key interventions and quality indicators extracted from evidence and international guidelines. The checklist distinguished the evidence level for each item and was validated by expert consensus. Results were verified by inviting participating hospitals to provide feedback. Fifteen out of 25 invited hospitals submitted care pathway documents for STEMI. The care pathway documents differed in timeframe, lay-out and size. Analysis of the care pathway documents showed important variation in formalizing adherence to evidence: between hospitals, inclusion of 24 key interventions in care pathway documents varied from 13 to 97%. Inclusion of 11 essential quality indicators varied from 0 to 40%. Care pathway documents for patients with STEMI differ considerably in lay-out, timeframe and size. This study showed variation in, and suboptimal inclusion of, evidence-based key interventions and quality indicators in care pathway documents. The use of these care pathway documents might result in suboptimal quality of care for STEMI patients. © The European Society of Cardiology 2015.

Biological pathways, candidate genes, and molecular markers associated with quality-of-life domains: an update.

PubMed

Sprangers, Mirjam A G; Thong, Melissa S Y; Bartels, Meike; Barsevick, Andrea; Ordoñana, Juan; Shi, Qiuling; Wang, Xin Shelley; Klepstad, Pål; Wierenga, Eddy A; Singh, Jasvinder A; Sloan, Jeff A

2014-09-01

There is compelling evidence of a genetic foundation of patient-reported quality of life (QOL). Given the rapid development of substantial scientific advances in this area of research, the current paper updates and extends reviews published in 2010. The objective was to provide an updated overview of the biological pathways, candidate genes, and molecular markers involved in fatigue, pain, negative (depressed mood) and positive (well-being/happiness) emotional functioning, social functioning, and overall QOL. We followed a purposeful search algorithm of existing literature to capture empirical papers investigating the relationship between biological pathways and molecular markers and the identified QOL domains. Multiple major pathways are involved in each QOL domain. The inflammatory pathway has the strongest evidence as a controlling mechanism underlying fatigue. Inflammation and neurotransmission are key processes involved in pain perception, and the catechol-O-methyltransferase (COMT) gene is associated with multiple sorts of pain. The neurotransmitter and neuroplasticity theories have the strongest evidence for their relationship with depression. Oxytocin-related genes and genes involved in the serotonergic and dopaminergic pathways play a role in social functioning. Inflammatory pathways, via cytokines, also play an important role in overall QOL. Whereas the current findings need future experiments and replication efforts, they will provide researchers supportive background information when embarking on studies relating candidate genes and/or molecular markers to QOL domains. The ultimate goal of this area of research is to enhance patients' QOL.

Implementation of an Inpatient Pediatric Sepsis Identification Pathway.

PubMed

Bradshaw, Chanda; Goodman, Ilyssa; Rosenberg, Rebecca; Bandera, Christopher; Fierman, Arthur; Rudy, Bret

2016-03-01

Early identification and treatment of severe sepsis and septic shock improves outcomes. We sought to identify and evaluate children with possible sepsis on a pediatric medical/surgical unit through successful implementation of a sepsis identification pathway. The sepsis identification pathway, a vital sign screen and subsequent physician evaluation, was implemented in October 2013. Quality improvement interventions were used to improve physician and nursing adherence with the pathway. We reviewed charts of patients with positive screens on a monthly basis to assess for nursing recognition/physician notification, physician evaluation for sepsis, and subsequent physician diagnosis of sepsis and severe sepsis/septic shock. Adherence data were analyzed on a run chart and statistical process control p-chart. Nursing and physician pathway adherence of >80% was achieved over a 6-month period and sustained for the following 6 months. The direction of improvements met standard criteria for special causes. Over a 1-year period, there were 963 admissions to the unit. Positive screens occurred in 161 (16.7%) of these admissions and 38 (23.5%) of these had a physician diagnosis of sepsis, severe sepsis, or septic shock. One patient with neutropenia and septic shock had a negative sepsis screen due to lack of initial fever. Using quality improvement methodology, we successfully implemented a sepsis identification pathway on our pediatric unit. The pathway provided a standardized process to identify and evaluate children with possible sepsis requiring timely evaluation and treatment. Copyright © 2016 by the American Academy of Pediatrics.

Cost analysis of enhanced recovery after surgery in microvascular breast reconstruction.

PubMed

Oh, Christine; Moriarty, James; Borah, Bijan J; Mara, Kristin C; Harmsen, William S; Saint-Cyr, Michel; Lemaine, Valerie

2018-06-01

Enhanced recovery after surgery (ERAS) pathways have been shown in multiple surgical specialties to decrease hospital length of stay (LOS) after surgery. ERAS in breast reconstruction has been found to decrease hospital LOS and inpatient opioid use. ERAS protocols can facilitate a patient's recovery and can potentially increase the quality of care while decreasing costs. A standardized ERAS pathway was developed through multidisciplinary collaboration. It addressed all phases of surgical care for patients undergoing free-flap breast reconstruction utilizing an abdominal donor site. In this retrospective cohort study, clinical variables associated with hospitalization costs for patients who underwent free-flap breast reconstruction with the ERAS pathway were compared with those of historical controls, termed traditional recovery after surgery (TRAS). All patients included in the study underwent surgery between September 2010 and September 2014. Predicted costs of the study groups were compared using generalized linear modeling. A total of 200 patients were analyzed: 82 in the ERAS cohort and 118 in the TRAS cohort. Clinical variables that were identified to potentially affect costs were found to have a statistically significant difference between groups and included unilateral versus bilateral procedures (p = 0.04) and the need for postoperative blood transfusion (p = 0.03). The cost regression analysis on the two cohorts was adjusted for these significant variables. Adjusted mean costs of patients with ERAS were found to be $4,576 lesser than those of the TRAS control group ($38,688 versus $43,264). Implementation of the ERAS pathway was associated with significantly decreased costs when compared to historical controls. There has been a healthcare focus toward prudent resource allocation, which dictates the need for plastic surgeons to recognize economic evaluation of clinical practice. The ERAS pathway can increase healthcare accountability by improving quality of care while simultaneously decreasing the costs associated with autologous breast reconstruction. Copyright © 2018 British Association of Plastic, Reconstructive and Aesthetic Surgeons. Published by Elsevier Ltd. All rights reserved.

A Decade of Boon or Burden: What Has the CHIP Ever Done for Cellular Protein Quality Control Mechanism Implicated in Neurodegeneration and Aging?

PubMed Central

Joshi, Vibhuti; Amanullah, Ayeman; Upadhyay, Arun; Mishra, Ribhav; Kumar, Amit; Mishra, Amit

2016-01-01

Cells regularly synthesize new proteins to replace old and abnormal proteins for normal cellular functions. Two significant protein quality control pathways inside the cellular milieu are ubiquitin proteasome system (UPS) and autophagy. Autophagy is known for bulk clearance of cytoplasmic aggregated proteins, whereas the specificity of protein degradation by UPS comes from E3 ubiquitin ligases. Few E3 ubiquitin ligases, like C-terminus of Hsc70-interacting protein (CHIP) not only take part in protein quality control pathways, but also plays a key regulatory role in other cellular processes like signaling, development, DNA damage repair, immunity and aging. CHIP targets misfolded proteins for their degradation through proteasome, as well as autophagy; simultaneously, with the help of chaperones, it also regulates folding attempts for misfolded proteins. The broad range of CHIP substrates and their associations with multiple pathologies make it a key molecule to work upon and focus for future therapeutic interventions. E3 ubiquitin ligase CHIP interacts and degrades many protein inclusions formed in neurodegenerative diseases. The presence of CHIP at various nodes of cellular protein-protein interaction network presents this molecule as a potential candidate for further research. In this review, we have explored a wide range of functionality of CHIP inside cells by a detailed presentation of its co-chaperone, E3 and E4 enzyme like functions, with central focus on its protein quality control roles in neurodegenerative diseases. We have also raised many unexplored but expected fundamental questions regarding CHIP functions, which generate hopes for its future applications in research, as well as drug discovery. PMID:27757073

Characterisation of sources and pathways of microbiological pollutants to protect remote private water supplies

NASA Astrophysics Data System (ADS)

Neill, Aaron; Tetzlaff, Doerthe; Strachan, Norval; Hough, Rupert; Soulsby, Chris

2016-04-01

In order to comply with legislation such as the Water Framework Directive and to safeguard public health, there is a critical need to maintain the quality of water sources that are used to supply drinking water. Private water supplies (PWS) are still common in many rural areas in the UK, and are especially vulnerable to poor water quality, owing to the limited treatment they often receive and variable raw water quality in groundwater and surface water sources. A significant issue affecting PWS quality is contamination by faecal pathogens derived from grazing animals or agricultural practices. In Scotland, approximately 20,000 PWS serve around 200,000 people, with a number of these PWS consistently failing to meet water quality targets relating to coliform bacteria and E. coli, both of which can be indicative of faecal contamination (faecal indicator organisms - FIOs). The purpose of our study was to employ integrated empirical and modelling approaches from hydrology and microbiology to elucidate the nature of the still poorly-understood interplay between hydrological flow pathways which connect sources of pathogens to PWS sources, antecedent conditions, seasonality and pathogen transfer risk, for two catchments with contrasting land uses in Scotland: an agricultural catchment (Tarland Burn) and a montane catchment (Bruntland Burn). In the Tarland Burn, 15 years of spatially-distributed samples collected at the catchment-scale of FIO counts were analysed alongside hydrometric data to identify "hot spots" of faecal pathogen transfer risk and possible spatial and temporal controls. We also used a combination of tracer-based and numerical modelling approaches to identify the relationship between hydrological connectivity, flow pathways, and the mobilisation of faecal pathogens from different sources. In the Bruntland Burn, we coupled a pathogen storage, mobilisation and transport scheme to a previously developed tracer-informed hydrological model for the catchment to investigate temporal patterns and controls of pathogen transfer risk from different hydrological source areas identified from extensive past tracer and numerical modelling work: groundwater, hillslopes and the dynamic riparian zone.

A multi-model assessment of the co-benefits of climate mitigation for global air quality

NASA Astrophysics Data System (ADS)

Rao, Shilpa; Klimont, Zbigniew; Leitao, Joana; Riahi, Keywan; van Dingenen, Rita; Aleluia Reis, Lara; Calvin, Katherine; Dentener, Frank; Drouet, Laurent; Fujimori, Shinichiro; Harmsen, Mathijs; Luderer, Gunnar; Heyes, Chris; Strefler, Jessica; Tavoni, Massimo; van Vuuren, Detlef P.

2016-12-01

We present a model comparison study that combines multiple integrated assessment models with a reduced-form global air quality model to assess the potential co-benefits of global climate mitigation policies in relation to the World Health Organization (WHO) goals on air quality and health. We include in our assessment, a range of alternative assumptions on the implementation of current and planned pollution control policies. The resulting air pollution emission ranges significantly extend those in the Representative Concentration Pathways. Climate mitigation policies complement current efforts on air pollution control through technology and fuel transformations in the energy system. A combination of stringent policies on air pollution control and climate change mitigation results in 40% of the global population exposed to PM levels below the WHO air quality guideline; with the largest improvements estimated for India, China, and Middle East. Our results stress the importance of integrated multisector policy approaches to achieve the Sustainable Development Goals.

A Guide to Pathways through the Pre-Five Quality Process.

ERIC Educational Resources Information Center

Strathclyde Regional Council, Glasgow (Scotland).

This guide describes a quality process for external and internal evaluation of the elementary school education department. The term "pathway" is used to define routes through the quality process that describe any school administrative activity in terms of the indicators and examples of good practice. There are five pathways: process…

Water quality degradation effects on freshwater availability: Impacts to human activities

USGS Publications Warehouse

Peters, N.E.; Meybeck, Michel

2000-01-01

The quality of freshwater at any point on the landscape reflects the combined effects of many processes along water pathways. Human activities on all spatial scales affect both water quality and quantity. Alteration of the landscape and associated vegetation has not only changed the water balance, but typically has altered processes that control water quality. Effects of human activities on a small scale are relevant to an entire drainage basin. Furthermore, local, regional, and global differences in climate and water flow are considerable, causing varying effects of human activities on land and water quality and quantity, depending on location within a watershed, geology, biology, physiographic characteristics, and climate. These natural characteristics also greatly control human activities, which will, in turn, modify (or affect) the natural composition of water. One of the most important issues for effective resource management is recognition of cyclical and cascading effects of human activities on the water quality and quantity along hydrologic pathways. The degradation of water quality in one part of a watershed can have negative effects on users downstream. Everyone lives downstream of the effects of some human activity. An extremely important factor is that substances added to the atmosphere, land, and water generally have relatively long time scales for removal or clean up. The nature of the substance, including its affinity for adhering to soil and its ability to be transformed, affects the mobility and the time scale for removal of the substance. Policy alone will not solve many of the degradation issues, but a combination of policy, education, scientific knowledge, planning, and enforcement of applicable laws can provide mechanisms for slowing the rate of degradation and provide human and environmental protection. Such an integrated approach is needed to effectively manage land and water resources.

Proteomic Biomarkers for Acute Interstitial Lung Disease in Gefitinib-Treated Japanese Lung Cancer Patients

PubMed Central

Kawakami, Takao; Nagasaka, Keiko; Takami, Sachiko; Wada, Kazuya; Tu, Hsiao-Kun; Otsuji, Makiko; Kyono, Yutaka; Dobashi, Tae; Komatsu, Yasuhiko; Kihara, Makoto; Akimoto, Shingo; Peers, Ian S.; South, Marie C.; Higenbottam, Tim; Fukuoka, Masahiro; Nakata, Koichiro; Ohe, Yuichiro; Kudoh, Shoji; Clausen, Ib Groth; Nishimura, Toshihide; Marko-Varga, György; Kato, Harubumi

2011-01-01

Interstitial lung disease (ILD) events have been reported in Japanese non-small-cell lung cancer (NSCLC) patients receiving EGFR tyrosine kinase inhibitors. We investigated proteomic biomarkers for mechanistic insights and improved prediction of ILD. Blood plasma was collected from 43 gefitinib-treated NSCLC patients developing acute ILD (confirmed by blinded diagnostic review) and 123 randomly selected controls in a nested case-control study within a pharmacoepidemiological cohort study in Japan. We generated ∼7 million tandem mass spectrometry (MS/MS) measurements with extensive quality control and validation, producing one of the largest proteomic lung cancer datasets to date, incorporating rigorous study design, phenotype definition, and evaluation of sample processing. After alignment, scaling, and measurement batch adjustment, we identified 41 peptide peaks representing 29 proteins best predicting ILD. Multivariate peptide, protein, and pathway modeling achieved ILD prediction comparable to previously identified clinical variables; combining the two provided some improvement. The acute phase response pathway was strongly represented (17 of 29 proteins, p = 1.0×10−25), suggesting a key role with potential utility as a marker for increased risk of acute ILD events. Validation by Western blotting showed correlation for identified proteins, confirming that robust results can be generated from an MS/MS platform implementing strict quality control. PMID:21799770

Effects of a digital clinical pathway for elective electrocardioversion for atrial fibrillation on quality of care.

PubMed

Valente, Mattia; Zwaan, Esther; Wit, Mirjam; Kimman, Geert P; Umans, Victor

2010-12-01

Clinical pathways attempt to increase efficiency by organizing the care-delivery process into individual analyzable steps. However, full advantage may only be taken if the process is governed by a "process care taker." Currently, new opportunities are emerging for nurses to become involved as health care experts and may become an intermediate between patient and clinical team. We evaluate a digital clinical pathway for electrocardioversion in atrial fibrillation with a nurse-coordinator in the ongoing consecutive experience in clinical practice. The introduction of a digital pathway into the hospital information system allows continuous surveillance of clinical outcome indicators as well as variance indicators. This article describes a service evaluation and the implementation and effects of introducing a clinical pathway. However, when comparing the 2 eras, the primary goals were improved guideline-adherence and reduced walk-through times in the 600 consecutive pathway patients versus 100 consecutive control patients. The pathway was launched in January 2008. Up to January 2009, 600 all-comer, elective patients were treated using this integrated digital clinical pathway, without exception. Treatment and outpatient check-up appointments are made immediately for all patients. The pathway enabled the cardiologist to complete the risk calculator and drug therapy recommendations significantly better when compared with control patients and also reduced walk-through times significantly. Patient satisfaction rose from 8.7 to 9.1 (P < 0.01) using the pathway. A nurse-led clinical pathway for cardioversion patients is safely and efficaciously introduced in a teaching hospital. The pathway improved guideline-adherence. These results emphasize the importance of a nurse-coordinator who is an intermediary between atrial fibrillation patients and the clinical care team.

Protecting the proteome: Eukaryotic cotranslational quality control pathways

PubMed Central

2014-01-01

The correct decoding of messenger RNAs (mRNAs) into proteins is an essential cellular task. The translational process is monitored by several quality control (QC) mechanisms that recognize defective translation complexes in which ribosomes are stalled on substrate mRNAs. Stalled translation complexes occur when defects in the mRNA template, the translation machinery, or the nascent polypeptide arrest the ribosome during translation elongation or termination. These QC events promote the disassembly of the stalled translation complex and the recycling and/or degradation of the individual mRNA, ribosomal, and/or nascent polypeptide components, thereby clearing the cell of improper translation products and defective components of the translation machinery. PMID:24535822

Protein quality control: the who’s who, the where’s and therapeutic escapes

PubMed Central

Yam, Gary Hin-Fai; Fan, Jingyu; Hirano, Kiyoko; Gaplovska-Kysela, Katarina; Le Fourn, Valerie; Guhl, Bruno; Santimaria, Roger; Torossi, Tania; Ziak, Martin

2007-01-01

In cells the quality of newly synthesized proteins is monitored in regard to proper folding and correct assembly in the early secretory pathway, the cytosol and the nucleoplasm. Proteins recognized as non-native in the ER will be removed and degraded by a process termed ERAD. ERAD of aberrant proteins is accompanied by various changes of cellular organelles and results in protein folding diseases. This review focuses on how the immunocytochemical labeling and electron microscopic analyses have helped to disclose the in situ subcellular distribution pattern of some of the key machinery proteins of the cellular protein quality control, the organelle changes due to the presence of misfolded proteins, and the efficiency of synthetic chaperones to rescue disease-causing trafficking defects of aberrant proteins. PMID:18075753

The health impacts of women's low control in their living environment: A theory-based systematic review of observational studies in societies with profound gender discrimination.

PubMed

Pennington, Andy; Orton, Lois; Nayak, Shilpa; Ring, Adele; Petticrew, Mark; Sowden, Amanda; White, Martin; Whitehead, Margaret

2018-05-01

We conducted a systematic review of observational evidence on the health impacts of women's low control/autonomy in the living environment in societies with profound gender discrimination and gender bias. Thirty observational studies of varying methodological quality were included. Overall, the evidence suggests that women's lower control or autonomy (for example lack of freedom of movement outside the home, lack of authority to access healthcare for sick children) was associated with poorer mental and physical health for women and higher morbidity and mortality for their children, after adjusting for their socioeconomic circumstances. Further studies are needed to disentangle and understand the pathways between low control and health outcomes in contexts of profound gender discrimination. This systematic review has highlighted the general low quality of the evidence base on this research question. It identifies the pressing need for high quality, longitudinal studies in the future. Crown Copyright © 2018. Published by Elsevier Ltd. All rights reserved.

Water quality assessment using the AREc32 reporter gene assay indicative of the oxidative stress response pathway.

PubMed

Escher, Beate I; Dutt, Mriga; Maylin, Erin; Tang, Janet Y M; Toze, Simon; Wolf, C Roland; Lang, Matti

2012-11-01

The reporter gene assay AREc32 is based on the induction of the Nrf2 mediated oxidative stress response pathway in the human breast cancer cell line MCF7, where eight copies of the antioxidant response element (ARE) are linked to a reporter gene encoding for luciferase. The Nrf2-ARE pathway is responsive to many chemicals that cause oxidative stress, among them a large number of pesticides and skin irritants. We adopted and validated the AREc32 bioassay for water quality testing. tert-Butylhydroquinone served as the positive control, phenol as the negative control and other reactive chemicals were assessed for their specificity. An environmentally relevant reference chemical, benzo(a)pyrene was the most potent inducer of all tested chemicals. The concentration causing an induction ratio (IR) of 1.5 (EC(IR1.5)) was chosen as the effect benchmark value. The assay was applied to 21 water samples ranging from sewage to drinking water, including secondary treatment and various tertiary treatment options (ozonation, biologically activated carbon filtration, membrane filtration, reverse osmosis, advanced oxidation, chlorination, chloramination). The samples were enriched by solid phase extraction. In most samples the oxidative stress response was far more sensitive than cytotoxicity. The primary and secondary treated effluent exceeded the effect threshold IR 1.5 at a relative enrichment factor (REF) of 1, i.e., the native samples were active. All tertiary treated samples were less potent and their EC(IR1.5) lay between REF 1 and 10. The Nrf2 pathway was induced at a REF of approximately 10 for surface waters and drinking water, and above this enrichment cytotoxicity took over in most samples and quenched the induction. The blank (ultrapure water run through the sample enrichment process) was cytotoxic at an REF of 100, which is the limit of concentrations range that can be evaluated. Treatment typically decreased both the cytotoxicity and oxidative stress response apart from drinking water treatment where chlorination caused an increase in oxidative stress response, presumably due to the formation of disinfection by-products. This study demonstrates the relevance and applicability of the oxidative stress response pathway for water quality monitoring.

Evaluating the potential of multi-purpose nature based solutions in peri-urban landscapes - a preliminary assessment

NASA Astrophysics Data System (ADS)

Geris, Josie; Wilkinson, Mark; Stutter, Marc; Guenther, Daniel; Soulsby, Chris

2016-04-01

Many communities across the world face the increasing challenge of balancing water quantity and quality protection and improvement with accommodating new growth and urban development. Urbanisation is typically associated with detrimental changes in water quality, sediment delivery, and effects on water storage and flow pathways (e.g. increases in flooding). Current mitigation solutions are typically based on isolated design strategies used at specific small scale sites and for storm water only. More holistic catchment scale approaches are urgently required to effectively manage the amount of water flows and protect the raw water quality in peri-urban landscapes. This project aims to provide a better understanding of the connectivity between natural and managed flow pathways, storage, and biogeochemical processes in the peri-urban landscape to eventually aid a more integrated water quantity and quality control design. For an actively urbanising catchment in NE Scotland we seek to understand the spatio-temporal character of the natural flow pathways and associated water quality, and how these may be used to support the design of nature based solutions during urbanisation. We present preliminary findings from a dense and multiscale monitoring network that includes hydrometric, tracer (stable water isotopes) and water quality (turbidity (sediment), nitrate, phosphate) data during a range of contrasting hydroclimatological conditions and at different stages of the development of urban infrastructure. These demonstrate a highly variable nature, both temporally and spatially, with water quality dynamics out of sync with storm responses and depending on management practices. This highlights potential difficulties for managing water quantity and quality simultaneously at the catchment scale, and suggests that a treatment train approach may be required. Well-designed nature based solutions that tackle both water quantity and quality issues will require adaptability and a focus on the whole spectrum of the flow regime.

Best strategies to implement clinical pathways in an emergency department setting: study protocol for a cluster randomized controlled trial

PubMed Central

2013-01-01

Background The clinical pathway is a tool that operationalizes best evidence recommendations and clinical practice guidelines in an accessible format for ‘point of care’ management by multidisciplinary health teams in hospital settings. While high-quality, expert-developed clinical pathways have many potential benefits, their impact has been limited by variable implementation strategies and suboptimal research designs. Best strategies for implementing pathways into hospital settings remain unknown. This study will seek to develop and comprehensively evaluate best strategies for effective local implementation of externally developed expert clinical pathways. Design/methods We will develop a theory-based and knowledge user-informed intervention strategy to implement two pediatric clinical pathways: asthma and gastroenteritis. Using a balanced incomplete block design, we will randomize 16 community emergency departments to receive the intervention for one clinical pathway and serve as control for the alternate clinical pathway, thus conducting two cluster randomized controlled trials to evaluate this implementation intervention. A minimization procedure will be used to randomize sites. Intervention sites will receive a tailored strategy to support full clinical pathway implementation. We will evaluate implementation strategy effectiveness through measurement of relevant process and clinical outcomes. The primary process outcome will be the presence of an appropriately completed clinical pathway on the chart for relevant patients. Primary clinical outcomes for each clinical pathway include the following: Asthma—the proportion of asthmatic patients treated appropriately with corticosteroids in the emergency department and at discharge; and Gastroenteritis—the proportion of relevant patients appropriately treated with oral rehydration therapy. Data sources include chart audits, administrative databases, environmental scans, and qualitative interviews. We will also conduct an overall process evaluation to assess the implementation strategy and an economic analysis to evaluate implementation costs and benefits. Discussion This study will contribute to the body of evidence supporting effective strategies for clinical pathway implementation, and ultimately reducing the research to practice gaps by operationalizing best evidence care recommendations through effective use of clinical pathways. Trial registration ClinicalTrials.gov: NCT01815710 PMID:23692634

Cellular homeostasis in fungi: impact on the aging process.

PubMed

Scheckhuber, Christian Q; Hamann, Andrea; Brust, Diana; Osiewacz, Heinz D

2012-01-01

Cellular quality control pathways are needed for maintaining the biological function of organisms. If these pathways become compromised, the results are usually highly detrimental. Functional impairments of cell components can lead to diseases and in extreme cases to organismal death. Dysfunction of cells can be induced by a number of toxic by-products that are formed during metabolic activity, like reactive oxygen and nitrogen species, for example. A key source of reactive oxygen species (ROS) are the organelles of oxidative phosphorylation, mitochondria. Therefore mitochondrial function is also directly affected by ROS, especially if there is a compromised ROS-scavenging capacity. Biological systems therefore depend on several lines of defence to counteract the toxic effects of ROS and other damaging agents. The first level is active at the molecular level and consists of various proteases that bind and degrade abnormally modified and / or aggregated mitochondrial proteins. The second level is concerned with maintaining the quality of whole mitochondria. Among the pathways of this level are mitochondrial dynamics and autophagy (mitophagy). Mitochondrial dynamics describes the time-dependent fusion and fission of mitochondria. It is argued that this kind of organellar dynamics has the power to restore the function of impaired organelles by content mixing with intact organelles. If the first and second lines of defence against damage fail and mitochondria become damaged too severely, there is the option to remove affected cells before they can elicit more damage to their surrounding environment by apoptosis. This form of programmed cell death is strictly regulated by a complex network of interacting components and can be divided into mitochondria-dependent and mitochondria-independent modes of action. In this review we give an overview on various biological quality control systems in fungi (yeasts and filamentous fungi) with an emphasis on autophagy (mitophagy) and apoptosis and how these pathways allow fungal organisms to maintain a balanced cellular homeostasis.

Lean Six Sigma: a new approach to the management of patients undergoing prosthetic hip replacement surgery.

PubMed

Improta, Giovanni; Balato, Giovanni; Romano, Maria; Carpentieri, Francesco; Bifulco, Paolo; Alessandro Russo, Mario; Rosa, Donato; Triassi, Maria; Cesarelli, Mario

2015-08-01

In 2012, health care spending in Italy reached €114.5 billion, accounting for 7.2% of the Gross Domestic Product (GDP) and 14.2% of total public spending. Therefore, reducing waste in health facilities could generate substantial cost savings. The objective of this study is to show that Lean Six Sigma represents an appropriate methodology for the development of a clinical pathway which allows to improve quality and to reduce costs in prosthetic hip replacement surgery. The methodology used for the development of a new clinical pathway was Lean Six Sigma. Problem solving in Lean Six Sigma is the DMAIC (Define, Measure, Analyse, Improve, Control) roadmap, characterized by five operational phases which make possible to reach fixed goals through a rigorous process of defining, measuring, analysing, improving and controlling business problems. The following project indicated several variables influencing the inappropriate prolongation of the length of stay for inpatient treatment and corrective actions were performed to improve the effectiveness and efficiency of the process of care. The average length of stay was reduced from 18.9 to 10.6 days (-44%). This article shows there is no trade-off between quality and costs: Lean Six Sigma improves quality and, at the same time, reduces costs. © 2015 John Wiley & Sons, Ltd.

The effect of long-range air mass transport pathways on PM10 and NO2 concentrations at urban and rural background sites in Ireland: Quantification using clustering techniques.

PubMed

Donnelly, Aoife A; Broderick, Brian M; Misstear, Bruce D

2015-01-01

The specific aims of this paper are to: (i) quantify the effects of various long range transport pathways nitrogen dioxide (NO2) and particulate matter with diameter less than 10μm (PM10) concentrations in Ireland and identify air mass movement corridors which may lead to incidences poor air quality for application in forecasting; (ii) compare the effects of such pathways at various sites; (iii) assess pathways associated with a period of decreased air quality in Ireland. The origin of and the regions traversed by an air mass 96h prior to reaching a receptor is modelled and k-means clustering is applied to create air-mass groups. Significant differences in air pollution levels were found between air mass cluster types at urban and rural sites. It was found that easterly or recirculated air masses lead to higher NO2 and PM10 levels with average NO2 levels varying between 124% and 239% of the seasonal mean and average PM10 levels varying between 103% and 199% of the seasonal mean at urban and rural sites. Easterly air masses are more frequent during winter months leading to higher overall concentrations. The span in relative concentrations between air mass clusters is highest at the rural site indicating that regional factors are controlling concentration levels. The methods used in this paper could be applied to assist in modelling and forecasting air quality based on long range transport pathways and forecast meteorology without the requirement for detailed emissions data over a large regional domain or the use of computationally demanding modelling techniques.

Cumulative sum control charts for assessing performance in arterial surgery.

PubMed

Beiles, C Barry; Morton, Anthony P

2004-03-01

The Melbourne Vascular Surgical Association (Melbourne, Australia) undertakes surveillance of mortality following aortic aneurysm surgery, patency at discharge following infrainguinal bypass and stroke and death following carotid endarterectomy. Quality improvement protocol employing the Deming cycle requires that the system for performing surgery first be analysed and optimized. Then process and outcome data are collected and these data require careful analysis. There must be a mechanism so that the causes of unsatisfactory outcomes can be determined and a good feedback mechanism must exist so that good performance is acknowledged and unsatisfactory performance corrected. A simple method for analysing these data that detects changes in average outcome rates is available using cumulative sum statistical control charts. Data have been analysed both retrospectively from 1999 to 2001, and prospectively during 2002 using cumulative sum control methods. A pathway to deal with control chart signals has been developed. The standard of arterial surgery in Victoria, Australia, is high. In one case a safe and satisfactory outcome was achieved by following the pathway developed by the audit committee. Cumulative sum control charts are a simple and effective tool for the identification of variations in performance standards in arterial surgery. The establishment of a pathway to manage problem performance is a vital part of audit activity.

Minimal impact of a care pathway for geriatric hip fracture patients.

PubMed

Panella, Massimiliano; Seys, Deborah; Sermeus, Walter; Bruyneel, Luk; Lodewijckx, Cathy; Deneckere, Svin; Sermon, An; Nijs, Stefaan; Boto, Paulo; Vanhaecht, Kris

2018-06-04

Adherence to guidelines for patients with proximal femur fracture is suboptimal. To evaluate the effect of a care pathway for the in-hospital management of older geriatric hip fracture patients on adherence to guidelines and patient outcomes. The European Quality of Care Pathways study is a cluster randomized controlled trial. 26 hospitals in Belgium, Italy and Portugal. Older adults with a proximal femur fracture (n = 514 patients) were included. Hospitals treating older adults (>65) with a proximal femur fracture were randomly assigned to an intervention group, i.e. implementation of a care pathway, or control group, i.e. usual care. Thirteen patient outcomes and 24 process indicators regarding in-hospital management, as well as three not-recommended care activities were measured. Adjusted and unadjusted regression analyses were conducted using intention-to-treat procedures. In the intervention group 301 patients in 15 hospitals were included, and in the control group 213 patients in 11 hospitals. Sixty-five percent of the patients were older than 80 years. The implementation of this care pathway had no significant impact on the thirteen patient outcomes. The preoperative management improved significantly. Eighteen of 24 process indicators improved, but only two improved significantly. Only for a few teams a geriatrician was an integral member of the treatment team. Implementation of a care pathway improved compliance to evidence, but no significant effect on patient outcomes was found. The impact of the collaboration between surgeons and geriatricians on adherence to guidelines and patient outcomes should be studied. ClinicalTrials.gov: NCT00962910. Copyright © 2018 Elsevier Ltd. All rights reserved.

PINK1-dependent phosphorylation of PINK1 and Parkin is essential for mitochondrial quality control.

PubMed

Zhuang, Na; Li, Lin; Chen, She; Wang, Tao

2016-12-01

Mitochondrial dysfunction has been linked to the pathogenesis of a large number of inherited diseases in humans, including Parkinson's disease, the second most common neurodegenerative disorder. The Parkinson's disease genes pink1 and parkin, which encode a mitochondrially targeted protein kinase, and an E3 ubiquitin ligase, respectively, participate in a key mitochondrial quality-control pathway that eliminates damaged mitochondria. In the current study, we established an in vivo PINK1/Parkin-induced photoreceptor neuron degeneration model in Drosophila with the aim of dissecting the PINK1/Parkin pathway in detail. Using LC-MS/MS analysis, we identified Serine 346 as the sole autophosphorylation site of Drosophila PINK1 and found that substitution of Serine 346 to Alanine completely abolished the PINK1 autophosphorylation. Disruption of either PINK1 or Parkin phosphorylation impaired the PINK1/Parkin pathway, and the degeneration phenotype of photoreceptor neurons was obviously alleviated. Phosphorylation of PINK1 is not only required for the PINK1-mediated mitochondrial recruitment of Parkin but also induces its kinase activity toward Parkin. In contrast, phosphorylation of Parkin by PINK1 is dispensable for its translocation but required for its activation. Moreover, substitution with autophosphorylation-deficient PINK1 failed to rescue pink1 null mutant phenotypes. Taken together, our findings suggest that autophosphorylation of PINK1 is essential for the mitochondrial translocation of Parkin and for subsequent phosphorylation and activation of Parkin.

Targeting Protein Quality Control Mechanisms by Natural Products to Promote Healthy Ageing.

PubMed

Wedel, Sophia; Manola, Maria; Cavinato, Maria; Trougakos, Ioannis P; Jansen-Dürr, Pidder

2018-05-19

Organismal ageing is associated with increased chance of morbidity or mortality and it is driven by diverse molecular pathways that are affected by both environmental and genetic factors. The progression of ageing correlates with the gradual accumulation of stressors and damaged biomolecules due to the time-dependent decline of stress resistance and functional capacity, which eventually compromise cellular homeodynamics. As protein machines carry out the majority of cellular functions, proteome quality control is critical for cellular functionality and is carried out through the curating activity of the proteostasis network (PN). Key components of the PN are the two main degradation machineries, namely the ubiquitin-proteasome and autophagy-lysosome pathways along with several stress-responsive pathways, such as that of nuclear factor erythroid 2-related factor 2 (Nrf2), which mobilises cytoprotective genomic responses against oxidative and/or xenobiotic damage. Reportedly, genetic or dietary interventions that activate components of the PN delay ageing in evolutionarily diverse organisms. Natural products (extracts or pure compounds) represent an extraordinary inventory of highly diverse structural scaffolds that offer promising activities towards meeting the challenge of increasing healthspan and/or delaying ageing (e.g., spermidine, quercetin or sulforaphane). Herein, we review those natural compounds that have been found to activate proteostatic and/or anti-stress cellular responses and hence have the potential to delay cellular senescence and/or in vivo ageing.

Role of Autophagy in Metabolic Syndrome-Associated Heart Disease

PubMed Central

Ren, Sidney Y.; Xu, Xihui

2014-01-01

Metabolic syndrome (MetS) is a constellation of multiple metabolic risk factors including abdominal obesity, glucose intolerance, insulin resistance, dyslipidemia and hypertension. Over the past decades, the prevalence of metabolic syndrome has increased dramatically, imposing a devastating, pandemic health threat. More importantly, individuals with metabolic syndrome are at an increased risk of diabetes mellitus and overall cardiovascular diseases. One of the common comorbidities of metabolic syndrome is heart anomalies leading to the loss of cardiomyocytes, cardiac dysfunction and ultimately heart failure. Up-to-date, a plethora cell signaling pathways have been postulated for the pathogenesis of cardiac complications in obesity including lipotoxicity, inflammation, oxidative stress, apoptosis and sympathetic overactivation although the precise mechanism of action underscoring obesity-associated heart dysfunction remains elusive. Recent evidence has indicated a potential role of protein quality control in components of metabolic syndrome. Within the protein quality control system, the autophagy-lysosome pathway is an evolutionarily conserved pathway responsible for bulk degradation of large intracellular organelles and protein aggregates. Autophagy has been demonstrated to play an indispensible role in the maintenance of cardiac geometry and function under both physiological and pathological conditions. Accumulating studies have demonstrated that autophagy plays a pivotal role in the etiology of cardiac anomalies under obesity and metabolic syndrome. In this mini review, we will discuss on how autophagy is involved in the regulation of cardiac function in obesity and metabolic syndrome. PMID:24810277

Effects of Long-Term Protein Restriction on Meat Quality, Muscle Amino Acids, and Amino Acid Transporters in Pigs.

PubMed

Yin, Jie; Li, Yuying; Zhu, Xiaotong; Han, Hui; Ren, Wenkai; Chen, Shuai; Bin, Peng; Liu, Gang; Huang, Xingguo; Fang, Rejun; Wang, Bin; Wang, Kai; Sun, Liping; Li, Tiejun; Yin, Yulong

2017-10-25

This study aimed to investigate the long-term effects of protein restriction from piglets to finishing pigs for 16 weeks on meat quality, muscle amino acids, and amino acid transporters. Thirty-nine piglets were randomly divided into three groups: a control (20-18-16% crude protein, CP) and two protein restricted groups (17-15-13% CP and 14-12-10% CP). The results showed that severe protein restriction (14-12-10% CP) inhibited feed intake and body weight, while moderate protein restriction (17-15-13% CP) had little effect on growth performance in pigs. Meat quality (i.e., pH, color traits, marbling, water-holding capacity, and shearing force) were tested, and the results exhibited that 14-12-10% CP treatment markedly improved muscle marbling score and increased yellowness (b*). pH value (45 min) was significantly higher in 17-15-13% CP group than that in other groups. In addition, protein restriction reduced muscle histone, arginine, valine, and isoleucine abundances and enhanced glycine and lysine concentrations compared with the control group, while the RT-PCR results showed that protein restriction downregulated amino acids transporters. Mechanistic target of rapamycin (mTOR) signaling pathway was inactivated in the moderate protein restricted group (17-15-13% CP), while severe protein restriction with dietary 14-12-10% CP markedly enhanced mTOR phosphorylation. In conclusion, long-term protein restriction affected meat quality and muscle amino acid metabolism in pigs, which might be associated with mTOR signaling pathway.

Ubiquitin facilitates a quality-control pathway that removes damaged chloroplasts

DOE PAGES

Woodson, Jesse D.; Joens, Matthew S.; Sinson, Andrew B.; ...

2015-10-23

Energy production by chloroplasts and mitochondria causes constant oxidative damage. A functioning photosynthetic cell requires quality-control mechanisms to turn over and degrade chloroplasts damaged by reactive oxygen species (ROS). Here in this study, we generated a conditionally lethal Arabidopsis mutant that accumulated excess protoporphyrin IX in the chloroplast and produced singlet oxygen. Damaged chloroplasts were subsequently ubiquitinated and selectively degraded. A genetic screen identified the plant U-box 4 (PUB4) E3 ubiquitin ligase as being necessary for this process. pub4-6 mutants had defects in stress adaptation and longevity. As a result, we have identified a signal that leads to the targetedmore » removal of ROS-overproducing chloroplasts.« less

Ubiquitin facilitates a quality-control pathway that removes damaged chloroplasts

DOE Office of Scientific and Technical Information (OSTI.GOV)

Woodson, Jesse D.; Joens, Matthew S.; Sinson, Andrew B.

Energy production by chloroplasts and mitochondria causes constant oxidative damage. A functioning photosynthetic cell requires quality-control mechanisms to turn over and degrade chloroplasts damaged by reactive oxygen species (ROS). Here in this study, we generated a conditionally lethal Arabidopsis mutant that accumulated excess protoporphyrin IX in the chloroplast and produced singlet oxygen. Damaged chloroplasts were subsequently ubiquitinated and selectively degraded. A genetic screen identified the plant U-box 4 (PUB4) E3 ubiquitin ligase as being necessary for this process. pub4-6 mutants had defects in stress adaptation and longevity. As a result, we have identified a signal that leads to the targetedmore » removal of ROS-overproducing chloroplasts.« less

Pathway Model of the Kinetics of the TGFbeta Antagonist Smad7 and Cross-Talk with the ATM and WNT Pathways

NASA Technical Reports Server (NTRS)

Carra, Claudio; Wang, Minli; Huff, Janice L.; Hada, Megumi; ONeill, Peter; Cucinotta, Francis A.

2010-01-01

Signal transduction controls cellular and tissue responses to radiation. Transforming growth factor beta (TGFbeta) is an important regulator of cell growth and differentiation and tissue homeostasis, and is often dis-regulated in tumor formation. Mathematical models of signal transduction pathways can be used to elucidate how signal transduction varies with radiation quality, and dose and dose-rate. Furthermore, modeling of tissue specific responses can be considered through mechanistic based modeling. We developed a mathematical model of the negative feedback regulation by Smad7 in TGFbeta-Smad signaling and are exploring possible connections to the WNT/beta -catenin, and ATM/ATF2 signaling pathways. A pathway model of TGFbeta-Smad signaling that includes Smad7 kinetics based on data in the scientific literature is described. Kinetic terms included are TGFbeta/Smad transcriptional regulation of Smad7 through the Smad3-Smad4 complex, Smad7-Smurf1 translocation from nucleus to cytoplasm, and Smad7 negative feedback regulation of the TGFO receptor through direct binding to the TGFO receptor complex. The negative feedback controls operating in this pathway suggests non-linear responses in signal transduction, which are described mathematically. We then explored possibilities for cross-talk mediated by Smad7 between DNA damage responses mediated by ATM, and with the WNT pathway and consider the design of experiments to test model driven hypothesis. Numerical comparisons of the mathematical model to experiments and representative predictions are described.

How to build and evaluate an integrated health care system for chronic patients: study design of a clustered randomised controlled trial in rural China.

PubMed

Tang, Wenxi; Sun, Xiaowei; Zhang, Yan; Ye, Ting; Zhang, Liang

2015-01-01

While integrated health care system has been proved an effective way to help improving patient health and system efficiency, the exact behaviour model and motivation approach are not so clear in poor rural areas where health human resources and continuous service provision are urgently needed. To gather solid evidence, we initiated a comprehensive intervention project in Qianjiang District, southwest part of rural China in 2012. And after one-year's pilot, we developed an intervention package of team service, comprehensive pathway and prospective- and performance-based payment system. To testify the potential influence of payment interventions, we use clustered randomised controlled trial, 60 clusters are grouped into two treatment groups and one control group to compare the time and group differences. Difference-in-differences model and structural equation modelling will be used to analyse the intervention effects and pathway. The outcomes are: quality of care, disease burden, supplier cooperative behaviour and patient utilisation behaviour and system efficiency. Repeated multivariate variance analysis will be used to statistically examine the outcome differences. This is the first trial of its kind to prove the effects and efficiency of integrated care. Though we adopted randomised controlled trial to gather the highest rank of evidence, still the fully randomisation was hard to realise in health policy reform experiment. To compensate, the designer should take efforts on control for the potential confounders as much as possible. With this trial, we assume the effects will come from: (1) improvement on the quality of life through risk factors control and lifestyles change on patient's behaviours; (2) improvement on quality of care through continuous care and coordinated supplier behaviours; (3) improvement on the system efficiency through active interaction between suppliers and patients. The integrated care system needs collaborative work from different levels of caregivers. So it is extremely important to consider the supplier cooperative behaviour. In this trial, we introduced payment system to help the delivery system integration through providing financial incentives to motivate people to play their roles. Also, the multidisciplinary team, the multi-institutional pathway and system global budget and pay-for-performance payment system could afford as a solution.

How to build and evaluate an integrated health care system for chronic patients: study design of a clustered randomised controlled trial in rural China

PubMed Central

Tang, Wenxi; Sun, Xiaowei; Zhang, Yan; Ye, Ting; Zhang, Liang

2015-01-01

Background While integrated health care system has been proved an effective way to help improving patient health and system efficiency, the exact behaviour model and motivation approach are not so clear in poor rural areas where health human resources and continuous service provision are urgently needed. To gather solid evidence, we initiated a comprehensive intervention project in Qianjiang District, southwest part of rural China in 2012. And after one-year's pilot, we developed an intervention package of team service, comprehensive pathway and prospective- and performance-based payment system. Methods To testify the potential influence of payment interventions, we use clustered randomised controlled trial, 60 clusters are grouped into two treatment groups and one control group to compare the time and group differences. Difference-in-differences model and structural equation modelling will be used to analyse the intervention effects and pathway. The outcomes are: quality of care, disease burden, supplier cooperative behaviour and patient utilisation behaviour and system efficiency. Repeated multivariate variance analysis will be used to statistically examine the outcome differences. Discussion This is the first trial of its kind to prove the effects and efficiency of integrated care. Though we adopted randomised controlled trial to gather the highest rank of evidence, still the fully randomisation was hard to realise in health policy reform experiment. To compensate, the designer should take efforts on control for the potential confounders as much as possible. With this trial, we assume the effects will come from: (1) improvement on the quality of life through risk factors control and lifestyles change on patient's behaviours; (2) improvement on quality of care through continuous care and coordinated supplier behaviours; (3) improvement on the system efficiency through active interaction between suppliers and patients. Conclusion The integrated care system needs collaborative work from different levels of caregivers. So it is extremely important to consider the supplier cooperative behaviour. In this trial, we introduced payment system to help the delivery system integration through providing financial incentives to motivate people to play their roles. Also, the multidisciplinary team, the multi-institutional pathway and system global budget and pay-for-performance payment system could afford as a solution. PMID:26034466

How Does Caregiver Well-Being Relate to Perceived Quality of Care in Patients With Cancer? Exploring Associations and Pathways

PubMed Central

Kent, Erin E.; Mollica, Michelle; Rowland, Julia H.

2016-01-01

Purpose Perceived quality of care (QOC) is an increasingly important metric of care quality and can be affected by such factors among patients with cancer as quality of life and physician trust. This study sought to evaluate whether informal caregiver well-being was also associated with perceived QOC among patients with cancer and assessed potential pathways that link these factors. Methods This study used data from the Cancer Care Outcomes Research and Surveillance (CanCORS) consortium. Patients with lung and colorectal cancer enrolled in CanCORS (N = 689) nominated an informal caregiver to participate in a caregiving survey. Both groups self-reported sociodemographic, psychosocial, and caregiving characteristics; cancer characteristics were obtained from the CanCORS core data set. Multivariable logistic regression was used to assess the association between caregiver psychosocial factors and subsequent patient-perceived QOC, controlling for earlier patient-perceived QOC and covariates. Secondary analysis examined potential pathways that link these factors. Results Patients whose informal caregiver had higher levels of depressive symptoms were significantly more likely to report fair or poor QOC (odds ratio, 1.06; 95% CI, 1.01 to 1.13). When caregivers reported fair or poor self-rated health, patients were more than three times more likely to report fair or poor perceived QOC (odds ratio, 3.76; 95% CI, 1.76 to 9.55). Controlling for patient psychosocial factors and physician communication and coordination of medical care reduced the effect size and/or statistical significance of these relationships. Conclusion Informal caregivers are an important part of the care team and their well-being is associated with patient-perceived QOC. Engaging informal cancer caregivers as part of the care team and conducting ongoing risk stratification screening and intervention to optimize their health may improve patient-reported outcomes and QOC. PMID:27573657

Protein quality control in the early secretory pathway

PubMed Central

Anelli, Tiziana; Sitia, Roberto

2008-01-01

Eukaryotic cells are able to discriminate between native and non-native polypeptides, selectively transporting the former to their final destinations. Secretory proteins are scrutinized at the endoplasmic reticulum (ER)–Golgi interface. Recent findings reveal novel features of the underlying molecular mechanisms, with several chaperone networks cooperating in assisting the maturation of complex proteins and being selectively induced to match changing synthetic demands. ‘Public' and ‘private' chaperones, some of which enriched in specializes subregions, operate for most or selected substrates, respectively. Moreover, sequential checkpoints are distributed along the early secretory pathway, allowing efficiency and fidelity in protein secretion. PMID:18216874

Mitochondrial Quality Control via the PGC1α-TFEB Signaling Pathway Is Compromised by Parkin Q311X Mutation But Independently Restored by Rapamycin.

PubMed

Siddiqui, Almas; Bhaumik, Dipa; Chinta, Shankar J; Rane, Anand; Rajagopalan, Subramanian; Lieu, Christopher A; Lithgow, Gordon J; Andersen, Julie K

2015-09-16

Following its activation by PINK1, parkin is recruited to depolarized mitochondria where it ubiquitinates outer mitochondrial membrane proteins, initiating lysosomal-mediated degradation of these organelles. Mutations in the gene encoding parkin, PARK2, result in both familial and sporadic forms of Parkinson's disease (PD) in conjunction with reductions in removal of damaged mitochondria. In contrast to what has been reported for other PARK2 mutations, expression of the Q311X mutation in vivo in mice appears to involve a downstream step in the autophagic pathway at the level of lysosomal function. This coincides with increased PARIS expression and reduced expression of a reciprocal signaling pathway involving the master mitochondrial regulator peroxisome proliferator-activated receptor-gamma coactivator (PGC1α) and the lysosomal regulator transcription factor EB (TFEB). Treatment with rapamycin was found to independently restore PGC1α-TFEB signaling in a manner not requiring parkin activity and to abrogate impairment of mitochondrial quality control and neurodegenerative features associated with this in vivo model. Losses in PGC1α-TFEB signaling in cultured rat DAergic cells expressing the Q311X mutation associated with reduced mitochondrial function and cell viability were found to be PARIS-dependent and to be independently restored by rapamycin in a manner requiring TFEB. Studies in human iPSC-derived neurons demonstrate that TFEB induction can restore mitochondrial function and cell viability in a mitochondrially compromised human cell model. Based on these data, we propose that the parkin Q311X mutation impacts on mitochondrial quality control via PARIS-mediated regulation of PGC1α-TFEB signaling and that this can be independently restored via upregulation of TFEB function. Mutations in PARK2 are generally associated with loss in ability to interact with PINK1, impacting on autophagic initiation. Our data suggest that, in the case of at least one parkin mutation, Q311X, detrimental effects are due to inhibition at the level of downstream lysosomal function. Mechanistically, this involves elevations in PARIS protein levels and subsequent effects on PGC1α-TFEB signaling that normally regulates mitochondrial quality control. Treatment with rapamycin independently restores PGC1α-TFEB signaling in a manner not requiring parkin activity and abrogates subsequent mitochondrial impairment and neuronal cell loss. Taken in total, our data suggest that the parkin Q311X mutation impacts on mitochondrial quality control via PARIS-mediated regulation of PGC1α-TFEB signaling and that this can be independently restored via rapamycin. Copyright © 2015 the authors 0270-6474/15/3512833-12$15.00/0.

Hydrograph Separations can Identify Contaminant-Specific Pathways for Conservation Targeting in a Tile-Drained Watershed

USDA-ARS?s Scientific Manuscript database

Water quality issues continue to vex agriculture. Understanding contaminant-specific pathways could help clarify effective water quality management strategies in watersheds. Hypothesis: If conducted at nested scales, hydrograph separation techniques can identify contaminant-specific pathways that co...

Quality Assurance of RNA Expression Profiling in Clinical Laboratories

PubMed Central

Tang, Weihua; Hu, Zhiyuan; Muallem, Hind; Gulley, Margaret L.

2012-01-01

RNA expression profiles are increasingly used to diagnose and classify disease, based on expression patterns of as many as several thousand RNAs. To ensure quality of expression profiling services in clinical settings, a standard operating procedure incorporates multiple quality indicators and controls, beginning with preanalytic specimen preparation and proceeding thorough analysis, interpretation, and reporting. Before testing, histopathological examination of each cellular specimen, along with optional cell enrichment procedures, ensures adequacy of the input tissue. Other tactics include endogenous controls to evaluate adequacy of RNA and exogenous or spiked controls to evaluate run- and patient-specific performance of the test system, respectively. Unique aspects of quality assurance for array-based tests include controls for the pertinent outcome signatures that often supersede controls for each individual analyte, built-in redundancy for critical analytes or biochemical pathways, and software-supported scrutiny of abundant data by a laboratory physician who interprets the findings in a manner facilitating appropriate medical intervention. Access to high-quality reagents, instruments, and software from commercial sources promotes standardization and adoption in clinical settings, once an assay is vetted in validation studies as being analytically sound and clinically useful. Careful attention to the well-honed principles of laboratory medicine, along with guidance from government and professional groups on strategies to preserve RNA and manage large data sets, promotes clinical-grade assay performance. PMID:22020152

Roles for the ubiquitin-proteasome pathway in protein quality control and signaling in the retina: implications in the pathogenesis of age-related macular degeneration

USDA-ARS?s Scientific Manuscript database

The accumulation of damaged or postsynthetically modified proteins and dysregulation of inflammatory responses and angiogenesis in the retina/RPE are thought be etiologically related to formation of drusen and choroidal neovascularization (CNV), hallmarks of age-related macular degeneration (AMD). T...

The transcriptome of corona radiata cells from individual MІІ oocytes that after ICSI developed to embryos selected for transfer: PCOS women compared to healthy women.

PubMed

Wissing, Marie Louise; Sonne, Si Brask; Westergaard, David; Nguyen, Kho do; Belling, Kirstine; Høst, Thomas; Mikkelsen, Anne Lis

2014-11-29

Corona radiata cells (CRCs) refer to the fraction of cumulus cells just adjacent to the oocyte. The CRCs are closely connected to the oocyte throughout maturation and their gene expression profiles might reflect oocyte quality. Polycystic ovary syndrome (PCOS) is a common cause of infertility. It is controversial whether PCOS associate with diminished oocyte quality. The purpose of this study was to compare individual human CRC samples between PCOS patients and controls. All patients were stimulated by the long gonadotropin-releasing hormone (GnRH) agonist protocol. The CRC samples originated from individual oocytes developing into embryos selected for transfer. CRCs were isolated in a two-step denudation procedure, separating outer cumulus cells from the inner CRCs. Extracted RNA was amplified and transcriptome profiling was performed with Human Agilent® arrays. The transcriptomes of CRCs showed no individual genes with significant differential expression between PCOS and controls, but gene set enrichment analysis identified several cell cycle- and DNA replication pathways overexpressed in PCOS CRCs (FDR < 0.05). Five of the genes contributing to the up-regulated cell cycle pathways in the PCOS CRCs were selected for qRT-PCR validation in ten PCOS and ten control CRC samples. qRT-PCR confirmed significant up-regulation in PCOS CRCs of cell cycle progression genes HIST1H4C (FC = 2.7), UBE2C (FC = 2.6) and cell cycle related transcription factor E2F4 (FC = 2.5). The overexpression of cell cycle-related genes and cell cycle pathways in PCOS CRCs could indicate a disturbed or delayed final maturation and differentiation of the CRCs in response to the human chorionic gonadotropin (hCG) surge. However, this had no effect on the in vitro development of the corresponding embryos. Future studies are needed to clarify whether the up-regulated cell cycle pathways in PCOS CRCs have any clinical implications.

Application of Pseudomonas fluorescens to Blackberry under Field Conditions Improves Fruit Quality by Modifying Flavonoid Metabolism

PubMed Central

Garcia-Seco, Daniel; Zhang, Yang; Gutierrez-Mañero, Francisco J.; Martin, Cathie; Ramos-Solano, Beatriz

2015-01-01

Application of a plant growth promoting rhizobacterium (PGPR), Pseudomonas fluorescens N21.4, to roots of blackberries (Rubus sp.) is part of an optimised cultivation practice to improve yields and quality of fruit throughout the year in this important fruit crop. Blackberries are especially rich in flavonoids and therefore offer potential benefits for human health in prevention or amelioration of chronic diseases. However, the phenylpropanoid pathway and its regulation during ripening have not been studied in detail, in this species. PGPR may trigger flavonoid biosynthesis as part of an induced systemic response (ISR) given the important role of this pathway in plant defence, to cause increased levels of flavonoids in the fruit. We have identified structural genes encoding enzymes of the phenylpropanoid and flavonoid biosynthetic pathways catalysing the conversion of phenylalanine to the final products including flavonols, anthocyanins and catechins from blackberry, and regulatory genes likely involved in controlling the activity of pathway branches. We have also measured the major flavonols, anthocyanins and catechins at three stages during ripening. Our results demonstrate the coordinated expression of flavonoid biosynthetic genes with the accumulation of anthocyanins, catechins, and flavonols in developing fruits of blackberry. Elicitation of blackberry plants by treatment of roots with P.fluorescens N21.4, caused increased expression of some flavonoid biosynthetic genes and an accompanying increase in the concentration of selected flavonoids in fruits. Our data demonstrate the physiological mechanisms involved in the improvement of fruit quality by PGPR under field conditions, and highlight some of the genetic targets of elicitation by beneficial bacteria. PMID:26559418

Application of Pseudomonas fluorescens to Blackberry under Field Conditions Improves Fruit Quality by Modifying Flavonoid Metabolism.

PubMed

Garcia-Seco, Daniel; Zhang, Yang; Gutierrez-Mañero, Francisco J; Martin, Cathie; Ramos-Solano, Beatriz

2015-01-01

Application of a plant growth promoting rhizobacterium (PGPR), Pseudomonas fluorescens N21.4, to roots of blackberries (Rubus sp.) is part of an optimised cultivation practice to improve yields and quality of fruit throughout the year in this important fruit crop. Blackberries are especially rich in flavonoids and therefore offer potential benefits for human health in prevention or amelioration of chronic diseases. However, the phenylpropanoid pathway and its regulation during ripening have not been studied in detail, in this species. PGPR may trigger flavonoid biosynthesis as part of an induced systemic response (ISR) given the important role of this pathway in plant defence, to cause increased levels of flavonoids in the fruit. We have identified structural genes encoding enzymes of the phenylpropanoid and flavonoid biosynthetic pathways catalysing the conversion of phenylalanine to the final products including flavonols, anthocyanins and catechins from blackberry, and regulatory genes likely involved in controlling the activity of pathway branches. We have also measured the major flavonols, anthocyanins and catechins at three stages during ripening. Our results demonstrate the coordinated expression of flavonoid biosynthetic genes with the accumulation of anthocyanins, catechins, and flavonols in developing fruits of blackberry. Elicitation of blackberry plants by treatment of roots with P.fluorescens N21.4, caused increased expression of some flavonoid biosynthetic genes and an accompanying increase in the concentration of selected flavonoids in fruits. Our data demonstrate the physiological mechanisms involved in the improvement of fruit quality by PGPR under field conditions, and highlight some of the genetic targets of elicitation by beneficial bacteria.

Harnessing Intracellular Biochemical Pathways for In Vitro Synthesis of Designer Tellurium Nanorods.

PubMed

Xiong, Ling-Hong; Cui, Ran; Zhang, Zhi-Ling; Tu, Jia-Wei; Shi, Yun-Bo; Pang, Dai-Wen

2015-10-28

Synthesizing nanomaterials of desired properties is a big challenge, which requires extremely harsh conditions and/or use of toxic materials. More recently developed in vivo methods have brought a different set of problems such as separation and purification of nanomaterials made in vivo. Here, a novel approach that harnesses cellular pathways for in vitro synthesis of high-quality tellurium nanorods with tunable lengths and optical properties is reported. It is first demonstrated that in vivo biochemical pathways could be used to synthesize Te nanorods via the intracellular reduction of TeO3(2-) in living Staphylococcus aureus cells. The pathways to set up a quasi-biological system for Te precursor formation are then utilized, which could further synthesize Te nanorods in vitro. This allows to successfully synthesize in vitro, under routine laboratory conditions, Te nanorods with uniform and tunable lengths, ranging from about 10 to 200 nm, and controllable optical properties with high molar extinction coefficients. The approach here should open new avenues for controllable, facile, and efficient synthesis of designer nanomaterials for diverse industrial and biomedical applications. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Structural Basis for Modulation of Quality Control Fate in a Marginally Stable Protein.

PubMed

Brock, Kelly P; Abraham, Ayelet-chen; Amen, Triana; Kaganovich, Daniel; England, Jeremy L

2015-07-07

The human von Hippel-Lindau (VHL) tumor suppressor is a marginally stable protein previously used as a model substrate of eukaryotic refolding and degradation pathways. When expressed in the absence of its cofactors, VHL cannot fold and is quickly degraded by the quality control machinery of the cell. We combined computational methods with in vivo experiments to examine the basis of the misfolding propensity of VHL. By expressing a set of randomly mutated VHL sequences in yeast, we discovered a more stable mutant form. Subsequent modeling suggested the mutation had caused a conformational change affecting cofactor and chaperone interaction, and this hypothesis was then confirmed by additional knockout and overexpression experiments targeting a yeast cofactor homolog. These findings offer a detailed structural basis for the modulation of quality control fate in a model misfolded protein and highlight burial mode modeling as a rapid means to detect functionally important conformational changes in marginally stable globular domains. Copyright © 2015 The Authors. Published by Elsevier Ltd.. All rights reserved.

Human High Temperature Requirement Serine Protease A1 (HTRA1) Degrades Tau Protein Aggregates*

PubMed Central

Tennstaedt, Annette; Pöpsel, Simon; Truebestein, Linda; Hauske, Patrick; Brockmann, Anke; Schmidt, Nina; Irle, Inga; Sacca, Barbara; Niemeyer, Christof M.; Brandt, Roland; Ksiezak-Reding, Hanna; Tirniceriu, Anca Laura; Egensperger, Rupert; Baldi, Alfonso; Dehmelt, Leif; Kaiser, Markus; Huber, Robert; Clausen, Tim; Ehrmann, Michael

2012-01-01

Protective proteases are key elements of protein quality control pathways that are up-regulated, for example, under various protein folding stresses. These proteases are employed to prevent the accumulation and aggregation of misfolded proteins that can impose severe damage to cells. The high temperature requirement A (HtrA) family of serine proteases has evolved to perform important aspects of ATP-independent protein quality control. So far, however, no HtrA protease is known that degrades protein aggregates. We show here that human HTRA1 degrades aggregated and fibrillar tau, a protein that is critically involved in various neurological disorders. Neuronal cells and patient brains accumulate less tau, neurofibrillary tangles, and neuritic plaques, respectively, when HTRA1 is expressed at elevated levels. Furthermore, HTRA1 mRNA and HTRA1 activity are up-regulated in response to elevated tau concentrations. These data suggest that HTRA1 is performing regulated proteolysis during protein quality control, the implications of which are discussed. PMID:22535953

Targeting the Autophagy/Lysosomal Degradation Pathway in Parkinson's Disease.

PubMed

Rivero-Ríos, Pilar; Madero-Pérez, Jesús; Fernández, Belén; Hilfiker, Sabine

2016-01-01

Autophagy is a cellular quality control mechanism crucial for neuronal homeostasis. Defects in autophagy are critically associated with mechanisms underlying Parkinson's disease (PD), a common and debilitating neurodegenerative disorder. Autophagic dysfunction in PD can occur at several stages of the autophagy/lysosomal degradative machinery, contributing to the formation of intracellular protein aggregates and eventual neuronal cell death. Therefore, autophagy inducers may comprise a promising new therapeutic approach to combat neurodegeneration in PD. Several currently available FDA-approved drugs have been shown to enhance autophagy, which may allow for their repurposing for use in novel clinical conditions including PD. This review summarizes our current knowledge of deficits in the autophagy/lysosomal degradation pathways associated with PD, and highlight current approaches which target this pathway as possible means towards novel therapeutic strategies.

From field notes to data portal - An operational QA/QC framework for tower networks

NASA Astrophysics Data System (ADS)

Sturtevant, C.; Hackley, S.; Meehan, T.; Roberti, J. A.; Holling, G.; Bonarrigo, S.

2016-12-01

Quality assurance and control (QA/QC) is one of the most important yet challenging aspects of producing research-quality data. This is especially so for environmental sensor networks collecting numerous high-frequency measurement streams at distributed sites. Here, the quality issues are multi-faceted, including sensor malfunctions, unmet theoretical assumptions, and measurement interference from the natural environment. To complicate matters, there are often multiple personnel managing different sites or different steps in the data flow. For large, centrally managed sensor networks such as NEON, the separation of field and processing duties is in the extreme. Tower networks such as Ameriflux, ICOS, and NEON continue to grow in size and sophistication, yet tools for robust, efficient, scalable QA/QC have lagged. Quality control remains a largely manual process relying on visual inspection of the data. In addition, notes of observed measurement interference or visible problems are often recorded on paper without an explicit pathway to data flagging during processing. As such, an increase in network size requires a near-proportional increase in personnel devoted to QA/QC, quickly stressing the human resources available. There is a need for a scalable, operational QA/QC framework that combines the efficiency and standardization of automated tests with the power and flexibility of visual checks, and includes an efficient communication pathway from field personnel to data processors to end users. Here we propose such a framework and an accompanying set of tools in development, including a mobile application template for recording tower maintenance and an R/shiny application for efficiently monitoring and synthesizing data quality issues. This framework seeks to incorporate lessons learned from the Ameriflux community and provide tools to aid continued network advancements.

Mitochondrial dynamics and Parkinson's disease: focus on parkin.

PubMed

Lim, Kah-Leong; Ng, Xiao-Hui; Grace, Lim Gui-Yin; Yao, Tso-Pang

2012-05-01

Parkinson's disease (PD) is a prevalent neurodegenerative disease affecting millions of individuals worldwide. Despite intensive efforts devoted to drug discovery, the disease remains incurable. To provide more effective medical therapy for PD, better understanding of the underlying causes of the disease is clearly necessary. A broad range of studies conducted over the past few decades have collectively implicated aberrant mitochondrial homeostasis as a key contributor to the development of PD. Supporting this, mutations in several PD-linked genes are directly or indirectly linked to mitochondrial dysfunction. In particular, recent discoveries have identified parkin, whose mutations are causative of recessive parkinsonism, as a key regulator of mitochondrial homeostasis. Parkin appears to be involved in the entire spectrum of mitochondrial dynamics, including organelle biogenesis, fusion/fission, and clearance via mitophagy. How a single protein can regulate such diverse mitochondrial events is as intriguing as it is amazing; the mechanism underlying this is currently under intense research. Here, we provide an overview of mitochondrial dynamics and its relationship with neurodegenerative diseases and discuss current evidence and controversies surrounding the role of parkin in mitochondrial quality control and its relevance to PD pathogenesis. Although the emerging field of parkin-mediated mitochondrial quality control has proven to be exciting, it is important to recognize that PD pathogenesis is likely to involve an intricate network of interacting pathways. Elucidating the reciprocity of pathways, particularly how other PD-related pathways potentially influence mitochondrial homeostasis, may hold the key to therapeutic development.

PINK1-dependent phosphorylation of PINK1 and Parkin is essential for mitochondrial quality control

PubMed Central

Zhuang, Na; Li, Lin; Chen, She; Wang, Tao

2016-01-01

Mitochondrial dysfunction has been linked to the pathogenesis of a large number of inherited diseases in humans, including Parkinson's disease, the second most common neurodegenerative disorder. The Parkinson's disease genes pink1 and parkin, which encode a mitochondrially targeted protein kinase, and an E3 ubiquitin ligase, respectively, participate in a key mitochondrial quality-control pathway that eliminates damaged mitochondria. In the current study, we established an in vivo PINK1/Parkin-induced photoreceptor neuron degeneration model in Drosophila with the aim of dissecting the PINK1/Parkin pathway in detail. Using LC-MS/MS analysis, we identified Serine 346 as the sole autophosphorylation site of Drosophila PINK1 and found that substitution of Serine 346 to Alanine completely abolished the PINK1 autophosphorylation. Disruption of either PINK1 or Parkin phosphorylation impaired the PINK1/Parkin pathway, and the degeneration phenotype of photoreceptor neurons was obviously alleviated. Phosphorylation of PINK1 is not only required for the PINK1-mediated mitochondrial recruitment of Parkin but also induces its kinase activity toward Parkin. In contrast, phosphorylation of Parkin by PINK1 is dispensable for its translocation but required for its activation. Moreover, substitution with autophosphorylation-deficient PINK1 failed to rescue pink1 null mutant phenotypes. Taken together, our findings suggest that autophosphorylation of PINK1 is essential for the mitochondrial translocation of Parkin and for subsequent phosphorylation and activation of Parkin. PMID:27906179

Protein quality control at the inner nuclear membrane

PubMed Central

Khmelinskii, Anton; Blaszczak, Ewa; Pantazopoulou, Marina; Fischer, Bernd; Omnus, Deike J.; Le Dez, Gaëlle; Brossard, Audrey; Gunnarsson, Alexander; Barry, Joseph D.; Meurer, Matthias; Kirrmaier, Daniel; Boone, Charles; Huber, Wolfgang; Rabut, Gwenaël; Ljungdahl, Per O.; Knop, Michael

2015-01-01

The nuclear envelope is a double membrane that separates the nucleus from the cytoplasm. The inner nuclear membrane (INM) functions in essential nuclear processes including chromatin organization and regulation of gene expression1. The outer nuclear membrane is continuous with the endoplasmic reticulum (ER) and is the site of membrane protein synthesis. Protein homeostasis in this compartment is ensured by ER-associated protein degradation (ERAD) pathways that in yeast involve the integral membrane E3 ubiquitin ligases Hrd1 and Doa10 operating with the E2 ubiquitin-conjugating enzymes Ubc6 and Ubc72,3. However, little is known regarding protein quality control at the INM. Here we describe a protein degradation pathway at the INM mediated by the Asi complex consisting of the RING domain proteins Asi1 and Asi34. We report that the As complex functions together with the ubiquitin conjugating enzymes Ubc6andUbc7to degrade soluble and integral membrane proteins. Genetic evidence suggest that the Asi ubiquitin ligase defines a pathway distinct from but complementary to ERAD. Using unbiased screening with a novel genome-wide yeast library based on a tandem fluorescent protein timer (tFT)5, we identify more than 50 substrates of the Asi, Hrd1 and Doa10 E3 ubiquity ligases. We show that the Asi ubiquitin ligase is involved in degradation of mislocalised integral membrane proteins, thus acting to maintain and safeguard the identity of the INM. PMID:25519137

The quality of metabolic pathway resources depends on initial enzymatic function assignments: a case for maize

DOE PAGES

Walsh, Jesse R.; Schaeffer, Mary L.; Zhang, Peifen; ...

2016-11-29

As metabolic pathway resources become more commonly available, researchers have unprecedented access to information about their organism of interest. Despite efforts to ensure consistency between various resources, information content and quality can vary widely. Two maize metabolic pathway resources for the B73 inbred line, CornCyc 4.0 and MaizeCyc 2.2, are based on the same gene model set and were developed using Pathway Tools software. These resources differ in their initial enzymatic function assignments and in the extent of manual curation. Here, we present an in-depth comparison between CornCyc and MaizeCyc to demonstrate the effect of initial computational enzymatic function assignmentsmore » on the quality and content of metabolic pathway resources.« less

The quality of metabolic pathway resources depends on initial enzymatic function assignments: a case for maize

DOE Office of Scientific and Technical Information (OSTI.GOV)

Walsh, Jesse R.; Schaeffer, Mary L.; Zhang, Peifen

As metabolic pathway resources become more commonly available, researchers have unprecedented access to information about their organism of interest. Despite efforts to ensure consistency between various resources, information content and quality can vary widely. Two maize metabolic pathway resources for the B73 inbred line, CornCyc 4.0 and MaizeCyc 2.2, are based on the same gene model set and were developed using Pathway Tools software. These resources differ in their initial enzymatic function assignments and in the extent of manual curation. Here, we present an in-depth comparison between CornCyc and MaizeCyc to demonstrate the effect of initial computational enzymatic function assignmentsmore » on the quality and content of metabolic pathway resources.« less

Saccharomyces cerevisiae proteinase A excretion and wine making.

PubMed

Song, Lulu; Chen, Yefu; Du, Yongjing; Wang, Xibin; Guo, Xuewu; Dong, Jian; Xiao, Dongguang

2017-11-09

Proteinase A (PrA), the major protease in Saccharomyces cerevisiae, plays an essential role in zymogen activation, sporulation, and other physiological processes in vivo. The extracellular secretion of PrA often occurs during alcoholic fermentation, especially in the later stages when the yeast cells are under stress conditions, and affects the quality and safety of fermented products. Thus, the mechanism underlying PrA excretion must be explored to improve the quality and safety of fermented products. This paper briefly introduces the structure and physiological function of PrA. Two transport routes of PrA, namely, the Golgi-to-vacuole pathway and the constitutive Golgi-to-plasma membrane pathway, are also discussed. Moreover, the research history and developments on the mechanism of extracellular PrA secretion are described. In addition, it is briefly discussed that calcium homeostasis plays an important role in the secretory pathway of proteins, implying that the regulation of PrA delivery to the plasma membrane requires the involvement of calcium ion. Finally, this review focuses on the effects of PrA excretion on wine making (including Chinese rice wine, grape wine, and beer brewage) and presents strategies to control PrA excretion.

Pathways into Teaching: Q&A with Dr. Pam Grossman. REL Mid-Atlantic Teacher Effectiveness Webinar Series

ERIC Educational Resources Information Center

Regional Educational Laboratory Mid-Atlantic, 2013

2013-01-01

This webinar explored several elements of teacher preparation pathways, including the history, popularity, and quality of various routes to certification, as well as the impact of these various pathways on teacher quality and retention and student achievement. This Q&A addressed the questions participants had for Dr. Grossman following the…

Altered mitochondrial quality control signaling in muscle of old gastric cancer patients with cachexia.

PubMed

Marzetti, Emanuele; Lorenzi, Maria; Landi, Francesco; Picca, Anna; Rosa, Fausto; Tanganelli, Fabiana; Galli, Marco; Doglietto, Giovanni Battista; Pacelli, Fabio; Cesari, Matteo; Bernabei, Roberto; Calvani, Riccardo; Bossola, Maurizio

2017-01-01

Mitochondrial dysfunction is involved in the loss of muscle featuring both aging and cancer cachexia (CC). Whether mitochondrial quality control (MQC) is altered in skeletal myocytes of old patients with CC is unclear. The present investigation therefore sought to preliminarily characterize MQC pathways in muscle of old gastric cancer patients with cachexia. The study followed a case-control cross-sectional design. Intraoperative biopsies of the rectus abdominis muscle were obtained from 18 patients with gastric adenocarcinoma (nine with CC and nine non-cachectic) and nine controls, and assayed for the expression of a set of MQC mediators. The mitofusin 2 expression was reduced in cancer patients compared with controls, independent of CC. Fission protein 1 was instead up-regulated in CC patients relative to the other groups. The mitophagy regulators PTEN-induced putative kinase 1 and Parkin were both down-regulated in cancer patients compared with controls. The ratio between the protein content of the lipidated and non-lipidated forms of microtubule-associated protein 1 light chain 3B was lower in CC patients relative to controls and non-cachectic cancer patients. Finally, the expression of autophagy-associated protein 7, lysosome-associated membrane protein 2, peroxisome proliferator-activated receptor-γ coactivator-1α, and mitochondrial transcription factor A was unvarying among groups. Collectively, our findings indicate that, in old patients with gastric cancer, cachexia is associated with derangements of the muscular MQC axis at several checkpoints: mitochondrial dynamics, mitochondrial tagging for disposal, and mitophagy signaling. Further investigations are needed to corroborate these preliminary findings and determine whether MQC pathways may become target for future interventions. Copyright © 2016 Elsevier Inc. All rights reserved.

The nuclear tRNA aminoacylation-dependent pathway may be the principal route used to export tRNA from the nucleus in Saccharomyces cerevisiae.

PubMed

Steiner-Mosonyi, Marta; Mangroo, Dev

2004-03-15

Nuclear tRNA export in Saccharomyces cerevisiae has been proposed to involve three pathways, designated Los1p-dependent, Los1p-independent nuclear aminoacylation-dependent, and Los1p- and nuclear aminoacylation-independent. Here, a comprehensive biochemical analysis was performed to identify tRNAs exported by the aminoacylation-dependent and -independent pathways of S. cerevisiae. Interestingly, the major tRNA species of at least 19 families were found in the aminoacylated form in the nucleus. tRNAs known to be exported by the export receptor Los1p were also aminoacylated in the nucleus of both wild-type and mutant Los1p strains. FISH (fluorescence in situ hybridization) analyses showed that tRNA(Tyr) co-localizes with the U18 small nucleolar RNA in the nucleolus of a tyrosyl-tRNA synthetase mutant strain defective in nuclear tRNA(Tyr) export because of a block in nuclear tRNA(Tyr) aminoacylation. tRNA(Tyr) was also found in the nucleolus of a utp8 mutant strain defective in nuclear tRNA export but not nuclear tRNA aminoacylation. These results strongly suggest that the nuclear aminoacylation-dependent pathway is principally responsible for tRNA export in S. cerevisiae and that Los1p is an export receptor of this pathway. It is also likely that in mammalian cells tRNAs are mainly exported from the nucleus by the nuclear aminoacylation-dependent pathway. In addition, the data are consistent with the idea that nuclear aminoacylation is used as a quality control mechanism for ensuring nuclear export of only mature and functional tRNAs, and that this quality assurance step occurs in the nucleolus.

Quality control of mRNP biogenesis: networking at the transcription site.

PubMed

Eberle, Andrea B; Visa, Neus

2014-08-01

Eukaryotic cells carry out quality control (QC) over the processes of RNA biogenesis to inactivate or eliminate defective transcripts, and to avoid their production. In the case of protein-coding transcripts, the quality controls can sense defects in the assembly of mRNA-protein complexes, in the processing of the precursor mRNAs, and in the sequence of open reading frames. Different types of defect are monitored by different specialized mechanisms. Some of them involve dedicated factors whose function is to identify faulty molecules and target them for degradation. Others are the result of a more subtle balance in the kinetics of opposing activities in the mRNA biogenesis pathway. One way or another, all such mechanisms hinder the expression of the defective mRNAs through processes as diverse as rapid degradation, nuclear retention and transcriptional silencing. Three major degradation systems are responsible for the destruction of the defective transcripts: the exosome, the 5'-3' exoribonucleases, and the nonsense-mediated mRNA decay (NMD) machinery. This review summarizes recent findings on the cotranscriptional quality control of mRNA biogenesis, and speculates that a protein-protein interaction network integrates multiple mRNA degradation systems with the transcription machinery. Copyright © 2014 Elsevier Ltd. All rights reserved.

Benchmarking organic micropollutants in wastewater, recycled water and drinking water with in vitro bioassays.

PubMed

Escher, Beate I; Allinson, Mayumi; Altenburger, Rolf; Bain, Peter A; Balaguer, Patrick; Busch, Wibke; Crago, Jordan; Denslow, Nancy D; Dopp, Elke; Hilscherova, Klara; Humpage, Andrew R; Kumar, Anu; Grimaldi, Marina; Jayasinghe, B Sumith; Jarosova, Barbora; Jia, Ai; Makarov, Sergei; Maruya, Keith A; Medvedev, Alex; Mehinto, Alvine C; Mendez, Jamie E; Poulsen, Anita; Prochazka, Erik; Richard, Jessica; Schifferli, Andrea; Schlenk, Daniel; Scholz, Stefan; Shiraishi, Fujio; Snyder, Shane; Su, Guanyong; Tang, Janet Y M; van der Burg, Bart; van der Linden, Sander C; Werner, Inge; Westerheide, Sandy D; Wong, Chris K C; Yang, Min; Yeung, Bonnie H Y; Zhang, Xiaowei; Leusch, Frederic D L

2014-01-01

Thousands of organic micropollutants and their transformation products occur in water. Although often present at low concentrations, individual compounds contribute to mixture effects. Cell-based bioassays that target health-relevant biological endpoints may therefore complement chemical analysis for water quality assessment. The objective of this study was to evaluate cell-based bioassays for their suitability to benchmark water quality and to assess efficacy of water treatment processes. The selected bioassays cover relevant steps in the toxicity pathways including induction of xenobiotic metabolism, specific and reactive modes of toxic action, activation of adaptive stress response pathways and system responses. Twenty laboratories applied 103 unique in vitro bioassays to a common set of 10 water samples collected in Australia, including wastewater treatment plant effluent, two types of recycled water (reverse osmosis and ozonation/activated carbon filtration), stormwater, surface water, and drinking water. Sixty-five bioassays (63%) showed positive results in at least one sample, typically in wastewater treatment plant effluent, and only five (5%) were positive in the control (ultrapure water). Each water type had a characteristic bioanalytical profile with particular groups of toxicity pathways either consistently responsive or not responsive across test systems. The most responsive health-relevant endpoints were related to xenobiotic metabolism (pregnane X and aryl hydrocarbon receptors), hormone-mediated modes of action (mainly related to the estrogen, glucocorticoid, and antiandrogen activities), reactive modes of action (genotoxicity) and adaptive stress response pathway (oxidative stress response). This study has demonstrated that selected cell-based bioassays are suitable to benchmark water quality and it is recommended to use a purpose-tailored panel of bioassays for routine monitoring.

Formation of distinct inclusion bodies by inhibition of ubiquitin-proteasome and autophagy-lysosome pathways.

PubMed

Lee, Junho; Yang, Kyu-Hwan; Joe, Cheol O; Kang, Seok-Seong

2011-01-14

Accumulation of misfolded proteins is caused by the impairment of protein quality control systems, such as ubiquitin-proteasome pathway (UPP) and autophagy-lysosome pathway (ALP). In this study, the formation of inclusion bodies was examined after the blockade of UPP and/or ALP in A549 cells. UPP inhibition induced a single and large inclusion body localized in microtubule-organizing center. Interestingly, however, ALP inhibition generated dispersed small inclusion bodies in the cytoplasm. Tuberous sclerosis complex 2 was selectively accumulated in the inclusion bodies of UPP-inhibited cells, but not those of ALP-inhibited cells. Blockade of transcription and translation entirely inhibited the formation of inclusion body induced by UPP inhibition, but partially by ALP inhibition. Moreover, the simultaneous inhibition of two protein catabolic pathways independently developed two distinct inclusion bodies within a single cell. These findings clearly demonstrated that dysfunction of each catabolic pathway induced formation and accumulation of unique inclusion bodies on the basis of morphology, localization and formation process in A549 cells. Copyright © 2010 Elsevier Inc. All rights reserved.

The Pathways from Parents' Marital Quality to Adolescents' School Adjustment in South Korea

ERIC Educational Resources Information Center

Jeong, Yu-Jin; Chun, Young-Ju

2010-01-01

This study tested the hypothesized pathways from parents' marital quality to Korean adolescents' school adjustment through the perception of self and parent-child relations. Based on previous literature and two major family theories, the authors hypothesized a path model to explain the process of how parents' marital quality influenced school…

Enhanced recovery pathways in pancreatic surgery: State of the art

PubMed Central

Pecorelli, Nicolò; Nobile, Sara; Partelli, Stefano; Cardinali, Luca; Crippa, Stefano; Balzano, Gianpaolo; Beretta, Luigi; Falconi, Massimo

2016-01-01

Pancreatic surgery is being offered to an increasing number of patients every year. Although postoperative outcomes have significantly improved in the last decades, even in high-volume centers patients still experience significant postoperative morbidity and full recovery after surgery takes longer than we think. In recent years, enhanced recovery pathways incorporating a large number of evidence-based perioperative interventions have proved to be beneficial in terms of improved postoperative outcomes, and accelerated patient recovery in the context of gastrointestinal, genitourinary and orthopedic surgery. The role of these pathways for pancreatic surgery is still unclear as high-quality randomized controlled trials are lacking. To date, non-randomized studies have shown that care pathways for pancreaticoduodenectomy and distal pancreatectomy are safe with no difference in postoperative morbidity, leading to early discharge and no increase in hospital readmissions. Hospital costs are reduced due to better organization of care and resource utilization. However, further research is needed to clarify the effect of enhanced recovery pathways on patient recovery and post-discharge outcomes following pancreatic resection. Future studies should be prospective and follow recent recommendations for the design and reporting of enhanced recovery pathways. PMID:27605881

YAP controls retinal stem cell DNA replication timing and genomic stability

PubMed Central

Cabochette, Pauline; Vega-Lopez, Guillermo; Bitard, Juliette; Parain, Karine; Chemouny, Romain; Masson, Christel; Borday, Caroline; Hedderich, Marie; Henningfeld, Kristine A; Locker, Morgane; Bronchain, Odile; Perron, Muriel

2015-01-01

The adult frog retina retains a reservoir of active neural stem cells that contribute to continuous eye growth throughout life. We found that Yap, a downstream effector of the Hippo pathway, is specifically expressed in these stem cells. Yap knock-down leads to an accelerated S-phase and an abnormal progression of DNA replication, a phenotype likely mediated by upregulation of c-Myc. This is associated with an increased occurrence of DNA damage and eventually p53-p21 pathway-mediated cell death. Finally, we identified PKNOX1, a transcription factor involved in the maintenance of genomic stability, as a functional and physical interactant of YAP. Altogether, we propose that YAP is required in adult retinal stem cells to regulate the temporal firing of replication origins and quality control of replicated DNA. Our data reinforce the view that specific mechanisms dedicated to S-phase control are at work in stem cells to protect them from genomic instability. DOI: http://dx.doi.org/10.7554/eLife.08488.001 PMID:26393999

The role of autosuggestion in geriatric patients' quality of life: a study on psycho-neuro-endocrine-immunology pathway.

PubMed

Sari, Nina Kemala; Setiati, Siti; Taher, Akmal; Wiwie, Martina; Djauzi, Samsuridjal; Pandelaki, Jacub; Purba, Jan Sudir; Sadikin, Mohamad

2017-10-01

There has been no study conducted about the effect of autosuggestion on quality of life for geriatric patients. Our aim was to evaluate the efficacy of autosuggestion for geriatric patients' quality of life and its impact on psycho-neuro-endocrine-immune pathway. Sixty geriatric patients aged ≥60 years in a ward were randomly assigned to either receive autosuggestion or not. Autosuggestion was recorded in a tape to be heard daily for 30 days. Both groups received the standard medical therapy. Primary outcome was quality of life by COOP chart. Secondary outcomes were serum cortisol level, interleukin-2, interleukin-6, interferon-γ, and N-acetylaspartate/creatine ratio in limbic/paralimbic system by magnetic resonance spectroscopy. The study was single blinded due to the nature of the intervention studied. Out of 60 subjects, 51 finished the study. The autosuggestion group reported better scores than the control one for quality of life, COOP chart 1.95 vs. 2.22 (95% CI, p = 0.02). There were increments of serum cortisol (p = 0.03) and interleukin-6 in the autosuggestion group (p = 0.04). Interleukin-2, interferon-γ, and N-acetylaspartate/creatine ratio in prefrontal cortex showed a tendency to increase in the autosuggestion groups. Autosuggestion is associated with improvement of geriatrics' quality of life, serum cortisol level, and adaptive immunity. There is a better trend for neuroplasticity in prefrontal cortex in the autosuggestion group.

Structural Elements Regulating AAA+ Protein Quality Control Machines.

PubMed

Chang, Chiung-Wen; Lee, Sukyeong; Tsai, Francis T F

2017-01-01

Members of the ATPases Associated with various cellular Activities (AAA+) superfamily participate in essential and diverse cellular pathways in all kingdoms of life by harnessing the energy of ATP binding and hydrolysis to drive their biological functions. Although most AAA+ proteins share a ring-shaped architecture, AAA+ proteins have evolved distinct structural elements that are fine-tuned to their specific functions. A central question in the field is how ATP binding and hydrolysis are coupled to substrate translocation through the central channel of ring-forming AAA+ proteins. In this mini-review, we will discuss structural elements present in AAA+ proteins involved in protein quality control, drawing similarities to their known role in substrate interaction by AAA+ proteins involved in DNA translocation. Elements to be discussed include the pore loop-1, the Inter-Subunit Signaling (ISS) motif, and the Pre-Sensor I insert (PS-I) motif. Lastly, we will summarize our current understanding on the inter-relationship of those structural elements and propose a model how ATP binding and hydrolysis might be coupled to polypeptide translocation in protein quality control machines.

Development of Future Scenario Emission Inventories for East Asia in Support of Multiple Modeling Studies

NASA Astrophysics Data System (ADS)

Kim, Y.; Woo, J. H.; Choi, K. C.; Lee, J. B.; Song, C. K.; Kim, S. K.; Hong, J.; Hong, S. C.; Zhang, Q.; Hong, C.; Tong, D.

2015-12-01

Future emission scenarios based on up-to-date regional socio-economic and control policy information were developed in support of climate-air quality integrated modeling research over East Asia. Two IPCC-participated Integrated Assessment Models(IAMs) were used to developed those scenario pathways. The two emission processing systems, KU-EPS and SMOKE-Asia, were used to convert these future scenario emissions to comprehensive chemical transport model-ready form. The NIER/KU-CREATE (Comprehensive Regional Emissions inventory for Atmospheric Transport Experiment) served as the regional base-year emission inventory. For anthropogenic emissions, it has 54 fuel classes, 201 sub-sectors and 13 pollutants, including CO2, CH4, N2O, SO2, NOx, CO, NMVOC, NH3, OC, BC, PM10, PM2.5, and mercury. Fast energy growth and aggressive penetration of the control measures make emissions projection very active for East Asia. Despite of more stringent air pollution control policies by the governments, however, air quality over the region seems not been improved as much - even worse in many cases. The needs of more scientific understanding of inter-relationship among emissions, transport, chemistry over the region are very high to effectively protect public health and ecosystems against ozone, fine particles, and other toxic pollutants in the air. After developing these long-term future emissions, therefore, we also tried to apply our future scenarios to develop the present emissions inventory for chemical weather forecasting and aircraft field campaign. On site, we will present; 1) the future scenario development framework and process methodologies, 2) initial development results of the future emission pathways, 3) present emission inventories from short-term projection, and 4) air quality modeling performance improvements over the region.

Pathways linking major depression and immunity in ambulatory female patients.

PubMed

Miller, G E; Cohen, S; Herbert, T B

1999-01-01

The goals of this study were to investigate whether depression is associated with cellular immunity in ambulatory patients and to identify neuroendocrine and behavioral pathways that might account for this relationship. We studied 32 women who met Diagnostic and Statistical Manual of Mental Disorder, fourth edition, criteria for major depressive disorder and 32 healthy female control subjects. The groups were matched for age and ethnicity. None were taking medication, and all were free of disease involving the immune system. Depressed subjects had reduced proliferative responses to the mitogens concanavalin A and phytohemagglutinin compared with control subjects. Natural killer cell activity was reduced among older depressed subjects but enhanced among younger depressed subjects. Although depression was associated with elevated circulating levels of norepinephrine and estradiol, these hormones could not account for the immunologic differences between depressed and control subjects. Depression was also associated with greater tobacco and caffeine consumption, less physical activity, and poorer sleep quality. Mediational analyses were consistent with physical activity acting as a pathway through which depression was associated with reduced lymphocyte proliferation. Ambulatory patients with mild to moderately severe depression exhibit reduced mitogen-stimulated lymphocyte proliferative responses and altered natural killer cell cytotoxicity. The relationship between depression and proliferative responses may be mediated by physical activity.

An Evaluation of Active Learning Causal Discovery Methods for Reverse-Engineering Local Causal Pathways of Gene Regulation

PubMed Central

Ma, Sisi; Kemmeren, Patrick; Aliferis, Constantin F.; Statnikov, Alexander

2016-01-01

Reverse-engineering of causal pathways that implicate diseases and vital cellular functions is a fundamental problem in biomedicine. Discovery of the local causal pathway of a target variable (that consists of its direct causes and direct effects) is essential for effective intervention and can facilitate accurate diagnosis and prognosis. Recent research has provided several active learning methods that can leverage passively observed high-throughput data to draft causal pathways and then refine the inferred relations with a limited number of experiments. The current study provides a comprehensive evaluation of the performance of active learning methods for local causal pathway discovery in real biological data. Specifically, 54 active learning methods/variants from 3 families of algorithms were applied for local causal pathways reconstruction of gene regulation for 5 transcription factors in S. cerevisiae. Four aspects of the methods’ performance were assessed, including adjacency discovery quality, edge orientation accuracy, complete pathway discovery quality, and experimental cost. The results of this study show that some methods provide significant performance benefits over others and therefore should be routinely used for local causal pathway discovery tasks. This study also demonstrates the feasibility of local causal pathway reconstruction in real biological systems with significant quality and low experimental cost. PMID:26939894

Contrasting Transcriptional Programs Control Postharvest Development of Apples (Malus x domestica Borkh.) Submitted to Cold Storage and Ethylene Blockage.

PubMed

Storch, Tatiane Timm; Finatto, Taciane; Bruneau, Maryline; Orsel-Baldwin, Mathilde; Renou, Jean-Pierre; Rombaldi, Cesar Valmor; Quecini, Vera; Laurens, François; Girardi, César Luis

2017-09-06

Apple is commercially important worldwide. Favorable genomic contexts and postharvest technologies allow year-round availability. Although ripening is considered a unidirectional developmental process toward senescence, storage at low temperatures, alone or in combination with ethylene blockage, is effective in preserving apple properties. Quality traits and genome wide expression were integrated to investigate the mechanisms underlying postharvest changes. Development and conservation techniques were responsible for transcriptional reprogramming and distinct programs associated with quality traits. A large portion of the differentially regulated genes constitutes a program involved in ripening and senescence, whereas a smaller module consists of genes associated with reestablishment and maintenance of juvenile traits after harvest. Ethylene inhibition was associated with a reversal of ripening by transcriptional induction of anabolic pathways. Our results demonstrate that the blockage of ethylene perception and signaling leads to upregulation of genes in anabolic pathways. We also associated complex phenotypes to subsets of differentially regulated genes.

Mechanisms of mitophagy: PINK1, Parkin, USP30 and beyond.

PubMed

Bingol, Baris; Sheng, Morgan

2016-11-01

Mitochondrial quality control is central for maintaining a healthy population of mitochondria. Two Parkinson's disease genes, mitochondrial kinase PINK1 and ubiquitin ligase Parkin, degrade damaged mitochondria though mitophagy. In this pathway, PINK1 senses mitochondrial damage and activates Parkin by phosphorylating Parkin and ubiquitin. Activated Parkin then builds ubiquitin chains on damaged mitochondria to tag them for degradation in lysosomes. USP30 deubiquitinase acts as a brake on mitophagy by opposing Parkin-mediated ubiquitination. Human genetic data point to a role for mitophagy defects in neurodegenerative diseases. This review highlights the molecular mechanisms of the mitophagy pathway and the recent advances in the understanding of mitophagy in vivo. Copyright © 2016 Elsevier Inc. All rights reserved.

Specificity and disease in the ubiquitin system

PubMed Central

Chaugule, Viduth K.; Walden, Helen

2016-01-01

Post-translational modification (PTM) of proteins by ubiquitination is an essential cellular regulatory process. Such regulation drives the cell cycle and cell division, signalling and secretory pathways, DNA replication and repair processes and protein quality control and degradation pathways. A huge range of ubiquitin signals can be generated depending on the specificity and catalytic activity of the enzymes required for attachment of ubiquitin to a given target. As a consequence of its importance to eukaryotic life, dysfunction in the ubiquitin system leads to many disease states, including cancers and neurodegeneration. This review takes a retrospective look at our progress in understanding the molecular mechanisms that govern the specificity of ubiquitin conjugation. PMID:26862208

Training in metabolomics research. II. Processing and statistical analysis of metabolomics data, metabolite identification, pathway analysis, applications of metabolomics and its future

PubMed Central

Barnes, Stephen; Benton, H. Paul; Casazza, Krista; Cooper, Sara; Cui, Xiangqin; Du, Xiuxia; Engler, Jeffrey; Kabarowski, Janusz H.; Li, Shuzhao; Pathmasiri, Wimal; Prasain, Jeevan K.; Renfrow, Matthew B.; Tiwari, Hemant K.

2017-01-01

Metabolomics, a systems biology discipline representing analysis of known and unknown pathways of metabolism, has grown tremendously over the past 20 years. Because of its comprehensive nature, metabolomics requires careful consideration of the question(s) being asked, the scale needed to answer the question(s), collection and storage of the sample specimens, methods for extraction of the metabolites from biological matrices, the analytical method(s) to be employed and the quality control of the analyses, how collected data are correlated, the statistical methods to determine metabolites undergoing significant change, putative identification of metabolites, and the use of stable isotopes to aid in verifying metabolite identity and establishing pathway connections and fluxes. This second part of a comprehensive description of the methods of metabolomics focuses on data analysis, emerging methods in metabolomics and the future of this discipline. PMID:28239968

Self-renewal of a purified Tie2+ hematopoietic stem cell population relies on mitochondrial clearance.

PubMed

Ito, Kyoko; Turcotte, Raphaël; Cui, Jinhua; Zimmerman, Samuel E; Pinho, Sandra; Mizoguchi, Toshihide; Arai, Fumio; Runnels, Judith M; Alt, Clemens; Teruya-Feldstein, Julie; Mar, Jessica C; Singh, Rajat; Suda, Toshio; Lin, Charles P; Frenette, Paul S; Ito, Keisuke

2016-12-02

A single hematopoietic stem cell (HSC) is capable of reconstituting hematopoiesis and maintaining homeostasis by balancing self-renewal and cell differentiation. The mechanisms of HSC division balance, however, are not yet defined. Here we demonstrate, by characterizing at the single-cell level a purified and minimally heterogeneous murine Tie2 + HSC population, that these top hierarchical HSCs preferentially undergo symmetric divisions. The induction of mitophagy, a quality control process in mitochondria, plays an essential role in self-renewing expansion of Tie2 + HSCs. Activation of the PPAR (peroxisome proliferator-activated receptor)-fatty acid oxidation pathway promotes expansion of Tie2 + HSCs through enhanced Parkin recruitment in mitochondria. These metabolic pathways are conserved in human TIE2 + HSCs. Our data thus identify mitophagy as a key mechanism of HSC expansion and suggest potential methods of cell-fate manipulation through metabolic pathways. Copyright © 2016, American Association for the Advancement of Science.

Self-renewal of a purified Tie2+ hematopoietic stem cell population relies on mitochondrial clearance

PubMed Central

Ito, Kyoko; Turcotte, Raphaël; Cui, Jinhua; Zimmerman, Samuel E.; Pinho, Sandra; Mizoguchi, Toshihide; Arai, Fumio; Runnels, Judith M.; Alt, Clemens; Teruya-Feldstein, Julie; Mar, Jessica C.; Singh, Rajat; Suda, Toshio; Lin, Charles P.; Frenette, Paul S.; Ito, Keisuke

2016-01-01

A single hematopoietic stem cell (HSC) is capable of reconstituting hematopoiesis and maintaining homeostasis by balancing self-renewal and cell differentiation. The mechanisms of HSC division balance, however, are not yet defined. Here we demonstrate, by characterizing at the single-cell level a purified and minimally heterogeneous murine Tie2+ HSC population, that these top hierarchical HSCs preferentially undergo symmetric divisions. The induction of mitophagy, a quality control process in mitochondria, plays an essential role in self-renewing expansion of Tie2+ HSCs. Activation of the PPAR (peroxisome proliferator–activated receptor)–fatty acid oxidation pathway promotes expansion of Tie2+ HSCs through enhanced Parkin recruitment in mitochondria. These metabolic pathways are conserved in human TIE2+ HSCs. Our data thus identify mitophagy as a key mechanism of HSC expansion and suggest potential methods of cell-fate manipulation through metabolic pathways. PMID:27738012

Statistical and methodological issues in the evaluation of case management studies.

PubMed

Lesser, M L; Robertson, S; Kohn, N; Cooper, D J; Dlugacz, Y D

1996-01-01

For the past 3 years, the nursing case management team at North Shore University Hospital in Manhasset, NY, has been involved in a project to implement more than 50 clinical pathways, which provide a written "time line" for clinical events that should occur during a patient's hospital stay. A major objective of this project was to evaluate the efficacy of these pathways with respect to a number of important outcomes, such as length of stay, hospital costs, quality of patient care, and nursing and patient satisfaction. This article discusses several statistics-related issues in the design and evaluation of such case management studies. In particular, the role of a research approach in implementing and evaluating hospital programs, the choice of a comparison (control) group, the exclusion of selected patients from analysis, and the problems of equating pathways with diagnosis-related groups are addressed.

The development, implementation and evaluation of clinical pathways for chronic obstructive pulmonary disease (COPD) in Saskatchewan: protocol for an interrupted times series evaluation.

PubMed

Rotter, Thomas; Plishka, Christopher; Hansia, Mohammed Rashaad; Goodridge, Donna; Penz, Erika; Kinsman, Leigh; Lawal, Adegboyega; O'Quinn, Sheryl; Buchan, Nancy; Comfort, Patricia; Patel, Prakesh; Anderson, Sheila; Winkel, Tanya; Lang, Rae Lynn; Marciniuk, Darcy D

2017-11-28

Chronic obstructive pulmonary disease (COPD) has substantial economic and human costs; it is expected to be the third leading cause of death worldwide by 2030. To minimize these costs high quality guidelines have been developed. However, guidelines alone rarely result in meaningful change. One method of integrating guidelines into practice is the use of clinical pathways (CPWs). CPWs bring available evidence to a range of healthcare professionals by detailing the essential steps in care and adapting guidelines to the local context. We are working with local stakeholders to develop CPWs for COPD with the aims of improving care while reducing utilization. The CPWs will employ several steps including: standardizing diagnostic training, unifying components of chronic disease care, coordinating education and reconditioning programs, and ensuring care uses best practices. Further, we have worked to identify evidence-informed implementation strategies which will be tailored to the local context. We will conduct a three-year research project using an interrupted time series (ITS) design in the form of a multiple baseline approach with control groups. The CPW will be implemented in two health regions (experimental groups) and two health regions will act as controls (control groups). The experimental and control groups will each contain an urban and rural health region. Primary outcomes for the study will be quality of care operationalized using hospital readmission rates and emergency department (ED) presentation rates. Secondary outcomes will be healthcare utilization and guideline adherence, operationalized using hospital admission rates, hospital length of stay and general practitioner (GP) visits. Results will be analyzed using segmented regression analysis. Funding has been procured from multiple stakeholders. The project has been deemed exempt from ethics review as it is a quality improvement project. Intervention implementation is expected to begin in summer of 2017. This project is expected to improve quality of care and reduce healthcare utilization. In addition it will provide evidence on the effects of CPWs in both urban and rural settings. If the CPWs are found effective we will work with all stakeholders to implement similar CPWs in surrounding health regions. Clinicaltrials.gov ( NCT03075709 ). Registered 8 March 2017.

Effect of pay for performance to improve quality of maternal and child care in low- and middle-income countries: a systematic review.

PubMed

Das, Ashis; Gopalan, Saji S; Chandramohan, Daniel

2016-04-14

Pay for Performance (P4P) mechanisms to health facilities and providers are currently being tested in several low- and middle-income countries (LMIC) to improve maternal and child health (MCH). This paper reviews the existing evidence on the effect of P4P program on quality of MCH care in LMICs. A systematic review of literature was conducted according to a registered protocol. MEDLINE, Web of Science, and Embase were searched using the key words maternal care, quality of care, ante natal care, emergency obstetric and neonatal care (EmONC) and child care. Of 4535 records retrieved, only eight papers met the inclusion criteria. Primary outcome of interest was quality of MCH disaggregated into structural quality, process quality and outcomes. Risk of bias across studies was assessed through a customized quality checklist. There were four controlled before after intervention studies, three cluster randomized controlled trials and one case control with post-intervention comparison of P4P programs for MCH care in Burundi, Democratic Republic of Congo, Egypt, the Philippines, and Rwanda. There is some evidence of positive effect of P4P only on process quality of MCH. The effect of P4P on delivery, EmONC, post natal care and under-five child care were not evaluated in these studies. There is weak evidence for P4P's positive effect on maternal and neonatal health outcomes and out-of-pocket expenses. P4P program had a few negative effects on structural quality. P4P is effective to improve process quality of ante natal care. However, further research is needed to understand P4P's impact on MCH and their causal pathways in LMICs. PROSPERO registration number CRD42014013077 .

Reduced in-hospital mortality for heart failure with clinical pathways: the results of a cluster randomised controlled trial.

PubMed

Panella, M; Marchisio, S; Demarchi, M L; Manzoli, L; Di Stanislao, F

2009-10-01

Hospital treatment of heart failure (HF) frequently does not follow published guidelines, potentially contributing to HF high morbidity, mortality and economic cost. The Experimental Prospective Study on the Effectiveness and Efficiency of the Implementation of Clinical Pathways was undertaken to determine how clinical pathways (CP) for hospital treatment of HF affected care variability, guidelines adherence, in-hospital mortality and outcomes at discharge. Methods/ Two-arm, cluster-randomised trial. Fourteen community hospitals were randomised either to the experimental arm (CP: appropriate therapeutic guidelines use, new organisation and procedures, patient education) or to the control arm (usual care). The main outcome was in-hospital mortality; secondary outcomes were length and appropriateness of the stay, rate of unscheduled readmissions, customer satisfaction, usage of diagnostic and therapeutic procedures during hospital stay and quality indicators at discharge. All outcomes were measured using validated instruments available in literature. In-hospital mortality was 5.6% in the experimental arm (n = 12); 15.4% in controls (n = 33, p = 0.001). In CP and usual care groups, the mean rates of unscheduled readmissions were 7.9% and 13.9%, respectively. Adjusting for age, smoking, New York Heart Association score, hypertension and source of referral, patients in the CP group, as compared to controls, had a significantly lower risk of in-hospital death (OR 0.18; 95% CI 0.07 to 0.46) and unscheduled readmissions (OR 0.42; 95% CI 0.20 to 0.87). No differences were found between CP and control with respect to the appropriateness of the stay, costs and patient's satisfaction. Except for electrocardiography, all recommended diagnostic procedures were used more in the CP group. Similarly, pharmaceuticals use was significantly greater in CP, with the exception of diuretics and anti-platelets agents. The introduction of a specifically tailored CP for the hospital treatment of HF was effective in reducing in-hospital mortality and unscheduled readmissions. This study adds to previous knowledge indicating that CP should be used to improve the quality of hospital treatment of HF. NCT00519038.

Role of N-linked oligosaccharides in the biosynthetic processing of the cystic fibrosis membrane conductance regulator

PubMed Central

Chang, Xiu-bao; Mengos, April; Hou, Yue-xian; Cui, Liying; Jensen, Timothy J.; Aleksandrov, Andrei; Riordan, John R.; Gentzsch, Martina

2009-01-01

Summary The epithelial chloride channel CFTR is a glycoprotein that is modified by two N-linked oligosaccharides. The most common mutant CFTR protein in patients with cystic fibrosis, ΔF508, is misfolded and retained by ER quality control. As oligosaccharide moieties of glycoproteins are known to mediate interactions with ER lectin chaperones, we investigated the role of N-linked glycosylation in the processing of wild-type and ΔF508 CFTR. We found that N-glycosylation and ER lectin interactions are not major determinants of trafficking of wild-type and ΔF508 from the ER to the plasma membrane. Unglycosylated CFTR, generated by removal of glycosylation sites or treatment of cells with the N-glycosylation inhibitor tunicamycin, did not bind calnexin, but did traffic to the cell surface and exhibited chloride channel activity. Most importantly, unglycosylated Δ F508 CFTR still could not escape quality control in the early secretory pathway and remained associated with the ER. However, the absence of N-linked oligosaccharides did reduce the stability of wild-type CFTR, causing significantly more-rapid turnover in post-ER compartments. Surprisingly, the individual N-linked carbohydrates do not play equivalent roles and modulate the fate of the wild-type protein in different ways in its early biosynthetic pathway. PMID:18682497

Role of N-linked oligosaccharides in the biosynthetic processing of the cystic fibrosis membrane conductance regulator.

PubMed

Chang, Xiu-Bao; Mengos, April; Hou, Yue-Xian; Cui, Liying; Jensen, Timothy J; Aleksandrov, Andrei; Riordan, John R; Gentzsch, Martina

2008-09-01

The epithelial chloride channel CFTR is a glycoprotein that is modified by two N-linked oligosaccharides. The most common mutant CFTR protein in patients with cystic fibrosis, DeltaF508, is misfolded and retained by ER quality control. As oligosaccharide moieties of glycoproteins are known to mediate interactions with ER lectin chaperones, we investigated the role of N-linked glycosylation in the processing of wild-type and DeltaF508 CFTR. We found that N-glycosylation and ER lectin interactions are not major determinants of trafficking of wild-type and DeltaF508 from the ER to the plasma membrane. Unglycosylated CFTR, generated by removal of glycosylation sites or treatment of cells with the N-glycosylation inhibitor tunicamycin, did not bind calnexin, but did traffic to the cell surface and exhibited chloride channel activity. Most importantly, unglycosylated DeltaF508 CFTR still could not escape quality control in the early secretory pathway and remained associated with the ER. However, the absence of N-linked oligosaccharides did reduce the stability of wild-type CFTR, causing significantly more-rapid turnover in post-ER compartments. Surprisingly, the individual N-linked carbohydrates do not play equivalent roles and modulate the fate of the wild-type protein in different ways in its early biosynthetic pathway.

A BAG3 chaperone complex maintains cardiomyocyte function during proteotoxic stress

PubMed Central

Judge, Luke M.; Perez-Bermejo, Juan A.; Truong, Annie; Ribeiro, Alexandre J.S.; Yoo, Jennie C.; Jensen, Christina L.; Mandegar, Mohammad A.; Huebsch, Nathaniel; Kaake, Robyn M.; So, Po-Lin; Srivastava, Deepak; Krogan, Nevan J.

2017-01-01

Molecular chaperones regulate quality control in the human proteome, pathways that have been implicated in many diseases, including heart failure. Mutations in the BAG3 gene, which encodes a co-chaperone protein, have been associated with heart failure due to both inherited and sporadic dilated cardiomyopathy. Familial BAG3 mutations are autosomal dominant and frequently cause truncation of the coding sequence, suggesting a heterozygous loss-of-function mechanism. However, heterozygous knockout of the murine BAG3 gene did not cause a detectable phenotype. To model BAG3 cardiomyopathy in a human system, we generated an isogenic series of human induced pluripotent stem cells (iPSCs) with loss-of-function mutations in BAG3. Heterozygous BAG3 mutations reduced protein expression, disrupted myofibril structure, and compromised contractile function in iPSC-derived cardiomyocytes (iPS-CMs). BAG3-deficient iPS-CMs were particularly sensitive to further myofibril disruption and contractile dysfunction upon exposure to proteasome inhibitors known to cause cardiotoxicity. We performed affinity tagging of the endogenous BAG3 protein and mass spectrometry proteomics to further define the cardioprotective chaperone complex that BAG3 coordinates in the human heart. Our results establish a model for evaluating protein quality control pathways in human cardiomyocytes and their potential as therapeutic targets and susceptibility factors for cardiac drug toxicity. PMID:28724793

A BAG3 chaperone complex maintains cardiomyocyte function during proteotoxic stress.

PubMed

Judge, Luke M; Perez-Bermejo, Juan A; Truong, Annie; Ribeiro, Alexandre Js; Yoo, Jennie C; Jensen, Christina L; Mandegar, Mohammad A; Huebsch, Nathaniel; Kaake, Robyn M; So, Po-Lin; Srivastava, Deepak; Pruitt, Beth L; Krogan, Nevan J; Conklin, Bruce R

2017-07-20

Molecular chaperones regulate quality control in the human proteome, pathways that have been implicated in many diseases, including heart failure. Mutations in the BAG3 gene, which encodes a co-chaperone protein, have been associated with heart failure due to both inherited and sporadic dilated cardiomyopathy. Familial BAG3 mutations are autosomal dominant and frequently cause truncation of the coding sequence, suggesting a heterozygous loss-of-function mechanism. However, heterozygous knockout of the murine BAG3 gene did not cause a detectable phenotype. To model BAG3 cardiomyopathy in a human system, we generated an isogenic series of human induced pluripotent stem cells (iPSCs) with loss-of-function mutations in BAG3. Heterozygous BAG3 mutations reduced protein expression, disrupted myofibril structure, and compromised contractile function in iPSC-derived cardiomyocytes (iPS-CMs). BAG3-deficient iPS-CMs were particularly sensitive to further myofibril disruption and contractile dysfunction upon exposure to proteasome inhibitors known to cause cardiotoxicity. We performed affinity tagging of the endogenous BAG3 protein and mass spectrometry proteomics to further define the cardioprotective chaperone complex that BAG3 coordinates in the human heart. Our results establish a model for evaluating protein quality control pathways in human cardiomyocytes and their potential as therapeutic targets and susceptibility factors for cardiac drug toxicity.

Perspectives on the Use of Clinical Pathways in Oncology Care.

PubMed

Chiang, Anne C; Ellis, Peter; Zon, Robin

2017-01-01

Pathways and guidelines are valuable tools to provide evidence-based care in oncology. Pathways may be more restrictive than guidelines because they attempt (where possible) to reduce cost, add efficiency, and remove unwarranted variability. Pathways offer an opportunity to measure, report, and improve quality of care; they can drive to evidence-based targeted therapy where appropriate; they can enhance efficiency through standardization; and, finally, they can be a vehicle to enhance participation in clinical trials. Pathway implementation requires understanding and commitment on the part of the physician and leadership as they may initially disrupt workflow, but ultimately have the ability to enhance patient care. ASCO criteria have been published for the development and implementation of high-quality oncology pathway programs. Future challenges for pathways include incorporation of molecular testing and appropriate targeted care in a real-time precision oncology approach.

Clinical pathways for acute coronary syndromes in China: protocol for a hospital quality improvement initiative.

PubMed

Rong, Ye; Turnbull, Fiona; Patel, Anushka; Du, Xin; Wu, Yangfeng; Gao, Runlin

2010-09-01

Clinical pathways have been shown to be effective in improving quality of care for patients admitted to hospital for acute coronary syndromes (ACS) in high-income countries. However, their utility has not formally been evaluated in low- or middle-income countries. The Clinical Pathways for Acute Coronary Syndromes in China program is a 7-year study with the overall goal of reducing evidence-practice gaps in the management of patients admitted to hospitals in China with suspected ACS. The program comprises 2 phases: a prospective survey of current management of ACS patients to identify the areas that evidence-based patient care can be potentially improved, and a quality care initiative to maximize the use of evidence-based investigations and treatments for ACS patients in China. In this article, we outline the details of the study protocol, including key aspects of the development, implementation, and evaluation of the quality improvement initiative (clinical pathway) for management of patients with suspected ACS.

Measuring the quality of end of life management in patients with advanced kidney disease: results from the pan-Thames renal audit group.

PubMed

McAdoo, Stephen P; Brown, Edwina A; Chesser, Alistair M; Farrington, Ken; Salisbury, Emma M

2012-04-01

Despite a recent increased awareness of the need for quality End of Life (EOL) care for patients with advanced kidney disease, there is no established method for measuring or auditing outcomes relating to EOL care in this population. We designed a one-page proforma, which was used to collect data on various aspects of EOL care relating to all deaths of patients on dialysis and patients dying on specialist renal wards, over a predefined 8-week period in 10 hospitals in London and South-East England. One hundred and thirty-eight deaths were recorded over the 8-week study period. The majority of patients (83%) were receiving maintenance haemodialysis prior to their terminal presentation. About 69% of deaths occurred during an in-patient hospital admission-of these, 36% were considered 'unexpected' and most quality markers of good EOL management were significantly less likely to be achieved in these patients, including use of palliative care strategies, good symptom control and overall quality of death. Thirty-six per cent of patients were from various ethnic minorities, and in this group, there was a trend towards lower use of palliative care pathways and lower rates of withdrawal from dialysis. This study confirms that it is possible to measure many important outcomes relating to quality of EOL care using a proforma completed at the time of death. Our findings suggest that many aspects of good EOL care are under-achieved in our region. This, in part, is due to a failure to recognize the worsening trajectory of the deteriorating patient, resulting in missed opportunities for EOL care planning and appropriate symptom control. Our observations suggest that there is a need for improved education and training in this area, particularly in detection of the dying patient, the value of advance care planning and the utility of tools such as the Liverpool Care Pathway.

ERK signaling pathway regulates sleep duration through activity-induced gene expression during wakefulness.

PubMed

Mikhail, Cyril; Vaucher, Angélique; Jimenez, Sonia; Tafti, Mehdi

2017-01-24

Wakefulness is accompanied by experience-dependent synaptic plasticity and an increase in activity-regulated gene transcription. Wake-induced genes are certainly markers of neuronal activity and may also directly regulate the duration of and need for sleep. We stimulated murine cortical cultures with the neuromodulatory signals that are known to control wakefulness in the brain and found that norepinephrine alone or a mixture of these neuromodulators induced activity-regulated gene transcription. Pharmacological inhibition of the various signaling pathways involved in the regulation of gene expression indicated that the extracellular signal-regulated kinase (ERK) pathway is the principal one mediating the effects of waking neuromodulators on gene expression. In mice, ERK phosphorylation in the cortex increased and decreased with wakefulness and sleep. Whole-body or cortical neuron-specific deletion of Erk1 or Erk2 significantly increased the duration of wakefulness in mice, and pharmacological inhibition of ERK phosphorylation decreased sleep duration and increased the duration of wakefulness bouts. Thus, this signaling pathway, which is highly conserved from Drosophila to mammals, is a key pathway that links waking experience-induced neuronal gene expression to sleep duration and quality. Copyright © 2017, American Association for the Advancement of Science.

Anesthesia for the patient undergoing total knee replacement: current status and future prospects

PubMed Central

Turnbull, Zachary A; Sastow, Dahniel; Giambrone, Gregory P; Tedore, Tiffany

2017-01-01

Total knee arthroplasty (TKA) has become one of the most common orthopedic surgical procedures performed nationally. As the population and surgical techniques for TKAs have evolved over time, so have the anesthesia and analgesia used for these procedures. General anesthesia has been the dominant form of anesthesia utilized for TKA in the past, but regional anesthetic techniques are on the rise. Multiple studies have shown the potential for regional anesthesia to improve patient outcomes, such as a decrease in intraoperative blood loss, length of stay, and patient mortality. Anesthesiologists are also moving toward multimodal analgesia, which includes peripheral nerve blockade, periarticular injection, and preemptive analgesia. The goal of multimodal analgesia is to improve perioperative pain control while minimizing systemic narcotic consumption. With improved postoperative pain management and rapid patient rehabilitation, new clinical pathways have been engineered to fast track patient recovery after orthopedic procedures. The aim of these clinical pathways was to improve quality of care, minimize unnecessary variations in care, and reduce cost by using streamlined procedures and protocols. The future of TKA care will be formalized clinical pathways and tracks to better optimize perioperative algorithms with regard to pain control and perioperative rehabilitation. PMID:28331362

Anesthesia for the patient undergoing total knee replacement: current status and future prospects.

PubMed

Turnbull, Zachary A; Sastow, Dahniel; Giambrone, Gregory P; Tedore, Tiffany

2017-01-01

Total knee arthroplasty (TKA) has become one of the most common orthopedic surgical procedures performed nationally. As the population and surgical techniques for TKAs have evolved over time, so have the anesthesia and analgesia used for these procedures. General anesthesia has been the dominant form of anesthesia utilized for TKA in the past, but regional anesthetic techniques are on the rise. Multiple studies have shown the potential for regional anesthesia to improve patient outcomes, such as a decrease in intraoperative blood loss, length of stay, and patient mortality. Anesthesiologists are also moving toward multimodal analgesia, which includes peripheral nerve blockade, periarticular injection, and preemptive analgesia. The goal of multimodal analgesia is to improve perioperative pain control while minimizing systemic narcotic consumption. With improved postoperative pain management and rapid patient rehabilitation, new clinical pathways have been engineered to fast track patient recovery after orthopedic procedures. The aim of these clinical pathways was to improve quality of care, minimize unnecessary variations in care, and reduce cost by using streamlined procedures and protocols. The future of TKA care will be formalized clinical pathways and tracks to better optimize perioperative algorithms with regard to pain control and perioperative rehabilitation.

Social constraints and quality of life among Chinese-speaking breast cancer survivors: a mediation model.

PubMed

You, Jin; Lu, Qian

2014-11-01

Literature has revealed detrimental effects of unsupportive interpersonal interactions on adjustment to cancer. However, no studies have examined this effect and the underlying psychological pathways among Chinese-speaking breast cancer survivors. The study investigated the relationship between social constraints and adjustment to cancer and the underlying psychological pathways among Chinese-speaking breast cancer survivors. Chinese-speaking breast cancer survivors (N = 120) completed a questionnaire package assessing social constraints, intrusive thoughts, affect, and quality of life. Results revealed a negative relationship between social constraints and quality of life. Such a relationship between social constraints and quality of life was mediated by negative affect and intrusive thoughts, while the association of intrusive thoughts and quality of life were completely mediated by positive and negative affect. Findings highlight the negative association between unsupportive interpersonal interactions and adjustment through cognitive and affective pathways among Chinese-speaking breast cancer survivors.

American Society for Enhanced Recovery (ASER) and Perioperative Quality Initiative (POQI) joint consensus statement on measurement to maintain and improve quality of enhanced recovery pathways for elective colorectal surgery.

PubMed

Moonesinghe, S Ramani; Grocott, Michael P W; Bennett-Guerrero, Elliott; Bergamaschi, Roberto; Gottumukkala, Vijaya; Hopkins, Thomas J; McCluskey, Stuart; Gan, Tong J; Mythen, Michael Monty G; Shaw, Andrew D; Miller, Timothy E

2017-01-01

This article sets out a framework for measurement of quality of care relevant to enhanced recovery pathways (ERPs) in elective colorectal surgery. The proposed framework is based on established measurement systems and/or theories, and provides an overview of the different approaches for improving clinical monitoring, and enhancing quality improvement or research in varied settings with different levels of available resources. Using a structure-process-outcome framework, we make recommendations for three hierarchical tiers of data collection. Core, Quality Improvement, and Best Practice datasets are proposed. The suggested datasets incorporate patient data to describe case-mix, process measures to describe delivery of enhanced recovery and clinical outcomes. The fundamental importance of routine collection of data for the initiation, maintenance, and enhancement of enhanced recovery pathways is emphasized.

Radiation Quality Effects on Transcriptome Profiles in 3-d Cultures After Particle Irradiation

NASA Technical Reports Server (NTRS)

Patel, Z. S.; Kidane, Y. H.; Huff, J. L.

2014-01-01

In this work, we evaluate the differential effects of low- and high-LET radiation on 3-D organotypic cultures in order to investigate radiation quality impacts on gene expression and cellular responses. Reducing uncertainties in current risk models requires new knowledge on the fundamental differences in biological responses (the so-called radiation quality effects) triggered by heavy ion particle radiation versus low-LET radiation associated with Earth-based exposures. We are utilizing novel 3-D organotypic human tissue models that provide a format for study of human cells within a realistic tissue framework, thereby bridging the gap between 2-D monolayer culture and animal models for risk extrapolation to humans. To identify biological pathway signatures unique to heavy ion particle exposure, functional gene set enrichment analysis (GSEA) was used with whole transcriptome profiling. GSEA has been used extensively as a method to garner biological information in a variety of model systems but has not been commonly used to analyze radiation effects. It is a powerful approach for assessing the functional significance of radiation quality-dependent changes from datasets where the changes are subtle but broad, and where single gene based analysis using rankings of fold-change may not reveal important biological information. We identified 45 statistically significant gene sets at 0.05 q-value cutoff, including 14 gene sets common to gamma and titanium irradiation, 19 gene sets specific to gamma irradiation, and 12 titanium-specific gene sets. Common gene sets largely align with DNA damage, cell cycle, early immune response, and inflammatory cytokine pathway activation. The top gene set enriched for the gamma- and titanium-irradiated samples involved KRAS pathway activation and genes activated in TNF-treated cells, respectively. Another difference noted for the high-LET samples was an apparent enrichment in gene sets involved in cycle cycle/mitotic control. It is plausible that the enrichment in these particular pathways results from the complex DNA damage resulting from high-LET exposure where repair processes are not completed during the same time scale as the less complex damage resulting from low-LET radiation.

Impact of 5'-amp-activated Protein Kinase on Male Gonad and Spermatozoa Functions.

PubMed

Nguyen, Thi Mong Diep

2017-01-01

As we already know, the male reproductive system requires less energetic investment than the female one. Nevertheless, energy balance is an important feature for spermatozoa production in the testis and for spermatozoa properties after ejaculation. The 5'-AMP-activated protein kinase, AMPK, is a sensor of cell energy, that regulates many metabolic pathways and that has been recently shown to control spermatozoa quality and functions. It is indeed involved in the regulation of spermatozoa quality through its action on the proliferation of testicular somatic cells (Sertoli and Leydig), on spermatozoa motility and acrosome reaction. It also favors spermatozoa quality through the management of lipid peroxidation and antioxidant enzymes. I review here the most recent data available on the roles of AMPK in vertebrate spermatozoa functions.

Insights into RNA processing pathways and associated-RNA degrading enzymes in Archaea.

PubMed

Clouet-d'Orval, Béatrice; Batista, Manon; Bouvier, Marie; Quentin, Yves; Fichant, Gwennaele; Marchfelder, Anita; Maier, Lisa-Katharina

2018-04-19

RNA processing pathways are at the center of regulation of gene expression. All RNA transcripts undergo multiple maturation steps in addition to covalent chemical modifications to become functional in the cell. This includes destroying unnecessary or defective cellular RNAs. In Archaea, information on mechanisms by which RNA species reach their mature forms and associated RNA-modifying enzymes is still fragmentary. To date, most archaeal actors and pathways have been proposed in light of information gathered from Bacteria and Eukarya. In this context, this review provides a state of the art overview of archaeal endoribonucleases and exoribonucleases that cleave and trim RNA species and also of the key small archaeal proteins that bind RNAs. Furthermore, synthetic up-to-date views of processing and biogenesis pathways of archaeal transfer and ribosomal RNAs as well as of maturation of stable small non-coding RNAs such as CRISPR RNAs, small C/D and H/ACA box guide RNAs, and other emerging classes of small RNAs are described. Finally prospective post-transcriptional mechanisms to control archaeal messenger RNA quality and quantity are discussed.

Benchmarking the perioperative process: II. Introducing anesthesia clinical pathways to improve processes and outcomes and to reduce nursing labor intensity in ambulatory orthopedic surgery.

PubMed

Williams, B A; DeRiso, B M; Engel, L B; Figallo, C M; Anders, J W; Sproul, K A; Ilkin, H; Harner, C D; Fu, F H; Nagarajan, N J; Evans, J H; Watkins, W D

1998-11-01

(1) To introduce anesthesia clinical pathways as a management tool to improve the quality of care; (2) to use the Procedural Times Glossary published by the Association of Anesthesia Clinical Directors (AACD) as a template for data collection and analysis; and (3) to determine the effects of anesthesia clinical pathways on surgical processes, outcomes, and costs in common ambulatory orthopedic surgery. Hospital database and patient chart review of consecutive patients undergoing anterior cruciate ligament reconstruction (ACLR) during academic years (AY) 1995-1996 and 1996-1997. Patient data from AY 1995-1996, during which no intraoperative anesthesia clinical pathways existed, served as historical controls. Data from AY 1996-1997, during which intraoperative anesthesia clinical pathways were used, served as the treatment group. Regional anesthesia options were routinely offered to patients in the clinical pathway. Ambulatory surgery center in a teaching hospital. The records of 503 ASA physical status I and II patients were reviewed. 1996-1997 patients underwent clinical pathway anesthesia care in which the intraoperative and postoperative anesthesia process was standardized with respect to symptom management, drugs, and equipment used. 1995-1996 patients did not have a standardized intraoperative and postoperative anesthetic course with respect to the management of common symptoms or to specific drugs and supplies used. Intervals described in the AACD Procedural Times Glossary, anesthesia drug and supply costs, and patient outcome variables (postoperative nursing interventions required and unexpected admissions), as influenced by the use of the anesthesia clinical pathway, were measured. Clinical pathway anesthesia care of ACLR in 1996-1997, which actively incorporated regional anesthesia options, reduced pharmacy and materials cost variability; slightly increased turnover time; improved intraoperative anesthesia and surgical efficiency, recovery times, and unexpected admission rates; and decreased the number of required nursing interventions for common postoperative symptoms. Clinical pathway patient management systems in anesthesia care are likely to produce useful outcome data of current practice patterns when compared with historical controls. This management tool may be useful in simultaneously containing costs and improving process efficiency and patient outcomes.

Integrating biomass quality variability in stochastic supply chain modeling and optimization for large-scale biofuel production

DOE Office of Scientific and Technical Information (OSTI.GOV)

Castillo-Villar, Krystel K.; Eksioglu, Sandra; Taherkhorsandi, Milad

The production of biofuels using second-generation feedstocks has been recognized as an important alternative source of sustainable energy and its demand is expected to increase due to regulations such as the Renewable Fuel Standard. However, the pathway to biofuel industry maturity faces unique, unaddressed challenges. Here, to address this challenges, this article presents an optimization model which quantifies and controls the impact of biomass quality variability on supply chain related decisions and technology selection. We propose a two-stage stochastic programming model and associated efficient solution procedures for solving large-scale problems to (1) better represent the random nature of the biomassmore » quality (defined by moisture and ash contents) in supply chain modeling, and (2) assess the impact of these uncertainties on the supply chain design and planning. The proposed model is then applied to a case study in the state of Tennessee. Results show that high moisture and ash contents negatively impact the unit delivery cost since poor biomass quality requires the addition of quality control activities. Experimental results indicate that supply chain cost could increase as much as 27%–31% when biomass quality is poor. We assess the impact of the biomass quality on the topological supply chain. Our case study indicates that biomass quality impacts supply chain costs; thus, it is important to consider the impact of biomass quality in supply chain design and management decisions.« less

Integrating biomass quality variability in stochastic supply chain modeling and optimization for large-scale biofuel production

DOE PAGES

Castillo-Villar, Krystel K.; Eksioglu, Sandra; Taherkhorsandi, Milad

2017-02-20

The production of biofuels using second-generation feedstocks has been recognized as an important alternative source of sustainable energy and its demand is expected to increase due to regulations such as the Renewable Fuel Standard. However, the pathway to biofuel industry maturity faces unique, unaddressed challenges. Here, to address this challenges, this article presents an optimization model which quantifies and controls the impact of biomass quality variability on supply chain related decisions and technology selection. We propose a two-stage stochastic programming model and associated efficient solution procedures for solving large-scale problems to (1) better represent the random nature of the biomassmore » quality (defined by moisture and ash contents) in supply chain modeling, and (2) assess the impact of these uncertainties on the supply chain design and planning. The proposed model is then applied to a case study in the state of Tennessee. Results show that high moisture and ash contents negatively impact the unit delivery cost since poor biomass quality requires the addition of quality control activities. Experimental results indicate that supply chain cost could increase as much as 27%–31% when biomass quality is poor. We assess the impact of the biomass quality on the topological supply chain. Our case study indicates that biomass quality impacts supply chain costs; thus, it is important to consider the impact of biomass quality in supply chain design and management decisions.« less

Pathologic and Therapeutic Implications for the Cell Biology of Parkin

PubMed Central

Charan, Rakshita A.; LaVoie, Matthew J.

2015-01-01

Mutations in the E3 ligase parkin are the most common cause of autosomal recessive Parkinson's disease (PD), but it is believed that parkin dysfunction may also contribute to idiopathic PD. Since its discovery, parkin has been implicated in supporting multiple neuroprotective pathways, many revolving around the maintenance of mitochondrial health quality control and governance of cell survival. Recent advances across the structure, biochemistry, and cell biology of parkin have provided great insights into the etiology of parkin-linked and idiopathic PD and may ultimately generate novel therapeutic strategies to slow or halt disease progression. This review describes the various pathways in which parkin acts and the mechanisms by which parkin may be targeted for therapeutic intervention. PMID:25697646

Integrated analyses for genetic markers of polycystic ovary syndrome with 9 case-control studies of gene expression profiles.

PubMed

Lu, Chenqi; Liu, Xiaoqin; Wang, Lin; Jiang, Ning; Yu, Jun; Zhao, Xiaobo; Hu, Hairong; Zheng, Saihua; Li, Xuelian; Wang, Guiying

2017-01-10

Due to genetic heterogeneity and variable diagnostic criteria, genetic studies of polycystic ovary syndrome are particularly challenging. Furthermore, lack of sufficiently large cohorts limits the identification of susceptibility genes contributing to polycystic ovary syndrome. Here, we carried out a systematic search of studies deposited in the Gene Expression Omnibus database through August 31, 2016. The present analyses included studies with: 1) patients with polycystic ovary syndrome and normal controls, 2) gene expression profiling of messenger RNA, and 3) sufficient data for our analysis. Ultimately, a total of 9 studies with 13 datasets met the inclusion criteria and were performed for the subsequent integrated analyses. Through comprehensive analyses, there were 13 genetic factors overlapped in all datasets and identified as significant specific genes for polycystic ovary syndrome. After quality control assessment, there were six datasets remained. Further gene ontology enrichment and pathway analyses suggested that differentially expressed genes mainly enriched in oocyte pathways. These findings provide potential molecular markers for diagnosis and prognosis of polycystic ovary syndrome, and need in-depth studies on the exact function and mechanism in polycystic ovary syndrome.

Sorting receptor Rer1 controls surface expression of muscle acetylcholine receptors by ER retention of unassembled alpha-subunits.

PubMed

Valkova, Christina; Albrizio, Marina; Röder, Ira V; Schwake, Michael; Betto, Romeo; Rudolf, Rüdiger; Kaether, Christoph

2011-01-11

The nicotinic acetylcholine receptor of skeletal muscle is composed of five subunits that are assembled in a stepwise manner. Quality control mechanisms ensure that only fully assembled receptors reach the cell surface. Here, we show that Rer1, a putative Golgi-ER retrieval receptor, is involved in the biogenesis of acetylcholine receptors. Rer1 is expressed in the early secretory pathway in the myoblast line C2C12 and in mouse skeletal muscle, and up-regulated during myogenesis. Upon down-regulation of Rer1 in C2C12 cells, unassembled acetylcholine receptor α-subunits escape from the ER and are transported to the plasma membrane and lysosomes, where they are degraded. As a result, the amount of fully assembled receptor at the cell surface is reduced. In vivo Rer1 knockdown and genetic inactivation of one Rer1 allele lead to significantly smaller neuromuscular junctions in mice. Our data show that Rer1 is a functionally important unique factor that controls surface expression of muscle acetylcholine receptors by localizing unassembled α-subunits to the early secretory pathway.

Identifying biomarkers of dietary patterns by using metabolomics123

PubMed Central

Derkach, Andriy; Reedy, Jill; Subar, Amy F; Sampson, Joshua N; Albanes, Demetrius; Gu, Fangyi; Kontto, Jukka; Lassale, Camille; Liao, Linda M; Männistö, Satu; Mondul, Alison M; Weinstein, Stephanie J; Irwin, Melinda L; Mayne, Susan T; Stolzenberg-Solomon, Rachael

2017-01-01

Background: Healthy dietary patterns that conform to national dietary guidelines are related to lower chronic disease incidence and longer life span. However, the precise mechanisms involved are unclear. Identifying biomarkers of dietary patterns may provide tools to validate diet quality measurement and determine underlying metabolic pathways influenced by diet quality. Objective: The objective of this study was to examine the correlation of 4 diet quality indexes [the Healthy Eating Index (HEI) 2010, the Alternate Mediterranean Diet Score (aMED), the WHO Healthy Diet Indicator (HDI), and the Baltic Sea Diet (BSD)] with serum metabolites. Design: We evaluated dietary patterns and metabolites in male Finnish smokers (n = 1336) from 5 nested case-control studies within the Alpha-Tocopherol, Beta-Carotene Cancer Prevention Study cohort. Participants completed a validated food-frequency questionnaire and provided a fasting serum sample before study randomization (1985–1988). Metabolites were measured with the use of mass spectrometry. We analyzed cross-sectional partial correlations of 1316 metabolites with 4 diet quality indexes, adjusting for age, body mass index, smoking, energy intake, education, and physical activity. We pooled estimates across studies with the use of fixed-effects meta-analysis with Bonferroni correction for multiple comparisons, and conducted metabolic pathway analyses. Results: The HEI-2010, aMED, HDI, and BSD were associated with 23, 46, 23, and 33 metabolites, respectively (17, 21, 11, and 10 metabolites, respectively, were chemically identified; r-range: −0.30 to 0.20; P = 6 × 10−15 to 8 × 10−6). Food-based diet indexes (HEI-2010, aMED, and BSD) were associated with metabolites correlated with most components used to score adherence (e.g., fruit, vegetables, whole grains, fish, and unsaturated fat). HDI correlated with metabolites related to polyunsaturated fat and fiber components, but not other macro- or micronutrients (e.g., percentages of protein and cholesterol). The lysolipid and food and plant xenobiotic pathways were most strongly associated with diet quality. Conclusions: Diet quality, measured by healthy diet indexes, is associated with serum metabolites, with the specific metabolite profile of each diet index related to the diet components used to score adherence. This trial was registered at clinicaltrials.gov as NCT00342992. PMID:28031192

Protein degradation pathways in Parkinson's disease: curse or blessing.

PubMed

Ebrahimi-Fakhari, Darius; Wahlster, Lara; McLean, Pamela J

2012-08-01

Protein misfolding, aggregation and deposition are common disease mechanisms in many neurodegenerative diseases including Parkinson's disease (PD). Accumulation of damaged or abnormally modified proteins may lead to perturbed cellular function and eventually to cell death. Thus, neurons rely on elaborated pathways of protein quality control and removal to maintain intracellular protein homeostasis. Molecular chaperones, the ubiquitin-proteasome system (UPS) and the autophagy-lysosomal pathway (ALP) are critical pathways that mediate the refolding or removal of abnormal proteins. The successive failure of these protein degradation pathways, as a cause or consequence of early pathological alterations in vulnerable neurons at risk, may present a key step in the pathological cascade that leads to spreading neurodegeneration. A growing number of studies in disease models and patients have implicated dysfunction of the UPS and ALP in the pathogenesis of Parkinson's disease and related disorders. Deciphering the exact mechanism by which the different proteolytic systems contribute to the elimination of pathogenic proteins, like α-synuclein, is therefore of paramount importance. We herein review the role of protein degradation pathways in Parkinson's disease and elaborate on the different contributions of the UPS and the ALP to the clearance of altered proteins. We examine the interplay between different degradation pathways and provide a model for the role of the UPS and ALP in the evolution and progression of α-synuclein pathology. With regards to exciting recent studies we also discuss the putative potential of using protein degradation pathways as novel therapeutic targets in Parkinson's disease.

Metabolic flux and nodes control analysis of brewer's yeasts under different fermentation temperature during beer brewing.

PubMed

Yu, Zhimin; Zhao, Haifeng; Zhao, Mouming; Lei, Hongjie; Li, Huiping

2012-12-01

The aim of this work was to further investigate the glycolysis performance of lager and ale brewer's yeasts under different fermentation temperature using a combined analysis of metabolic flux, glycolytic enzyme activities, and flux control. The results indicated that the fluxes through glycolytic pathway decreased with the change of the fermentation temperature from 15 °C to 10 °C, which resulted in the prolonged fermentation times. The maximum activities (V (max)) of hexokinase (HK), phosphofructokinase (PFK), and pyruvate kinase (PK) at key nodes of glycolytic pathway decreased with decreasing fermentation temperature, which was estimated to have different control extent (22-84 %) on the glycolytic fluxes in exponential or flocculent phase. Moreover, the decrease of V (max) of PFK or PK displayed the crucial role in down-regulation of flux in flocculent phase. In addition, the metabolic state of ale strain was more sensitive to the variation of temperature than that of lager strain. The results of the metabolic flux and nodes control analysis in brewer's yeasts under different fermentation temperature may provide an alternative approach to regulate glycolytic flux by changing V (max) and improve the production efficiency and beer quality.

A Randomized, Placebo-controlled Trial of Roflumilast. Effect on Proline-Glycine-Proline and Neutrophilic Inflammation in Chronic Obstructive Pulmonary Disease.

PubMed

Wells, J Michael; Jackson, Patricia L; Viera, Liliana; Bhatt, Surya P; Gautney, Joshua; Handley, Guy; King, R Wilson; Xu, Xin; Gaggar, Amit; Bailey, William C; Dransfield, Mark T; Blalock, J Edwin

2015-10-15

Roflumilast is a therapeutic agent in the treatment of chronic obstructive pulmonary disease (COPD). It has antiinflammatory effects; however, it is not known whether it can affect a biologic pathway implicated in COPD pathogenesis and progression. The self-propagating acetyl-proline-glycine-proline (AcPGP) pathway is a novel means of neutrophilic inflammation that is pathologic in the development of COPD. AcPGP is produced by extracellular matrix collagen breakdown with prolyl endopeptidase and leukotriene A4 hydrolase serving as the enzymes responsible for its production and degradation, respectively. We hypothesized that roflumilast would decrease AcPGP, halting the feed-forward cycle of inflammation. We conducted a single-center, placebo-controlled, randomized study investigating 12 weeks of roflumilast treatment added to current therapy in moderate-to-severe COPD with chronic bronchitis. Subjects underwent sputum and blood analyses, pulmonary function testing, exercise tolerance, and quality-of-life assessment at 0, 4, and 12 weeks. Twenty-seven patients were enrolled in the intention-to-treat analysis. Roflumilast treatment decreased sputum AcPGP by more than 50% (P < 0.01) and prolyl endopeptidase by 46% (P = 0.02), without significant improvement in leukotriene A4 hydrolase activity compared with placebo. Roflumilast also reduces other inflammatory markers. There were no significant changes in lung function, quality of life, or exercise tolerance between roflumilast- and placebo-treated groups. Roflumilast reduces pulmonary inflammation through decreasing prolyl endopeptidase activity and AcPGP. As expected for lower AcPGP levels, markers of neutrophilic inflammation are blunted. Inhibiting this self-propagating pathway lessens the overall inflammatory burden, which may alter the natural history of COPD, including the risk of exacerbation. Clinical trial registered with www.clinicaltrials.gov (NCT 01572948).

Mechanisms of sterol uptake and transport in yeast.

PubMed

Jacquier, Nicolas; Schneiter, Roger

2012-03-01

Sterols are essential lipid components of eukaryotic membranes. Here we summarize recent advances in understanding how sterols are transported between different membranes. Baker's yeast is a particularly attractive organism to dissect this lipid transport pathway, because cells can synthesize their own major sterol, ergosterol, in the membrane of the endoplasmic reticulum from where it is then transported to the plasma membrane. However, Saccharomyces cerevisiae is also a facultative anaerobic organism, which becomes sterol auxotroph in the absence of oxygen. Under these conditions, cells take up sterol from the environment and transport the lipid back into the membrane of the endoplasmic reticulum, where the free sterol becomes esterified and is then stored in lipid droplets. Steryl ester formation is thus a reliable readout to assess the back-transport of exogenously provided sterols from the plasma membrane to the endoplasmic reticulum. Structure/function analysis has revealed that the bulk membrane function of the fungal ergosterol can be provided by structurally related sterols, including the mammalian cholesterol. Foreign sterols, however, are subject to a lipid quality control cycle in which the sterol is reversibly acetylated. Because acetylated sterols are efficiently excreted from cells, the substrate specificity of the deacetylating enzymes determines which sterols are retained. Membrane-bound acetylated sterols are excreted by the secretory pathway, more soluble acetylated sterol derivatives such as the steroid precursor pregnenolone, on the other hand, are excreted by a pathway that is independent of vesicle formation and fusion. Further analysis of this lipid quality control cycle is likely to reveal novel insight into the mechanisms that ensure sterol homeostasis in eukaryotic cells. Article from a special issue on Steroids and Microorganisms. Copyright © 2010. Published by Elsevier Ltd.

The ventral visual pathway: an expanded neural framework for the processing of object quality.

PubMed

Kravitz, Dwight J; Saleem, Kadharbatcha S; Baker, Chris I; Ungerleider, Leslie G; Mishkin, Mortimer

2013-01-01

Since the original characterization of the ventral visual pathway, our knowledge of its neuroanatomy, functional properties, and extrinsic targets has grown considerably. Here we synthesize this recent evidence and propose that the ventral pathway is best understood as a recurrent occipitotemporal network containing neural representations of object quality both utilized and constrained by at least six distinct cortical and subcortical systems. Each system serves its own specialized behavioral, cognitive, or affective function, collectively providing the raison d'être for the ventral visual pathway. This expanded framework contrasts with the depiction of the ventral visual pathway as a largely serial staged hierarchy culminating in singular object representations and more parsimoniously incorporates attentional, contextual, and feedback effects. Published by Elsevier Ltd.

Regulation of gene expression in mammalian nervous system through alternative pre-mRNA splicing coupled with RNA quality control mechanisms.

PubMed

Yap, Karen; Makeyev, Eugene V

2013-09-01

Eukaryotic gene expression is orchestrated on a genome-wide scale through several post-transcriptional mechanisms. Of these, alternative pre-mRNA splicing expands the proteome diversity and modulates mRNA stability through downstream RNA quality control (QC) pathways including nonsense-mediated decay (NMD) of mRNAs containing premature termination codons and nuclear retention and elimination (NRE) of intron-containing transcripts. Although originally identified as mechanisms for eliminating aberrant transcripts, a growing body of evidence suggests that NMD and NRE coupled with deliberate changes in pre-mRNA splicing patterns are also used in a number of biological contexts for deterministic control of gene expression. Here we review recent studies elucidating molecular mechanisms and biological significance of these gene regulation strategies with a specific focus on their roles in nervous system development and physiology. This article is part of a Special Issue entitled 'RNA and splicing regulation in neurodegeneration'. Copyright © 2013 Elsevier Inc. All rights reserved.

Building Data-Driven Pathways From Routinely Collected Hospital Data: A Case Study on Prostate Cancer

PubMed Central

Clark, Jeremy; Cooper, Colin S; Mills, Robert; Rayward-Smith, Victor J; de la Iglesia, Beatriz

2015-01-01

Background Routinely collected data in hospitals is complex, typically heterogeneous, and scattered across multiple Hospital Information Systems (HIS). This big data, created as a byproduct of health care activities, has the potential to provide a better understanding of diseases, unearth hidden patterns, and improve services and cost. The extent and uses of such data rely on its quality, which is not consistently checked, nor fully understood. Nevertheless, using routine data for the construction of data-driven clinical pathways, describing processes and trends, is a key topic receiving increasing attention in the literature. Traditional algorithms do not cope well with unstructured processes or data, and do not produce clinically meaningful visualizations. Supporting systems that provide additional information, context, and quality assurance inspection are needed. Objective The objective of the study is to explore how routine hospital data can be used to develop data-driven pathways that describe the journeys that patients take through care, and their potential uses in biomedical research; it proposes a framework for the construction, quality assessment, and visualization of patient pathways for clinical studies and decision support using a case study on prostate cancer. Methods Data pertaining to prostate cancer patients were extracted from a large UK hospital from eight different HIS, validated, and complemented with information from the local cancer registry. Data-driven pathways were built for each of the 1904 patients and an expert knowledge base, containing rules on the prostate cancer biomarker, was used to assess the completeness and utility of the pathways for a specific clinical study. Software components were built to provide meaningful visualizations for the constructed pathways. Results The proposed framework and pathway formalism enable the summarization, visualization, and querying of complex patient-centric clinical information, as well as the computation of quality indicators and dimensions. A novel graphical representation of the pathways allows the synthesis of such information. Conclusions Clinical pathways built from routinely collected hospital data can unearth information about patients and diseases that may otherwise be unavailable or overlooked in hospitals. Data-driven clinical pathways allow for heterogeneous data (ie, semistructured and unstructured data) to be collated over a unified data model and for data quality dimensions to be assessed. This work has enabled further research on prostate cancer and its biomarkers, and on the development and application of methods to mine, compare, analyze, and visualize pathways constructed from routine data. This is an important development for the reuse of big data in hospitals. PMID:26162314

[Exploration of common biological pathways for attention deficit hyperactivity disorder and low birth weight].

PubMed

Xiang, Bo; Yu, Minglan; Liang, Xuemei; Lei, Wei; Huang, Chaohua; Chen, Jing; He, Wenying; Zhang, Tao; Li, Tao; Liu, Kezhi

2017-12-10

To explore common biological pathways for attention deficit hyperactivity disorder (ADHD) and low birth weight (LBW). Thei-Gsea4GwasV2 software was used to analyze the result of genome-wide association analysis (GWAS) for LBW (pathways were derived from Reactome), and nominally significant (P< 0.05, FDR< 0.25) pathways were tested for replication in ADHD.Significant pathways were analyzed with DAPPLE and Reatome FI software to identify genes involved in such pathways, with each cluster enriched with the gene ontology (GO). The Centiscape2.0 software was used to calculate the degree of genetic networks and the betweenness value to explore the core node (gene). Weighed gene co-expression network analysis (WGCNA) was then used to explore the co-expression of genes in these pathways.With gene expression data derived from BrainSpan, GO enrichment was carried out for each gene module. Eleven significant biological pathways was identified in association with LBW, among which two (Selenoamino acid metabolism and Diseases associated with glycosaminoglycan metabolism) were replicated during subsequent ADHD analysis. Network analysis of 130 genes in these pathways revealed that some of the sub-networksare related with morphology of cerebellum, development of hippocampus, and plasticity of synaptic structure. Upon co-expression network analysis, 120 genes passed the quality control and were found to express in 3 gene modules. These modules are mainly related to the regulation of synaptic structure and activity regulation. ADHD and LBW share some biological regulation processes. Anomalies of such proces sesmay predispose to ADHD.

[Killing effect of Huaier combined with DC-CIK on nude mice bearing colon cancer HT29 stem cells in vivo].

PubMed

Sun, Wen-Wen; Dou, Jin-Xia; Zhang, Lin; Qiao, Li-Kui; Shen, Na; Gao, Wen-Yuan

2018-01-01

To compare the therapeutic effects of different treatment methods on the nude mice bearing colon cancer HT29 cells. BalB/C nude mice colon cancer stem cell models were established and randomly divided into the following four groups, with 8 nude mice in each group: blank control group, DC-CIK group, Huaier group, and Huaier combined with DC-CIK group (combined treatment group). The mice in DC-CIK group and combined treatment group received 1×10⁶ DC-CIK cells treatment by tail vein injectionafter the tumor stem cells were inoculated for 4 days,2 times a week for three weeks. The mice in Huaier group and combined treatment group received intragastric administration at the dose of 20 g/60 kg body weight, 0.2 mL/time, once a day for a total of three weeks. The mice in control group received equal volume of normal saline. Tumor size and body weight of nude mice were measured every 2 days during treatment for three weeks in each group. After the treatment, the nude mice were sacrificed to measure the tumor weight and the tumor inhibition rate was calculated. The RT-PCR method was used to detect the expression levels of the key genes in the signal pathway. After the end of the treatment, the quality of the tumor in the Huaier group, DC-CIK group and combined treatment group was significantly lower than that in the control group; the quality in combined treatment group was significantly lower than that in Huaier group and DC-CIK group.Among them, the tumor inhibition rate reached 46.77% in the combined treatment group. In respect of changes in expression levels of key genes in the signaling pathway, the mRNA expression levels of key genes PI3KR1 and Akt in PI3K/Akt pathway, key genes Wnt1 and CTTNB1 in Wnt/ β -catenin pathway, and key genes Notch1, Notch2, Notch3 in Notch pathway in the combined treatment group were lower than those in DC-CIK group and Huaier group. The Huaier combined with DC-CIK group showed best therapeutic effect among different treatment methods for HT29 stemcell colon tumors in nude mice, providing a new idea for clinical treatment of colon cancer. Copyright© by the Chinese Pharmaceutical Association.

Global Air Quality and Climate

NASA Technical Reports Server (NTRS)

Fiore, Arlene M.; Naik, Vaishali; Steiner, Allison; Unger, Nadine; Bergmann, Dan; Prather, Michael; Righi, Mattia; Rumbold, Steven T.; Shindell, Drew T.; Skeie, Ragnhild B.;

Southern Pennsylvania's Industrial Pipeline: "Pathways" Program Helps Local Manufacturers Find Quality Workers

ERIC Educational Resources Information Center

Dixon, John; Girifalco, Tony; Yakabosky, Walt

2008-01-01

This article describes the Applied Engineering Technology (AET) Career and Educational Pathways Program, which helps local manufacturers find quality workers. The program features 32 high schools, three community colleges, and 10 four-year institutions offering an integrated regional system of applied engineering education. The goal is to enroll…

Distinct transcriptional responses elicited by unfolded nuclear or cytoplasmic protein in mammalian cells

PubMed Central

Miyazaki, Yusuke; Chen, Ling-chun; Chu, Bernard W; Swigut, Tomek; Wandless, Thomas J

2015-01-01

Eukaryotic cells possess a variety of signaling pathways that prevent accumulation of unfolded and misfolded proteins. Chief among these is the heat shock response (HSR), which is assumed to respond to unfolded proteins in the cytosol and nucleus alike. In this study, we probe this axiom further using engineered proteins called ‘destabilizing domains’, whose folding state we control with a small molecule. The sudden appearance of unfolded protein in mammalian cells elicits a robust transcriptional response, which is distinct from the HSR and other known pathways that respond to unfolded proteins. The cellular response to unfolded protein is strikingly different in the nucleus and the cytosol, although unfolded protein in either compartment engages the p53 network. This response provides cross-protection during subsequent proteotoxic stress, suggesting that it is a central component of protein quality control networks, and like the HSR, is likely to influence the initiation and progression of human pathologies. DOI: http://dx.doi.org/10.7554/eLife.07687.001 PMID:26314864

TGFbeta regulation of membrane mucin Muc4 via proteosome degradation.

PubMed

Lomako, Wieslawa M; Lomako, Joseph; Soto, Pedro; Carraway, Coralie A Carothers; Carraway, Kermit L

2009-07-01

Muc4 is a heterodimeric membrane mucin implicated in epithelial differentiation and tumor progression. It is expressed from a single gene as a 300 kDa precursor protein which is cleaved in the endoplasmic reticulum to its two subunits. Our previous work has shown that Muc4 is regulated by TGFbeta, which represses the precursor cleavage. Working with Muc4-transfected A375 tumor cells, we now show that Muc4 undergoes proteosomal degradation. Proteosome inhibitors prolong the life of the precursor, shunt the Muc4 into cytoplasmic aggresomes, increase the level of Muc4 associated with the endoplasmic reticulum chaperones calnexin and calreticulin and increase the levels of ubiquitinated Muc4. Most importantly, proteosome inhibitors repress the TGFbeta inhibition of Muc4 expression. These results suggest a model in which TGFbeta inhibits precursor cleavage, shunting the precursor into the proteosomal degradation pathway. Thus, the cells have evolved a mechanism to use the quality control pathway for glycoproteins to control the quantity of the protein produced. 2009 Wiley-Liss, Inc.

Impact of Tortuosity on Charge-Carrier Transport in Organic Bulk Heterojunction Blends

NASA Astrophysics Data System (ADS)

Heiber, Michael C.; Kister, Klaus; Baumann, Andreas; Dyakonov, Vladimir; Deibel, Carsten; Nguyen, Thuc-Quyen

2017-11-01

The impact of the tortuosity of the charge-transport pathways through a bulk heterojunction film on the charge-carrier mobility is theoretically investigated using model morphologies and kinetic Monte Carlo simulations. The tortuosity descriptor provides a quantitative metric to characterize the quality of the charge-transport pathways, and model morphologies with controlled domain size and tortuosity are created using an anisotropic domain growth procedure. The tortuosity is found to be dependent on the anisotropy of the domain structure and is highly tunable. Time-of-flight charge-transport simulations on morphologies with a range of tortuosity values reveal that tortuosity can significantly reduce the magnitude of the mobility and the electric-field dependence relative to a neat material. These reductions are found to be further controlled by the energetic disorder and temperature. Most significantly, the sensitivity of the electric-field dependence to the tortuosity can explain the different experimental relationships previously reported, and exploiting this sensitivity could lead to simpler methods for characterizing and optimizing charge transport in organic solar cells.

Phenotypic characterization of a photomorphogenic mutant.

PubMed

Fankhauser, Christian; Casal, Jorge J

2004-09-01

Light is arguably the most important abiotic factor controlling plant growth and development throughout their life cycle. Plants have evolved sophisticated light-sensing mechanisms to monitor fluctuations in light quality, intensity, direction and periodicity (day length). In Arabidopsis, three families of photoreceptors have been identified by molecular genetic studies. The UV-A/blue light receptors cryptochromes and the red/far-red receptors phytochromes control an overlapping set of responses including photoperiodic flowering induction and de-etiolation. Phototropins are the primary photoreceptors for a set of specific responses to UV-A/blue light such as phototropism, chloroplast movement and stomatal opening. Mutants affecting a photoreceptor have a characteristic phenotype. It is therefore possible to determine the specific developmental responses and the photoreceptor pathway(s) affected in a mutant by performing an appropriate set of photobiological and genetic experiments. In this paper, we outline the principal and easiest experiments that can be performed to obtain a first indication about the nature of the photobiological defect in a given mutant.

Certification Criteria for Linked Learning Pathways

ERIC Educational Resources Information Center

ConnectEd: The California Center for College and Career, 2010

2010-01-01

Pathways offer a promising strategy for transforming high schools and improving student outcomes. However, to achieve these desired results, pathways must be of high quality. To guide sites in planning and implementing such pathways, a design team of experts developed the criteria outlined in this document. Sites can choose to go through a…

From Field Notes to Data Portal - A Scalable Data QA/QC Framework for Tower Networks: Progress and Preliminary Results

NASA Astrophysics Data System (ADS)

Sturtevant, C.; Hackley, S.; Lee, R.; Holling, G.; Bonarrigo, S.

2017-12-01

Quality assurance and control (QA/QC) is one of the most important yet challenging aspects of producing research-quality data. Data quality issues are multi-faceted, including sensor malfunctions, unmet theoretical assumptions, and measurement interference from humans or the natural environment. Tower networks such as Ameriflux, ICOS, and NEON continue to grow in size and sophistication, yet tools for robust, efficient, scalable QA/QC have lagged. Quality control remains a largely manual process heavily relying on visual inspection of data. In addition, notes of measurement interference are often recorded on paper without an explicit pathway to data flagging. As such, an increase in network size requires a near-proportional increase in personnel devoted to QA/QC, quickly stressing the human resources available. We present a scalable QA/QC framework in development for NEON that combines the efficiency and standardization of automated checks with the power and flexibility of human review. This framework includes fast-response monitoring of sensor health, a mobile application for electronically recording maintenance activities, traditional point-based automated quality flagging, and continuous monitoring of quality outcomes and longer-term holistic evaluations. This framework maintains the traceability of quality information along the entirety of the data generation pipeline, and explicitly links field reports of measurement interference to quality flagging. Preliminary results show that data quality can be effectively monitored and managed for a multitude of sites with a small group of QA/QC staff. Several components of this framework are open-source, including a R-Shiny application for efficiently monitoring, synthesizing, and investigating data quality issues.

Calibration and validation of an activated sludge model for greenhouse gases no. 1 (ASMG1): prediction of temperature-dependent N₂O emission dynamics.

PubMed

Guo, Lisha; Vanrolleghem, Peter A

2014-02-01

An activated sludge model for greenhouse gases no. 1 was calibrated with data from a wastewater treatment plant (WWTP) without control systems and validated with data from three similar plants equipped with control systems. Special about the calibration/validation approach adopted in this paper is that the data are obtained from simulations with a mathematical model that is widely accepted to describe effluent quality and operating costs of actual WWTPs, the Benchmark Simulation Model No. 2 (BSM2). The calibration also aimed at fitting the model to typical observed nitrous oxide (N₂O) emission data, i.e., a yearly average of 0.5% of the influent total nitrogen load emitted as N₂O-N. Model validation was performed by challenging the model in configurations with different control strategies. The kinetic term describing the dissolved oxygen effect on the denitrification by ammonia-oxidizing bacteria (AOB) was modified into a Haldane term. Both original and Haldane-modified models passed calibration and validation. Even though their yearly averaged values were similar, the two models presented different dynamic N₂O emissions under cold temperature conditions and control. Therefore, data collected in such situations can potentially permit model discrimination. Observed seasonal trends in N₂O emissions are simulated well with both original and Haldane-modified models. A mechanistic explanation based on the temperature-dependent interaction between heterotrophic and autotrophic N₂O pathways was provided. Finally, while adding the AOB denitrification pathway to a model with only heterotrophic N₂O production showed little impact on effluent quality and operating cost criteria, it clearly affected N2O emission productions.

Clinical implementation of RNA signatures for pharmacogenomic decision-making

PubMed Central

Tang, Weihua; Hu, Zhiyuan; Muallem, Hind; Gulley, Margaret L

2011-01-01

RNA profiling is increasingly used to predict drug response, dose, or toxicity based on analysis of drug pharmacokinetic or pharmacodynamic pathways. Before implementing multiplexed RNA arrays in clinical practice, validation studies are carried out to demonstrate sufficient evidence of analytic and clinical performance, and to establish an assay protocol with quality assurance measures. Pathologists assure quality by selecting input tissue and by interpreting results in the context of the input tissue as well as the technologies that were used and the clinical setting in which the test was ordered. A strength of RNA profiling is the array-based measurement of tens to thousands of RNAs at once, including redundant tests for critical analytes or pathways to promote confidence in test results. Instrument and reagent manufacturers are crucial for supplying reliable components of the test system. Strategies for quality assurance include careful attention to RNA preservation and quality checks at pertinent steps in the assay protocol, beginning with specimen collection and proceeding through the various phases of transport, processing, storage, analysis, interpretation, and reporting. Specimen quality is checked by probing housekeeping transcripts, while spiked and exogenous controls serve as a check on analytic performance of the test system. Software is required to manipulate abundant array data and present it for interpretation by a laboratory physician who reports results in a manner facilitating therapeutic decision-making. Maintenance of the assay requires periodic documentation of personnel competency and laboratory proficiency. These strategies are shepherding genomic arrays into clinical settings to provide added value to patients and to the larger health care system. PMID:23226056

Deciphering signature of selection affecting beef quality traits in Angus cattle.

PubMed

Taye, Mengistie; Yoon, Joon; Dessie, Tadelle; Cho, Seoae; Oh, Sung Jong; Lee, Hak-Kyo; Kim, Heebal

2018-01-01

Artificial selection towards a desired phenotype/trait has modified the genomes of livestock dramatically that generated breeds that greatly differ in morphology, production and environmental adaptation traits. Angus cattle are among the famous cattle breeds developed for superior beef quality. This paper aimed at exploring genomic regions under selection in Angus cattle that are associated with meat quality traits and other associated phenotypes. The whole genome of 10 Angus cattle was compared with 11 Hanwoo (A-H) and 9 Jersey (A-J) cattle breeds using a cross-population composite likelihood ratio (XP-CLR) statistical method. The top 1% of the empirical distribution was taken as significant and annotated using UMD3.1. As a result, 255 and 210 genes were revealed under selection from A-H and A-J comparisons, respectively. The WebGestalt gene ontology analysis resulted in sixteen (A-H) and five (A-J) significantly enriched KEGG pathways. Several pathways associated with meat quality traits (insulin signaling, type II diabetes mellitus pathway, focal adhesion pathway, and ECM-receptor interaction), and feeding efficiency (olfactory transduction, tight junction, and metabolic pathways) were enriched. Genes affecting beef quality traits (e.g., FABP3, FTO, DGAT2, ACS, ACAA2, CPE, TNNI1), stature and body size (e.g., PLAG1, LYN, CHCHD7, RPS20), fertility and dystocia (e.g., ESR1, RPS20, PPP2R1A, GHRL, PLAG1), feeding efficiency (e.g., PIK3CD, DNAJC28, DNAJC3, GHRL, PLAG1), coat color (e.g., MC1-R) and genetic disorders (e.g., ITGB6, PLAG1) were found to be under positive selection in Angus cattle. The study identified genes and pathways that are related to meat quality traits and other phenotypes of Angus cattle. The findings in this study, after validation using additional or independent dataset, will provide useful information for the study of Angus cattle in particular and beef cattle in general.

Short- and long-term effects of clinical pathway on the quality of surgical non-small cell lung cancer care in China: an interrupted time series study.

PubMed

Wang, Xinyu; Su, Shaofei; Jiang, Hao; Wang, Jiaying; Li, Xi; Liu, Meina

2018-05-01

To examine the short- and long-term effect of clinical pathway for non-small cell lung cancer surgery on the length of stay, the compliance of quality indicators and risk-adjusted post-operative complication rate. A retrospective quasi-experimental study from June 2011 to October 2015. A tertiary cancer hospital in China. Patients diagnosed as non-small cell lung cancer who underwent curative resection. Clinical pathway was implemented at January 2013. Hence, the study period was divided into three periods: pre-pathway, from June 2011 to December 2012; short-term period, from January 2013 to December 2013; long-term period, from January 2014 to October 2015. Three length of hospital stay indicators, four process performance indicators and one outcome indicator. ITS showed there was a significant decline of 2 days (P = 0.0421) for total length of stay and 2.23 days (P = 0.0199) for post-operative length of stay right after the implementation of clinical pathway. Short-term level changes were found in the compliance rate of required number of lymph node sampling (-8.08%, P = 0.0392), and risk-adjusted complication rate (9.02%, P = 0.0001). There were no statistically significant changes in other quality of care indicators. The clinical pathway had a positive impact on the length of stay but showed a transient negative effect on complication rate and the quality of lymph node sampling.

Androgen receptor polyglutamine expansion drives age-dependent quality control defects and muscle dysfunction.

PubMed

Nath, Samir R; Yu, Zhigang; Gipson, Theresa A; Marsh, Gregory B; Yoshidome, Eriko; Robins, Diane M; Todi, Sokol V; Housman, David E; Lieberman, Andrew P

2018-05-29

Skeletal muscle has emerged as a critical, disease-relevant target tissue in spinal and bulbar muscular atrophy, a degenerative disorder of the neuromuscular system caused by a CAG/polyglutamine (polyQ) expansion in the androgen receptor (AR) gene. Here, we used RNA-Seq to identify pathways that are disrupted in diseased muscle using AR113Q knock-in mice. This analysis unexpectedly identified significantly diminished expression of numerous ubiquitin-proteasome pathway genes in AR113Q muscle, encoding approximately 30% of proteasome subunits and 20% of E2 ubiquitin conjugases. These changes were age-, hormone- and glutamine length-dependent and arose due to a toxic gain-of-function conferred by the mutation. Moreover, altered gene expression was associated with decreased level of the proteasome transcription factor NRF1 and its activator DDI2 and resulted in diminished proteasome activity. Ubiquitinated ADRM1 was detected in AR113Q muscle, indicating the occurrence of stalled proteasomes in mutant mice. Finally, diminished expression of Drosophila orthologues of NRF1 or ADRM1 promoted the accumulation of polyQ AR protein and increased toxicity. Collectively, these data indicate that AR113Q muscle develops progressive proteasome dysfunction that leads to the impairment of quality control and the accumulation of polyQ AR protein, key features that contribute to the age-dependent onset and progression of this disorder.

Molecular mechanism of ER stress-induced pre-emptive quality control involving association of the translocon, Derlin-1, and HRD1.

PubMed

Kadowaki, Hisae; Satrimafitrah, Pasjan; Takami, Yasunari; Nishitoh, Hideki

2018-05-09

The maintenance of endoplasmic reticulum (ER) homeostasis is essential for cell function. ER stress-induced pre-emptive quality control (ERpQC) helps alleviate the burden to a stressed ER by limiting further protein loading. We have previously reported the mechanisms of ERpQC, which includes a rerouting step and a degradation step. Under ER stress conditions, Derlin family proteins (Derlins), which are components of ER-associated degradation, reroute specific ER-targeting proteins to the cytosol. Newly synthesized rerouted polypeptides are degraded via the cytosolic chaperone Bag6 and the AAA-ATPase p97 in the ubiquitin-proteasome system. However, the mechanisms by which ER-targeting proteins are rerouted from the ER translocation pathway to the cytosolic degradation pathway and how the E3 ligase ubiquitinates ERpQC substrates remain unclear. Here, we show that ERpQC substrates are captured by the carboxyl-terminus region of Derlin-1 and ubiquitinated by the HRD1 E3 ubiquitin ligase prior to degradation. Moreover, HRD1 forms a large ERpQC-related complex composed of Sec61α and Derlin-1 during ER stress. These findings indicate that the association of the degradation factor HRD1 with the translocon and the rerouting factor Derlin-1 may be necessary for the smooth and effective clearance of ERpQC substrates.

Developability studies before initiation of process development: improving manufacturability of monoclonal antibodies.

PubMed

Yang, Xiaoyu; Xu, Wei; Dukleska, Svetlana; Benchaar, Sabrina; Mengisen, Selina; Antochshuk, Valentyn; Cheung, Jason; Mann, Leslie; Babadjanova, Zulfia; Rowand, Jason; Gunawan, Rico; McCampbell, Alexander; Beaumont, Maribel; Meininger, David; Richardson, Daisy; Ambrogelly, Alexandre

2013-01-01

Monoclonal antibodies constitute a robust class of therapeutic proteins. Their stability, resistance to stress conditions and high solubility have allowed the successful development and commercialization of over 40 antibody-based drugs. Although mAbs enjoy a relatively high probability of success compared with other therapeutic proteins, examples of projects that are suspended due to the instability of the molecule are not uncommon. Developability assessment studies have therefore been devised to identify early during process development problems associated with stability, solubility that is insufficient to meet expected dosing or sensitivity to stress. This set of experiments includes short-term stability studies at 2-8 þC, 25 þC and 40 þC, freeze-thaw studies, limited forced degradation studies and determination of the viscosity of high concentration samples. We present here three case studies reflecting three typical outcomes: (1) no major or unexpected degradation is found and the study results are used to inform early identification of degradation pathways and potential critical quality attributes within the Quality by Design framework defined by US Food and Drug Administration guidance documents; (2) identification of specific degradation pathway(s) that do not affect potency of the molecule, with subsequent definition of proper process control and formulation strategies; and (3) identification of degradation that affects potency, resulting in program termination and reallocation of resources.

The ventral visual pathway: An expanded neural framework for the processing of object quality

PubMed Central

Kravitz, Dwight J.; Saleem, Kadharbatcha S.; Baker, Chris I.; Ungerleider, Leslie G.; Mishkin, Mortimer

2012-01-01

Since the original characterization of the ventral visual pathway our knowledge of its neuroanatomy, functional properties, and extrinsic targets has grown considerably. Here we synthesize this recent evidence and propose that the ventral pathway is best understood as a recurrent occipitotemporal network containing neural representations of object quality both utilized and constrained by at least six distinct cortical and subcortical systems. Each system serves its own specialized behavioral, cognitive, or affective function, collectively providing the raison d’etre for the ventral visual pathway. This expanded framework contrasts with the depiction of the ventral visual pathway as a largely serial staged hierarchy that culminates in singular object representations for utilization mainly by ventrolateral prefrontal cortex and, more parsimoniously than this account, incorporates attentional, contextual, and feedback effects. PMID:23265839

Pathway Analysis of Metabolic Syndrome Using a Genome-Wide Association Study of Korea Associated Resource (KARE) Cohorts.

PubMed

Shim, Unjin; Kim, Han-Na; Sung, Yeon-Ah; Kim, Hyung-Lae

2014-12-01

Metabolic syndrome (MetS) is a complex disorder related to insulin resistance, obesity, and inflammation. Genetic and environmental factors also contribute to the development of MetS, and through genome-wide association studies (GWASs), important susceptibility loci have been identified. However, GWASs focus more on individual single-nucleotide polymorphisms (SNPs), explaining only a small portion of genetic heritability. To overcome this limitation, pathway analyses are being applied to GWAS datasets. The aim of this study is to elucidate the biological pathways involved in the pathogenesis of MetS through pathway analysis. Cohort data from the Korea Associated Resource (KARE) was used for analysis, which include 8,842 individuals (age, 52.2 ± 8.9 years; body mass index, 24.6 ± 3.2 kg/m(2)). A total of 312,121 autosomal SNPs were obtained after quality control. Pathway analysis was conducted using Meta-analysis Gene-Set Enrichment of Variant Associations (MAGENTA) to discover the biological pathways associated with MetS. In the discovery phase, SNPs from chromosome 12, including rs11066280, rs2074356, and rs12229654, were associated with MetS (p < 5 × 10(-6)), and rs11066280 satisfied the Bonferroni-corrected cutoff (unadjusted p < 1.38 × 10(-7), Bonferroni-adjusted p < 0.05). Through pathway analysis, biological pathways, including electron carrier activity, signaling by platelet-derived growth factor (PDGF), the mitogen-activated protein kinase kinase kinase cascade, PDGF binding, peroxisome proliferator-activated receptor (PPAR) signaling, and DNA repair, were associated with MetS. Through pathway analysis of MetS, pathways related with PDGF, mitogen-activated protein kinase, and PPAR signaling, as well as nucleic acid binding, protein secretion, and DNA repair, were identified. Further studies will be needed to clarify the genetic pathogenesis leading to MetS.

Catchment Legacies and Trajectories: Understanding Time Lags in Catchment Response as a Function of Hydrologic and Biogeochemical Controls

NASA Astrophysics Data System (ADS)

Basu, N. B.; Van Meter, K. J.

2012-12-01

Increased nutrient loads delivered from watersheds due to agricultural intensification, industrialization, and urbanization have contributed globally to the persistence of large hypoxic zones in inland and coastal waters. Watershed management practices targeting these non-point source pollutants often lead to little or no improvement in water quality, even after extensive implementation of conservation measures or Best Management Practices (BMPs). The lag time between implementation of a conservation measure and resultant water quality benefits has recently been recognized as an important factor in the "apparent" failure of these BMPs. When conservation measures are implemented without explicit consideration of the lag time and with expectations that they will lead to immediate benefits, the resulting failure to meet such expectations can discourage vital restoration efforts. It is therefore important to quantify the lag times associated with watershed management efforts a priori and to implement restoration strategies targeted specifically at minimizing lag times and maximizing restoration benefits. The focus of this research is to develop a framework for understanding the time lags between land-use changes and stream water quality benefits. We hypothesize that such time lags arise from nutrient legacies building over decades of fertilizer application. For nitrogen (N), one can conceptualize this as either hydrologic legacy, in the form of dissolved nitrate that is delayed due to slow groundwater transport, or as biogeochemical legacy, in the form of organic N, possibly in dissolved or readily mineralizable forms. Indeed, mass-balance studies across the Mississippi and Thames river basins indicate the possibility of missing N mass in these landscapes, with inputs being consistently greater than the outputs even when accounting for all possible pathways of nitrogen transformation. Historical soil data within the upper Mississippi River Basin (MRB) indicate that agriculture depletes organic N in surface soil, but leads to N accumulations deeper in the profile. Nitrogen accumulation estimates (approximately 2 million Mt/yr) based on the historical data are startlingly close to the deficit suggested by mass-balance studies of the MRB (3 million Mt/yr). Understanding the lag times associated with such biogeochemical legacies requires quantification of this accumulation as a function of landscape attributes, climate, and management controls, as well as the rate of mineralization of accumulated N after implementation of management practices. Understanding hydrologic legacy requires a partitioning of flow along various pathways (e.g., overland flow, tile flow, or groundwater pathways), and the distribution of travel times along the pathways. Based on this framework, we developed a coupled hydrologic and biogeochemical model to quantify these legacies and predict landscape recovery times as a function of natural and anthropogenic controls.

Training in metabolomics research. II. Processing and statistical analysis of metabolomics data, metabolite identification, pathway analysis, applications of metabolomics and its future.

PubMed

Barnes, Stephen; Benton, H Paul; Casazza, Krista; Cooper, Sara J; Cui, Xiangqin; Du, Xiuxia; Engler, Jeffrey; Kabarowski, Janusz H; Li, Shuzhao; Pathmasiri, Wimal; Prasain, Jeevan K; Renfrow, Matthew B; Tiwari, Hemant K

2016-08-01

Metabolomics, a systems biology discipline representing analysis of known and unknown pathways of metabolism, has grown tremendously over the past 20 years. Because of its comprehensive nature, metabolomics requires careful consideration of the question(s) being asked, the scale needed to answer the question(s), collection and storage of the sample specimens, methods for extraction of the metabolites from biological matrices, the analytical method(s) to be employed and the quality control of the analyses, how collected data are correlated, the statistical methods to determine metabolites undergoing significant change, putative identification of metabolites and the use of stable isotopes to aid in verifying metabolite identity and establishing pathway connections and fluxes. This second part of a comprehensive description of the methods of metabolomics focuses on data analysis, emerging methods in metabolomics and the future of this discipline. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

A Risk and Maintenance Model for Bulimia Nervosa: From Impulsive Action to Compulsive Behavior

PubMed Central

Pearson, Carolyn M.; Wonderlich, Stephen A.; Smith, Gregory T.

2015-01-01

This paper offers a new model for bulimia nervosa (BN) that explains both the initial impulsive nature of binge eating and purging as well as the compulsive quality of the fully developed disorder. The model is based on a review of advances in research on BN and advances in relevant basic psychological science. It integrates transdiagnostic personality risk, eating disorder specific risk, reinforcement theory, cognitive neuroscience, and theory drawn from the drug addiction literature. We identify both a state-based and a trait-based risk pathway, and we then propose possible state-by-trait interaction risk processes. The state-based pathway emphasizes depletion of self-control. The trait-based pathway emphasizes transactions between the trait of negative urgency (the tendency to act rashly when distressed) and high-risk psychosocial learning. We then describe a process by which initially impulsive BN behaviors become compulsive over time, and we consider the clinical implications of our model. PMID:25961467

Selective Targeting of Proteins within Secretory Pathway for Endoplasmic Reticulum-associated Degradation

PubMed Central

Vecchi, Lara; Petris, Gianluca; Bestagno, Marco; Burrone, Oscar R.

2012-01-01

The endoplasmic reticulum-associated degradation (ERAD) is a cellular quality control mechanism to dispose of misfolded proteins of the secretory pathway via proteasomal degradation. SEL1L is an ER-resident protein that participates in identification of misfolded molecules as ERAD substrates, therefore inducing their ER-to-cytosol retrotranslocation and degradation. We have developed a novel class of fusion proteins, termed degradins, composed of a fragment of SEL1L fused to a target-specific binding moiety located on the luminal side of the ER. The target-binding moiety can be a ligand of the target or derived from specific mAbs. Here, we describe the ability of degradins with two different recognition moieties to promote degradation of a model target. Degradins recognize the target protein within the ER both in secretory and membrane-bound forms, inducing their degradation following retrotranslocation to the cytosol. Thus, degradins represent an effective technique to knock-out proteins within the secretory pathway with high specificity. PMID:22523070

Economical analysis of saturation mutagenesis experiments

PubMed Central

Acevedo-Rocha, Carlos G.; Reetz, Manfred T.; Nov, Yuval

2015-01-01

Saturation mutagenesis is a powerful technique for engineering proteins, metabolic pathways and genomes. In spite of its numerous applications, creating high-quality saturation mutagenesis libraries remains a challenge, as various experimental parameters influence in a complex manner the resulting diversity. We explore from the economical perspective various aspects of saturation mutagenesis library preparation: We introduce a cheaper and faster control for assessing library quality based on liquid media; analyze the role of primer purity and supplier in libraries with and without redundancy; compare library quality, yield, randomization efficiency, and annealing bias using traditional and emergent randomization schemes based on mixtures of mutagenic primers; and establish a methodology for choosing the most cost-effective randomization scheme given the screening costs and other experimental parameters. We show that by carefully considering these parameters, laboratory expenses can be significantly reduced. PMID:26190439

Biological pathways, candidate genes and molecular markers associated with quality-of-life domains: an update

PubMed Central

Sprangers, Mirjam A.G.; Thong, Melissa S.Y.; Bartels, Meike; Barsevick, Andrea; Ordoñana, Juan; Shi, Qiuling; Wang, Xin Shelley; Klepstad, Pål; Wierenga, Eddy A.; Singh, Jasvinder A.; Sloan, Jeff A.

2014-01-01

Background There is compelling evidence of a genetic foundation of patient-reported QOL. Given the rapid development of substantial scientific advances in this area of research, the current paper updates and extends reviews published in 2010. Objectives The objective is to provide an updated overview of the biological pathways, candidate genes and molecular markers involved in fatigue, pain, negative (depressed mood) and positive (well-being/happiness) emotional functioning, social functioning, and overall QOL. Methods We followed a purposeful search algorithm of existing literature to capture empirical papers investigating the relationship between biological pathways and molecular markers and the identified QOL domains. Results Multiple major pathways are involved in each QOL domain. The inflammatory pathway has the strongest evidence as a controlling mechanism underlying fatigue. Inflammation and neurotransmission are key processes involved in pain perception and the COMT gene is associated with multiple sorts of pain. The neurotransmitter and neuroplasticity theories have the strongest evidence for their relationship with depression. Oxytocin-related genes and genes involved in the serotonergic and dopaminergic pathways play a role in social functioning. Inflammatory pathways, via cytokines, also play an important role in overall QOL. Conclusions Whereas the current findings need future experiments and replication efforts, they will provide researchers supportive background information when embarking on studies relating candidate genes and/or molecular markers to QOL domains. The ultimate goal of this area of research is to enhance patients’ QOL. PMID:24604075

NutrimiRAging: Micromanaging Nutrient Sensing Pathways through Nutrition to Promote Healthy Aging.

PubMed

Micó, Víctor; Berninches, Laura; Tapia, Javier; Daimiel, Lidia

2017-04-26

Current sociodemographic predictions point to a demographic shift in developed and developing countries that will result in an unprecedented increase of the elderly population. This will be accompanied by an increase in age-related conditions that will strongly impair human health and quality of life. For this reason, aging is a major concern worldwide. Healthy aging depends on a combination of individual genetic factors and external environmental factors. Diet has been proved to be a powerful tool to modulate aging and caloric restriction has emerged as a valuable intervention in this regard. However, many questions about how a controlled caloric restriction intervention affects aging-related processes are still unanswered. Nutrient sensing pathways become deregulated with age and lose effectiveness with age. These pathways are a link between diet and aging. Thus, fully understanding this link is a mandatory step before bringing caloric restriction into practice. MicroRNAs have emerged as important regulators of cellular functions and can be modified by diet. Some microRNAs target genes encoding proteins and enzymes belonging to the nutrient sensing pathways and, therefore, may play key roles in the modulation of the aging process. In this review, we aimed to show the relationship between diet, nutrient sensing pathways and microRNAs in the context of aging.

Agriculture and nutrition in India: mapping evidence to pathways.

PubMed

Kadiyala, Suneetha; Harris, Jody; Headey, Derek; Yosef, Sivan; Gillespie, Stuart

2014-12-01

In India, progress against undernutrition has been slow. Given its importance for income generation, improving diets, care practices, and maternal health, the agriculture sector is widely regarded as playing an important role in accelerating the reduction in undernutrition. This paper comprehensively maps existing evidence along agriculture-nutrition pathways in India and assesses both the quality and coverage of the existing literature. We present a conceptual framework delineating six key pathways between agriculture and nutrition. Three pathways pertain to the nutritional impacts of farm production, farm incomes, and food prices. The other three pertain to agriculture-gender linkages. After an extensive search, we found 78 research papers that provided evidence to populate these pathways. The literature suggests that Indian agriculture has a range of important influences on nutrition. Agriculture seems to influence diets even when controlling for income, and relative food prices could partly explain observed dietary changes in recent decades. The evidence on agriculture-gender linkages to nutrition is relatively weak. Sizeable knowledge gaps remain. The root causes of these gaps include an interdisciplinary disconnect between nutrition and economics/agriculture, a related problem of inadequate survey data, and limited policy-driven experimentation. Closing these gaps is essential to strengthening the agriculture sector's contribution to reducing undernutrition. © 2014 New York Academy of Sciences.

Compensatory changes accompanying chronic forced use of the nondominant hand by unilateral amputees.

PubMed

Philip, Benjamin A; Frey, Scott H

2014-03-05

Amputation of the dominant hand forces patients to use the nondominant hand exclusively, including for tasks (e.g., writing and drawing) that were formerly the sole domain of the dominant hand. The behavioral and neurological effects of this chronic forced use of the nondominant hand remain largely unknown. Yet, these effects may shed light on the potential to compensate for degradation or loss of dominant hand function, as well as the mechanisms that support motor learning under conditions of very long-term training. We used a novel precision drawing task and fMRI to investigate 8 adult human amputees with chronic (mean 33 years) unilateral dominant (right) hand absence, and right-handed matched controls (8 for fMRI, 19 for behavior). Amputees' precision drawing performances with their left hands reached levels of smoothness (associated with left hemisphere control), acceleration time (associated with right hemisphere control), and speed equivalent to controls' right hands, whereas accuracy maintained a level comparable with controls' left hands. This compensation is supported by an experience-dependent shift from heavy reliance on the dorsodorsal parietofrontal pathway (feedback control) to the ventrodorsal pathway and prefrontal regions involved in the cognitive control of goal-directed actions. Relative to controls, amputees also showed increased activity within the former cortical sensorimotor hand territory in the left (ipsilateral) hemisphere. These data demonstrate that, with chronic and exclusive forced use, the speed and quality of nondominant hand precision endpoint control in drawing can achieve levels nearly comparable with the dominant hand.

Improvement in resource utilization after development of a clinical pathway for patients with pressure ulcers.

PubMed

Dzwierzynski, W W; Spitz, K; Hartz, A; Guse, C; Larson, D L

1998-11-01

Clinical pathways are interdisciplinary patient care plans intended to reduce variance and improve quality of care while lowering health care cost. This study was undertaken to determine whether the development of a clinical pathway for care of patients with pressure ulcers can indeed decrease health care costs while preserving quality of care. A clinical pathway for surgical reconstruction of pressure ulcers was developed by standardizing the current practices of our plastic surgeon group. The pathway provided direction in optimal scheduling of physician interventions along with nursing, physical and occupational therapies, and spinal cord rehabilitation interventions. It covered all potential elements of patient care, including laboratory, radiology, dietary services, intravenous fluids, and use of specialty beds. It defined patient outcomes and outlined discharge planning. Pathways were distributed throughout all services caring for patients with pressure ulcers. Patient charts and billing data were reviewed for the 16-month periods before and after initiation of the pathway. No other significant changes in treatment occurred during this time frame. Ninety-seven patient charts were examined (54 before pathway and 43 after pathway implementation). Parameters evaluated included length of stay and total charges (including bed use, medications, laboratory tests, and radiology). Patient readmission rate was also examined. A significant reduction in patient length of stay and total charges was achieved after implementation of the clinical pathway. Reduction was seen not only for patients treated with flaps by plastic surgery but also for patients with pressure ulcers who were not specifically targeted such as those from other services. The readmission rate decreased slightly, although not significantly, after the pathway inception. Total cost saving was almost $11,000 per patient (23 percent). In conclusion, implementation of a clinical pathway, because it standardizes care and reduces variations and duplication of care, can reduce health care cost without impairing quality of care in the treatment of decubitus ulcer patients.

The cost effectiveness of an early transition from hospital to nursing home for stroke patients: design of a comparative study

PubMed Central

2010-01-01

Background As the incidence of stroke has increased, its impact on society has increased accordingly, while it continues to have a major impact on the individual. New strategies to further improve the quality, efficiency and logistics of stroke services are necessary. Early discharge from hospital to a nursing home with an adequate rehabilitation programme could help to optimise integrated care for stroke patients. The objective is to describe the design of a non-randomised comparative study evaluating early admission to a nursing home, with multidisciplinary assessment, for stroke patients. The study is comprised of an effect evaluation, an economic evaluation and a process evaluation. Methods/design The design involves a non-randomised comparative trial for two groups. Participants are followed for 6 months from the time of stroke. The intervention consists of a redesigned care pathway for stroke patients. In this care pathway, patients are discharged from hospital to a nursing home within 5 days, in comparison with 12 days in the usual situation. In the nursing home a structured assessment takes place, aimed at planning adequate rehabilitation. People in the control group receive the usual care. The main outcome measures of the effect evaluation are quality of life and daily functioning. In addition, an economic evaluation will be performed from a societal perspective. A process evaluation will be carried out to evaluate the feasibility of the intervention as well as the experiences and opinions of patients and professionals. Discussion The results of this study will provide information about the cost effectiveness of the intervention and its effects on clinical outcomes and quality of life. Relevant strengths and weaknesses of the study are addressed in this article. Trial registration Current Controlled Trails ISRCTN58135104 PMID:20504313

Life review and life story books for people with mild to moderate dementia: a randomised controlled trial

PubMed Central

Subramaniam, Ponnusamy; Woods, Bob; Whitaker, Chris

2013-01-01

Objectives To evaluate the effect of different pathways for developing a life story book (LSB) for people with dementia. Method Preliminary randomised control trial; 23 people with dementia in care homes (mean age 86) randomly assigned to receive either 12 individual life review sessions and co-creating a LSB or a personal LSB created by their relatives as a ‘gift’ Results No difference in quality of life (quality of life–Alzheimer's disease (QOL–AD)) was observed between the two groups, six weeks after having received the LSB (F(1,20) = 0.08, p = 0.77). At this point, QOL–AD had improved for both groups, but there was a significant between-group difference at an intermediate assessment immediately after the life review sessions had been completed, before the LSBs were received (F(1, 20) = 5.11, p = 0.035), in favour of life review. A similar pattern was observed on autobiographical memory (extended autobiographical memory interview), with the life review group improving significantly more than the gift group during the life review sessions, but no difference was observed once all participants had had their LSB for six weeks. After the LSBs were produced – by either pathway – quality of relationship as rated by relatives improved significantly (F(2, 39) = 19.37, p < 0.001) and staff knowledge regarding the resident and attitudes to dementia improved. Conclusion The creation of LSBs – either through a life review process or by relatives without involving the person with dementia – has benefits for people with dementia, relatives and staff in care homes. However, undertaking a life review requires training and supervision. PMID:24063317

The cost effectiveness of an early transition from hospital to nursing home for stroke patients: design of a comparative study.

PubMed

Heijnen, Ron W H; Evers, Silvia M A A; van der Weijden, Trudy D E M; Limburg, Martien; Schols, Jos M G A

2010-05-26

As the incidence of stroke has increased, its impact on society has increased accordingly, while it continues to have a major impact on the individual. New strategies to further improve the quality, efficiency and logistics of stroke services are necessary. Early discharge from hospital to a nursing home with an adequate rehabilitation programme could help to optimise integrated care for stroke patients.The objective is to describe the design of a non-randomised comparative study evaluating early admission to a nursing home, with multidisciplinary assessment, for stroke patients. The study is comprised of an effect evaluation, an economic evaluation and a process evaluation. The design involves a non-randomised comparative trial for two groups. Participants are followed for 6 months from the time of stroke. The intervention consists of a redesigned care pathway for stroke patients. In this care pathway, patients are discharged from hospital to a nursing home within 5 days, in comparison with 12 days in the usual situation. In the nursing home a structured assessment takes place, aimed at planning adequate rehabilitation. People in the control group receive the usual care. The main outcome measures of the effect evaluation are quality of life and daily functioning. In addition, an economic evaluation will be performed from a societal perspective. A process evaluation will be carried out to evaluate the feasibility of the intervention as well as the experiences and opinions of patients and professionals. The results of this study will provide information about the cost effectiveness of the intervention and its effects on clinical outcomes and quality of life. Relevant strengths and weaknesses of the study are addressed in this article. Current Controlled Trails ISRCTN58135104.

Dysregulation of the Mitochondrial Unfolded Protein Response Induces Non-Apoptotic Dopaminergic Neurodegeneration in C. elegans Models of Parkinson's Disease

PubMed Central

Martinez, Bryan A.; Petersen, Daniel A.; Gaeta, Anthony L.

2017-01-01

Due to environmental insult or innate genetic deficiency, protein folding environments of the mitochondrial matrix are prone to dysregulation, prompting the activation of a specific organellar stress-response mechanism, the mitochondrial unfolded protein response (UPRMT). In Caenorhabditis elegans, mitochondrial damage leads to nuclear translocation of the ATFS-1 transcription factor to activate the UPRMT. After short-term acute stress has been mitigated, the UPRMT is eventually suppressed to restore homeostasis to C. elegans hermaphrodites. In contrast, and reflective of the more chronic nature of progressive neurodegenerative disorders such as Parkinson's disease (PD), here, we report the consequences of prolonged, cell-autonomous activation of the UPRMT in C. elegans dopaminergic neurons. We reveal that neuronal function and integrity decline rapidly with age, culminating in activity-dependent, non-apoptotic cell death. In a PD-like context wherein transgenic nematodes express the Lewy body constituent protein α-synuclein (αS), we not only find that this protein and its PD-associated disease variants have the capacity to induce the UPRMT, but also that coexpression of αS and ATFS-1-associated dysregulation of the UPRMT synergistically potentiate dopaminergic neurotoxicity. This genetic interaction is in parallel to mitophagic pathways dependent on the C. elegans PINK1 homolog, which is necessary for cellular resistance to chronic malfunction of the UPRMT. Given the increasingly recognized role of mitochondrial quality control in neurodegenerative diseases, these studies illustrate, for the first time, an insidious aspect of mitochondrial signaling in which the UPRMT pathway, under disease-associated, context-specific dysregulation, exacerbates disruption of dopaminergic neurons in vivo, resulting in the neurodegeneration characteristic of PD. SIGNIFICANCE STATEMENT Disruptions or alterations in the activation of pathways that regulate mitochondrial quality control have been linked to neurodegenerative diseases due in part to the central role of mitochondria in metabolism, ROS regulation, and proteostasis. The extent to which these pathways, including the mitochondrial unfolded protein response (UPRMT) and mitophagy, are active may predict severity and progression of these disorders, as well as sensitivity to compounding stressors. Furthermore, therapeutic strategies that aim to induce these pathways may benefit from increased study into cellular responses that arise from long-term or ectopic stimulation, especially in neuronal compartments. By demonstrating the detrimental consequences of prolonged cellular activation of the UPRMT, we provide evidence that this pathway is not a universally beneficial mechanism because dysregulation has neurotoxic consequences. PMID:29030433

Levels of metacaspase1 and chaperones related to protein quality control in alcoholic and nonalcoholic steatohepatitis.

PubMed

Mendoza, Alejandro S; Dorce, Jacques; Peng, Yue; French, Barbara A; Tillman, Brittany; Li, Jun; French, Samuel W

2015-02-01

Efficient management of misfolded or aggregated proteins in ASH and NASH is crucial for continued hepatic viability. Cellular protein quality control systems play an important role in the pathogenesis and progression of ASH and NASH. In a recent study, elevated Mca1 expression counteracted aggregation and accumulation of misfolded proteins and extended the life span of the yeast Saccharomyces cerevisiae (Hill et al, 2014). Mca1 may also associate with Ssa1 and Hsp104 in disaggregation and fragmentation of aggregated proteins and their subsequent degradation through the ER-associated degradation (ERAD) pathway. If degradation is not available, protection of the cellular environment from a misfolded protein is accomplished by its sequestration into two distinct inclusion bodies (Kaganovich et al., 2008) called the JUNQ (JUxta Nuclear Quality control compartment) and the IPOD (Insoluble Protein Deposit). Mca1, Hsp104, Hsp40, Ydj1, Ssa1, VCP/p97, and p62 all play important roles in protein quality control systems. This study aims to measure the expression of Mca1 and related chaperones involved in protein quality control in alcoholic steatohepatitis (ASH), and nonalcoholic steatohepatitis (NASH) compared with normal control liver biopsies. Mca1, Hsp104, Hsp40, Ydj1, Ssa1, VCP/p97, and p62 expressions were measured in three to six formalin-fixed paraffin embedded ASH and NASH liver biopsies and control normal liver specimens by immunofluorescence staining and quantified by immunofluorescence intensity. Mca1, Hsp104, Ydj1 and p62 were significantly upregulated compared to control (p<0.05) in ASH specimens. Hsp40 and VCP/p97 were also uptrending in ASH. In NASH, the only significant difference was the increased expression of Hsp104 compared to control (p<0.05). Ssa1 levels were uptrending in both ASH and NASH specimens. The upregulation of Mca1, Hsp104, Ydj1 and p62 in ASH may be elicited as a response to the chronic exposure of the hepatocytes to the toxicity of alcohol. Recruitment of Mca1, Hsp104, Ydj1 and p62 may indicate that autophagy, the ERAD, JUNQ, and IPOD systems are active in ASH. Whereas in NASH, elevated Hsp104 and uptrending Ssa1 levels may indicate that autophagy and IPOD may be the only active protein quality control systems involved. Published by Elsevier Inc.

Use of a bovine genome chip to identify new biological pathways for beef quality in cattle.

PubMed

Guifen, Liu; Xiaomu, Liu; Fachun, Wan; Xiuwen, Tan; Haijian, Cheng; Enliang, Song

2012-12-01

The accumulation of muscle is largely influenced by the genetic background of cattle. Muscle tissue was collected from the longissimus muscle of Lilu beef cattle at 12, 18, 24 and 30 months old. Using meat quality analysis, we found that the Lilu beef cattle have good production and slaughter performance, the performance meets the criterion of beef cattle. Microarray analysis was able to identify a total of 4,219 genes that are differentially expressed (P ≤ 0.01) between the two groups of cattle (12 vs 18; 18 vs 24; 24 vs 30). Bioinformatics analysis results suggested that most of the differentially expressed genes are involved in the metabolic pathways and neuroactive ligand-receptor interaction pathways. In the future study that aims to look for genes relating to growth and meat quality, we will focus on the genes that have been shown to have a significant variation between groups and are involved in the two pathways.

Evaluating between-pathway models with expression data.

PubMed

Hescott, B J; Leiserson, M D M; Cowen, L J; Slonim, D K

2010-03-01

Between-pathway models (BPMs) are network motifs consisting of pairs of putative redundant pathways. In this article, we show how adding another source of high-throughput data--microarray gene expression data from knockout experiments--allows us to identify a compensatory functional relationship between genes from the two BPM pathways. We evaluate the quality of the BPMs from four different studies, and we describe how our methods might be extended to refine pathways.

Heme oxygenase-1 regulates mitochondrial quality control in the heart

PubMed Central

Hull, Travis D.; Boddu, Ravindra; Guo, Lingling; Tisher, Cornelia C.; Traylor, Amie M.; Patel, Bindiya; Joseph, Reny; Prabhu, Sumanth D.; Suliman, Hagir B.; Piantadosi, Claude A.; George, James F.

2016-01-01

The cardioprotective inducible enzyme heme oxygenase-1 (HO-1) degrades prooxidant heme into equimolar quantities of carbon monoxide, biliverdin, and iron. We hypothesized that HO-1 mediates cardiac protection, at least in part, by regulating mitochondrial quality control. We treated WT and HO-1 transgenic mice with the known mitochondrial toxin, doxorubicin (DOX). Relative to WT mice, mice globally overexpressing human HO-1 were protected from DOX-induced dilated cardiomyopathy, cardiac cytoarchitectural derangement, and infiltration of CD11b+ mononuclear phagocytes. Cardiac-specific overexpression of HO-1 ameliorated DOX-mediated dilation of the sarcoplasmic reticulum as well as mitochondrial disorganization in the form of mitochondrial fragmentation and increased numbers of damaged mitochondria in autophagic vacuoles. HO-1 overexpression promotes mitochondrial biogenesis by upregulating protein expression of NRF1, PGC1α, and TFAM, which was inhibited in WT animals treated with DOX. Concomitantly, HO-1 overexpression inhibited the upregulation of the mitochondrial fission mediator Fis1 and resulted in increased expression of the fusion mediators, Mfn1 and Mfn2. It also prevented dynamic changes in the levels of key mediators of the mitophagy pathway, PINK1 and parkin. Therefore, these findings suggest that HO-1 has a novel role in protecting the heart from oxidative injury by regulating mitochondrial quality control. PMID:27110594

NFκB is a central regulator of protein quality control in response to protein aggregation stresses via autophagy modulation

PubMed Central

Nivon, Mathieu; Fort, Loïc; Muller, Pascale; Richet, Emma; Simon, Stéphanie; Guey, Baptiste; Fournier, Maëlenn; Arrigo, André-Patrick; Hetz, Claudio; Atkin, Julie D.; Kretz-Remy, Carole

2016-01-01

During cell life, proteins often misfold, depending on particular mutations or environmental changes, which may lead to protein aggregates that are toxic for the cell. Such protein aggregates are the root cause of numerous diseases called “protein conformational diseases,” such as myofibrillar myopathy and familial amyotrophic lateral sclerosis. To fight against aggregates, cells are equipped with protein quality control mechanisms. Here we report that NFκB transcription factor is activated by misincorporation of amino acid analogues into proteins, inhibition of proteasomal activity, expression of the R120G mutated form of HspB5 (associated with myofibrillar myopathy), or expression of the G985R and G93A mutated forms of superoxide dismutase 1 (linked to familial amyotrophic lateral sclerosis). This noncanonical stimulation of NFκB triggers the up-regulation of BAG3 and HspB8 expression, two activators of selective autophagy, which relocalize to protein aggregates. Then NFκB-dependent autophagy allows the clearance of protein aggregates. Thus NFκB appears as a central and major regulator of protein aggregate clearance by modulating autophagic activity. In this context, the pharmacological stimulation of this quality control pathway might represent a valuable strategy for therapies against protein conformational diseases. PMID:27075172

Microbial production of isoquinoline alkaloids as plant secondary metabolites based on metabolic engineering research.

PubMed

Sato, Fumihiko; Kumagai, Hidehiko

2013-01-01

Plants produce a variety of secondary metabolites that possess strong physiological activities. Unfortunately, however, their production can suffer from a variety of serious problems, including low levels of productivity and heterogeneous quality, as well as difficulty in raw material supply. In contrast, microorganisms can be used to produce their primary and some of their secondary metabolites in a controlled environment, thus assuring high levels of efficiency and uniform quality. In an attempt to overcome the problems associated with secondary metabolite production in plants, we developed a microbial platform for the production of plant isoquinoline alkaloids involving the unification of the microbial and plant metabolic pathways into a single system. The potential applications of this system have also been discussed.

Microbial production of isoquinoline alkaloids as plant secondary metabolites based on metabolic engineering research

PubMed Central

SATO, Fumihiko; KUMAGAI, Hidehiko

2013-01-01

Plants produce a variety of secondary metabolites that possess strong physiological activities. Unfortunately, however, their production can suffer from a variety of serious problems, including low levels of productivity and heterogeneous quality, as well as difficulty in raw material supply. In contrast, microorganisms can be used to produce their primary and some of their secondary metabolites in a controlled environment, thus assuring high levels of efficiency and uniform quality. In an attempt to overcome the problems associated with secondary metabolite production in plants, we developed a microbial platform for the production of plant isoquinoline alkaloids involving the unification of the microbial and plant metabolic pathways into a single system. The potential applications of this system have also been discussed. PMID:23666088

Bundled Payments in Total Joint Replacement: Keeping Our Care Affordable and High in Quality.

PubMed

McLawhorn, Alexander S; Buller, Leonard T

2017-09-01

The purpose of this review was to evaluate the literature regarding bundle payment reimbursement models for total joint arthroplasty (TJA). From an economic standpoint, TJA are cost-effective, but they represent a substantial expense to the Centers for Medicare & Medicaid Services (CMS). Historically, fee-for-service payment models resulted in highly variable cost and quality. CMS introduced Bundled Payments for Care Improvement (BPCI) in 2012 and subsequently the Comprehensive Care for Joint Replacement (CJR) reimbursement model in 2016 to improve the value of TJA from the perspectives of both CMS and patients, by improving quality via cost control. Early results of bundled payments are promising, but preserving access to care for patients with high comorbidity burdens and those requiring more complex care is a lingering concern. Hospitals, regardless of current participation in bundled payments, should develop care pathways for TJA to maximize efficiency and patient safety.

Assessment of inter-city transport of particulate matter in the Beijing-Tianjin-Hebei region

NASA Astrophysics Data System (ADS)

Chang, Xing; Wang, Shuxiao; Zhao, Bin; Cai, Siyi; Hao, Jiming

2018-04-01

The regional transport of particulate matter with diameter less than 2.5 µm (PM2.5) plays an important role in the air pollution of the Beijing-Tianjin-Hebei (BTH) region in China. However, previous studies on regional transport of PM2.5 mainly aim at province level, which is insufficient for the development of an optimal joint PM2.5 control strategy. In this study, we calculate PM2.5 inflows and outflows through the administrative boundaries of three major cities in the BTH region, i.e., Beijing, Tianjin and Shijiazhuang, using the WRF (Weather Research and Forecasting model)-CMAQ (Community Multiscale Air Quality) modeling system. The monthly average inflow fluxes indicate the major directions of PM2.5 transport. For Beijing, the PM2.5 inflow fluxes from Zhangjiakou (in the northwest) and Baoding (in the southwest) constitute 57 % of the total in winter, and Langfang (in the southeast) and Baoding constitute 73 % in summer. Based on the net PM2.5 fluxes and their vertical distributions, we find there are three major transport pathways in the BTH region: the northwest-southeast pathway in winter (at all levels below 1000 m), the northwest-southeast pathway in summer (at all levels below 1000 m), and the southwest-northeast pathway in both winter and in summer (mainly at 300-1000 m). In winter, even if surface wind speeds are low, the transport at above 300 m can still be strong. Among the three pathways, the southwest-northeast happens along with PM2.5 concentrations 30 and 55 % higher than the monthly average in winter and summer, respectively. Analysis of two heavy pollution episodes in January and July in Beijing show a much (8-16 times) stronger transport than the monthly average, emphasizing the joint air pollution control of the cities located on the transport pathways, especially during heavy pollution episodes.

Evaluating Between-Pathway Models with Expression Data

PubMed Central

Leiserson, M.D.M.; Cowen, L.J.; Slonim, D.K.

2010-01-01

Abstract Between-pathway models (BPMs) are network motifs consisting of pairs of putative redundant pathways. In this article, we show how adding another source of high-throughput data—microarray gene expression data from knockout experiments—allows us to identify a compensatory functional relationship between genes from the two BPM pathways. We evaluate the quality of the BPMs from four different studies, and we describe how our methods might be extended to refine pathways. PMID:20377458

THE DELICATE BALANCE BETWEEN SECRETED PROTEIN FOLDING AND ENDOPLASMIC RETICULUM-ASSOCIATED DEGRADATION IN HUMAN PHYSIOLOGY

PubMed Central

Guerriero, Christopher J.; Brodsky, Jeffrey L.

2014-01-01

Protein folding is a complex, error-prone process that often results in an irreparable protein by-product. These by-products can be recognized by cellular quality control machineries and targeted for proteasome-dependent degradation. The folding of proteins in the secretory pathway adds another layer to the protein folding “problem,” as the endoplasmic reticulum maintains a unique chemical environment within the cell. In fact, a growing number of diseases are attributed to defects in secretory protein folding, and many of these by-products are targeted for a process known as endoplasmic reticulum-associated degradation (ERAD). Since its discovery, research on the mechanisms underlying the ERAD pathway has provided new insights into how ERAD contributes to human health during both normal and diseases states. Links between ERAD and disease are evidenced from the loss of protein function as a result of degradation, chronic cellular stress when ERAD fails to keep up with misfolded protein production, and the ability of some pathogens to coopt the ERAD pathway. The growing number of ERAD substrates has also illuminated the differences in the machineries used to recognize and degrade a vast array of potential clients for this pathway. Despite all that is known about ERAD, many questions remain, and new paradigms will likely emerge. Clearly, the key to successful disease treatment lies within defining the molecular details of the ERAD pathway and in understanding how this conserved pathway selects and degrades an innumerable cast of substrates. PMID:22535891

ER stress response mechanisms in the pathogenic yeast Candida glabrata and their roles in virulence

PubMed Central

Miyazaki, Taiga; Kohno, Shigeru

2014-01-01

The maintenance of endoplasmic reticulum (ER) homeostasis is critical for numerous aspects of cell physiology. Eukaryotic cells respond to the accumulation of misfolded proteins in the ER (ER stress) by activating the unfolded protein response (UPR), an intracellular signaling pathway that adjusts the folding capacity of the ER. Recent studies of several pathogenic fungi have revealed that the UPR is important for antifungal resistance and virulence; therefore, the pathway has attracted much attention as a potential therapeutic target. While the UPR is highly conserved among eukaryotes, our group recently discovered that the pathogenic yeast Candida glabrata lacks the typical fungal UPR, but possesses alternative mechanisms to cope with ER stress. This review summarizes how C. glabrata responds to ER stress and discusses the impacts of ER quality control systems on antifungal resistance and virulence. PMID:24335436

Heat Shock Proteins and Autophagy Pathways in Neuroprotection: From Molecular Bases to Pharmacological Interventions

PubMed Central

Penke, Botond; Bogár, Ferenc; Sántha, Miklós; Tóth, Melinda E.; Vígh, László

2018-01-01

Neurodegenerative diseases (NDDs) such as Alzheimer’s disease, Parkinson’s disease and Huntington’s disease (HD), amyotrophic lateral sclerosis, and prion diseases are all characterized by the accumulation of protein aggregates (amyloids) into inclusions and/or plaques. The ubiquitous presence of amyloids in NDDs suggests the involvement of disturbed protein homeostasis (proteostasis) in the underlying pathomechanisms. This review summarizes specific mechanisms that maintain proteostasis, including molecular chaperons, the ubiquitin-proteasome system (UPS), endoplasmic reticulum associated degradation (ERAD), and different autophagic pathways (chaperon mediated-, micro-, and macro-autophagy). The role of heat shock proteins (Hsps) in cellular quality control and degradation of pathogenic proteins is reviewed. Finally, putative therapeutic strategies for efficient removal of cytotoxic proteins from neurons and design of new therapeutic targets against the progression of NDDs are discussed. PMID:29361800

Alkaloid profiling of the traditional Chinese medicine Rhizoma corydalis using high performance liquid chromatography-tandem quadrupole time-of-flight mass spectrometry

PubMed Central

Sun, Mingqian; Liu, Jianxun; Lin, Chengren; Miao, Lan; Lin, Li

2014-01-01

Since alkaloids are the major active constituents of Rhizoma corydalis (RC), a convenient and accurate analytical method is needed for their identification and characterization. Here we report a method to profile the alkaloids in RC based on liquid chromatography-tandem quadrupole time-of-flight mass spectrometry (LC–Q-TOF-MS/MS). A total of 16 alkaloids belonging to four different classes were identified by comparison with authentic standards. The fragmentation pathway of each class of alkaloid was clarified and their differences were elucidated. Furthermore, based on an analysis of fragmentation pathways and alkaloid profiling, a rapid and accurate method for the identification of unknown alkaloids in RC is proposed. The method could also be useful for the quality control of RC. PMID:26579385

The Occurrence and Diversity of Waterborne Fungi in African Aquatic Systems: Their Impact on Water Quality and Human Health.

PubMed

Magwaza, Nontokozo M; Nxumalo, Edward N; Mamba, Bhekie B; Msagati, Titus A M

2017-05-20

Currently, there is a worldwide growing interest in the occurrence and diversity of fungi and their secondary metabolites in aquatic systems, especially concerning their role in water quality and human health. However, this concern is hampered by the scant information that is available in the literature about aquatic fungi and how they affect water quality. There are only few published reports that link certain species of aquatic fungi to human health. The common aquatic fungal species that have been reported so far in African aquatic systems belong to the hyphomycetes kingdom. This paper thus aims to survey the information about the occurrence and factors that control the distribution of different species of fungi in African aquatic systems, as well as their effect on water quality and the possible metabolic pathways that lead to the formation of toxic secondary metabolites that are responsible for the deterioration of water quality. This review will also investigate the analytical and bioanalytical procedures that have been reported for the identification of different species of waterborne fungi and their secondary metabolites.

The Occurrence and Diversity of Waterborne Fungi in African Aquatic Systems: Their Impact on Water Quality and Human Health

PubMed Central

Magwaza, Nontokozo M.; Nxumalo, Edward N.; Mamba, Bhekie B.; Msagati, Titus A. M.

2017-01-01

Currently, there is a worldwide growing interest in the occurrence and diversity of fungi and their secondary metabolites in aquatic systems, especially concerning their role in water quality and human health. However, this concern is hampered by the scant information that is available in the literature about aquatic fungi and how they affect water quality. There are only few published reports that link certain species of aquatic fungi to human health. The common aquatic fungal species that have been reported so far in African aquatic systems belong to the hyphomycetes kingdom. This paper thus aims to survey the information about the occurrence and factors that control the distribution of different species of fungi in African aquatic systems, as well as their effect on water quality and the possible metabolic pathways that lead to the formation of toxic secondary metabolites that are responsible for the deterioration of water quality. This review will also investigate the analytical and bioanalytical procedures that have been reported for the identification of different species of waterborne fungi and their secondary metabolites. PMID:28531124

Pathways to Youth Empowerment and Community Connectedness: A Study of Youth-Adult Partnership in Malaysian After-School, Co-Curricular Programs.

PubMed

Zeldin, Shepherd; Krauss, Steven Eric; Kim, Taehan; Collura, Jessica; Abdullah, Haslinda

2016-08-01

After-school programs are prevalent across the world, but there is a paucity of research that examines quality within the "black box" of programs at the point of service. Grounded in current theory, this research examined hypothesized pathways between the experience of youth-adult partnership (youth voice in decision-making; supportive adult relationships), the mediators of program safety and engagement, and the developmental outcomes of youth empowerment (leadership competence, policy control) and community connectedness (community connections, school attachment). Surveys were administered to 207 ethnically diverse (47.3 % female; 63.3 % Malay) youth, age 15-16, attending after-school co-curricular programs in Kuala Lumpur, Malaysia. Results showed that youth voice in program decision-making predicted both indicators of youth empowerment. Neither youth voice nor supportive adult relationships was directly associated with community connectedness, however. Program engagement mediated the associations between youth-adult partnership and empowerment. In contrast, program safety mediated the associations between youth-adult partnership and community connectedness. The findings indicate that the two core components of youth-adult partnership-youth voice and supportive adult relationships-may operate through different, yet complementary, pathways of program quality to predict developmental outcomes. Implications for future research are highlighted. For reasons of youth development and youth rights, the immediate challenge is to create opportunities for youth to speak on issues of program concern and to elevate those adults who are able and willing to help youth exercise their voice.

The role of the PI3K-Akt signaling pathway in the developmental competence of bovine oocytes.

PubMed

Andrade, Gabriella Mamede; da Silveira, Juliano Coelho; Perrini, Claudia; Del Collado, Maite; Gebremedhn, Samuel; Tesfaye, Dawit; Meirelles, Flávio Vieira; Perecin, Felipe

2017-01-01

The ovarian follicle encloses oocytes in a microenvironment throughout their growth and acquisition of competence. Evidence suggests a dynamic interplay among follicular cells and oocytes, since they are constantly exchanging "messages". We dissected bovine ovarian follicles and recovered follicular cells (FCs-granulosa and cumulus cells) and cumulus-oocyte complexes (COCs) to investigate whether the PI3K-Akt signaling pathway impacted oocyte quality. Following follicle rupture, COCs were individually selected for in vitro cultures to track the follicular cells based on oocyte competence to reach the blastocyst stage after parthenogenetic activation. Levels of PI3K-Akt signaling pathway components in FCs correlated with oocyte competence. This pathway is upregulated in FCs from follicles with high-quality oocytes that are able to reach the blastocyst stage, as indicated by decreased levels of PTEN and increased levels of the PTEN regulators bta-miR-494 and bta-miR-20a. Using PI3K-Akt responsive genes, we showed decreased FOXO3a levels and BAX levels in lower quality groups, indicating changes in cell cycle progression, oxidative response and apoptosis. Based on these results, the measurement of levels of PI3K-Akt pathway components in FCs from ovarian follicles carrying oocytes with distinct developmental competences is a useful tool to identify putative molecular pathways involved in the acquisition of oocyte competence.

Degradation of misfolded proteins in neurodegenerative diseases: therapeutic targets and strategies.

PubMed

Ciechanover, Aaron; Kwon, Yong Tae

2015-03-13

Mammalian cells remove misfolded proteins using various proteolytic systems, including the ubiquitin (Ub)-proteasome system (UPS), chaperone mediated autophagy (CMA) and macroautophagy. The majority of misfolded proteins are degraded by the UPS, in which Ub-conjugated substrates are deubiquitinated, unfolded and cleaved into small peptides when passing through the narrow chamber of the proteasome. The substrates that expose a specific degradation signal, the KFERQ sequence motif, can be delivered to and degraded in lysosomes via the CMA. Aggregation-prone substrates resistant to both the UPS and the CMA can be degraded by macroautophagy, in which cargoes are segregated into autophagosomes before degradation by lysosomal hydrolases. Although most misfolded and aggregated proteins in the human proteome can be degraded by cellular protein quality control, some native and mutant proteins prone to aggregation into β-sheet-enriched oligomers are resistant to all known proteolytic pathways and can thus grow into inclusion bodies or extracellular plaques. The accumulation of protease-resistant misfolded and aggregated proteins is a common mechanism underlying protein misfolding disorders, including neurodegenerative diseases such as Huntington's disease (HD), Alzheimer's disease (AD), Parkinson's disease (PD), prion diseases and Amyotrophic Lateral Sclerosis (ALS). In this review, we provide an overview of the proteolytic pathways in neurons, with an emphasis on the UPS, CMA and macroautophagy, and discuss the role of protein quality control in the degradation of pathogenic proteins in neurodegenerative diseases. Additionally, we examine existing putative therapeutic strategies to efficiently remove cytotoxic proteins from degenerating neurons.

Demonstration that endoplasmic reticulum-associated degradation of glycoproteins can occur downstream of processing by endomannosidase.

PubMed

Kukushkin, Nikolay V; Alonzi, Dominic S; Dwek, Raymond A; Butters, Terry D

2011-08-15

During quality control in the ER (endoplasmic reticulum), nascent glycoproteins are deglucosylated by ER glucosidases I and II. In the post-ER compartments, glycoprotein endo-α-mannosidase provides an alternative route for deglucosylation. Previous evidence suggests that endomannosidase non-selectively deglucosylates glycoproteins that escape quality control in the ER, facilitating secretion of aberrantly folded as well as normal glycoproteins. In the present study, we employed FOS (free oligosaccharides) released from degrading glycoproteins as biomarkers of ERAD (ER-associated degradation), allowing us to gain a global rather than single protein-centred view of ERAD. Glucosidase inhibition was used to discriminate between glucosidase- and endomannosidase-mediated ERAD pathways. Endomannosidase expression was manipulated in CHO (Chinese-hamster ovary)-K1 cells, naturally lacking a functional version of the enzyme, and HEK (human embryonic kidney)-293T cells. Endomannosidase was shown to decrease the levels of total FOS, suggesting decreased rates of ERAD. However, following pharmacological inhibition of ER glucosidases I and II, endomannosidase expression resulted in a partial switch between glucosylated FOS, released from ER-confined glycoproteins, to deglucosylated FOS, released from endomannosidase-processed glycoproteins transported from the Golgi/ERGIC (ER/Golgi intermediate compartment) to the ER. Using this approach, we have identified a previously unknown pathway of glycoprotein flow, undetectable by the commonly employed methods, in which secretory cargo is targeted back to the ER after being processed by endomannosidase. © The Authors Journal compilation © 2011 Biochemical Society

Global air quality and climate.

PubMed

Fiore, Arlene M; Naik, Vaishali; Spracklen, Dominick V; Steiner, Allison; Unger, Nadine; Prather, Michael; Bergmann, Dan; Cameron-Smith, Philip J; Cionni, Irene; Collins, William J; Dalsøren, Stig; Eyring, Veronika; Folberth, Gerd A; Ginoux, Paul; Horowitz, Larry W; Josse, Béatrice; Lamarque, Jean-François; MacKenzie, Ian A; Nagashima, Tatsuya; O'Connor, Fiona M; Righi, Mattia; Rumbold, Steven T; Shindell, Drew T; Skeie, Ragnhild B; Sudo, Kengo; Szopa, Sophie; Takemura, Toshihiko; Zeng, Guang

2012-10-07

Emissions of air pollutants and their precursors determine regional air quality and can alter climate. Climate change can perturb the long-range transport, chemical processing, and local meteorology that influence air pollution. We review the implications of projected changes in methane (CH(4)), ozone precursors (O(3)), and aerosols for climate (expressed in terms of the radiative forcing metric or changes in global surface temperature) and hemispheric-to-continental scale air quality. Reducing the O(3) precursor CH(4) would slow near-term warming by decreasing both CH(4) and tropospheric O(3). Uncertainty remains as to the net climate forcing from anthropogenic nitrogen oxide (NO(x)) emissions, which increase tropospheric O(3) (warming) but also increase aerosols and decrease CH(4) (both cooling). Anthropogenic emissions of carbon monoxide (CO) and non-CH(4) volatile organic compounds (NMVOC) warm by increasing both O(3) and CH(4). Radiative impacts from secondary organic aerosols (SOA) are poorly understood. Black carbon emission controls, by reducing the absorption of sunlight in the atmosphere and on snow and ice, have the potential to slow near-term warming, but uncertainties in coincident emissions of reflective (cooling) aerosols and poorly constrained cloud indirect effects confound robust estimates of net climate impacts. Reducing sulfate and nitrate aerosols would improve air quality and lessen interference with the hydrologic cycle, but lead to warming. A holistic and balanced view is thus needed to assess how air pollution controls influence climate; a first step towards this goal involves estimating net climate impacts from individual emission sectors. Modeling and observational analyses suggest a warming climate degrades air quality (increasing surface O(3) and particulate matter) in many populated regions, including during pollution episodes. Prior Intergovernmental Panel on Climate Change (IPCC) scenarios (SRES) allowed unconstrained growth, whereas the Representative Concentration Pathway (RCP) scenarios assume uniformly an aggressive reduction, of air pollutant emissions. New estimates from the current generation of chemistry-climate models with RCP emissions thus project improved air quality over the next century relative to those using the IPCC SRES scenarios. These two sets of projections likely bracket possible futures. We find that uncertainty in emission-driven changes in air quality is generally greater than uncertainty in climate-driven changes. Confidence in air quality projections is limited by the reliability of anthropogenic emission trajectories and the uncertainties in regional climate responses, feedbacks with the terrestrial biosphere, and oxidation pathways affecting O(3) and SOA.

Estimating environmental co-benefits of U.S. low-carbon pathways using an integrated assessment model with state-level resolution

EPA Science Inventory

There are many technological pathways that can lead to reduced carbon dioxide emissions. However, these pathways can have substantially different impacts on other environmental endpoints, such as air quality and energy-related water demand. This study uses an integrated assessmen...

Estimating Environmental Co-benefits of U.S. CO2 Reduction Pathways Using the GCAM-USA Integrated Assessment Model

EPA Science Inventory

Various technological pathways can lead to reduced CO2 emissions. However, different pathways can have substantially different impacts on other environmental endpoints, such as air quality and energy-related water demand. The Global Change Assessment Model (GCAM) is a high resolu...

Elicitation and treatment with precursors of phenolics synthesis improve low-molecular antioxidants and antioxidant capacity of buckwheat sprouts.

PubMed

Świeca, Michał

2016-01-01

Recently, an increase of interest in the modification of food products on each step of production (breeding, production technology, storage condition) is observed. Nutritional properties as well as level and activity of bioactive compounds in plant-origin food may be modified using a range of technological and biotechnological practices and elicitation should be mentioned between them. Elicitation with willow bark infusion supported by feeding with the phenylpropanoid pathway precursors were used for improving the quality of buckwheat sprouts. Special emphasis has been placed on the metabolomic and biochemical changes and the mechanism of overproduction of low-molecular antioxidants. The accumulation of phenolics is caused by stimulation of two main enzymes the phenylpropanoid pathway (tyrosine ammonia-lyase and phenylalanine ammonia-lyase). Tyrosine ammonia-lyase activities were effectively induced by feeding with tyrosine (about four times that of the control), whereas phenylalanine ammonia-lyase activity was the highest in the elicited control sprouts and those fed with shikimic acid (an increase by 60% compared to the control). Shikimic acid feeding (both elicited and non-elicited sprouts) effectively improved the total phenolics (by about 10% and 20%, respectively), condensed tannins (by about 30% and 28%, respectively), and flavonoids (by about 46% and 70%, respectively). Significant increase of vitexin, rutin, chlorogenic acid and isoorientin contents was also observed. The treatments increased the ascorbic acid content, too. Total antioxidant capacity of sprouts was most effectively increased by feeding with shikimic acid and further elicitation. The studies transfer biotechnology commonly used for the induction of overproduction of secondary metabolites in plant cell line systems to low-processed food production. The obtained results could be used for better understanding of the effect of elicitation and precursor feeding on antioxidants production and contribute to improving the buckwheat sprouts quality.

Laser in Glaucoma and Ocular Hypertension (LiGHT) trial. A multicentre, randomised controlled trial: design and methodology.

PubMed

Gazzard, Gus; Konstantakopoulou, Evgenia; Garway-Heath, David; Barton, Keith; Wormald, Richard; Morris, Stephen; Hunter, Rachael; Rubin, Gary; Buszewicz, Marta; Ambler, Gareth; Bunce, Catey

2018-05-01

The Laser in Glaucoma and Ocular Hypertension (LiGHT) Trial aims to establish whether initial treatment with selective laser trabeculoplasty (SLT) is superior to initial treatment with topical medication for primary open-angle glaucoma (POAG) or ocular hypertension (OHT). The LiGHT Trial is a prospective, unmasked, multicentre, pragmatic, randomised controlled trial. 718 previously untreated patients with POAG or OHT were recruited at six collaborating centres in the UK between 2012 and 2014. The trial comprises two treatment arms: initial SLT followed by conventional medical therapy as required, and medical therapy without laser therapy. Randomisation was provided online by a web-based randomisation service. Participants will be monitored for 3 years, according to routine clinical practice. The target intraocular pressure (IOP) was set at baseline according to an algorithm, based on disease severity and lifetime risk of loss of vision at recruitment, and subsequently adjusted on the basis of IOP control, optic disc and visual field. The primary outcome measure is health-related quality of life (HRQL) (EQ-5D five-level). Secondary outcomes are treatment pathway cost and cost-effectiveness, Glaucoma Utility Index, Glaucoma Symptom Scale, Glaucoma Quality of Life, objective measures of pathway effectiveness, visual function and safety profiles and concordance. A single main analysis will be performed at the end of the trial on an intention-to-treat basis. The LiGHT Trial is a multicentre, pragmatic, randomised clinical trial that will provide valuable data on the relative HRQL, clinical effectiveness and cost-effectiveness of SLT and topical IOP-lowering medication. ISRCTN32038223, Pre-results. © Article author(s) (or their employer(s) unless otherwise stated in the text of the article) 2018. All rights reserved. No commercial use is permitted unless otherwise expressly granted.

PINK1 Primes Parkin-Mediated Ubiquitination of PARIS in Dopaminergic Neuronal Survival.

PubMed

Lee, Yunjong; Stevens, Daniel A; Kang, Sung-Ung; Jiang, Haisong; Lee, Yun-Il; Ko, Han Seok; Scarffe, Leslie A; Umanah, George E; Kang, Hojin; Ham, Sangwoo; Kam, Tae-In; Allen, Kathleen; Brahmachari, Saurav; Kim, Jungwoo Wren; Neifert, Stewart; Yun, Seung Pil; Fiesel, Fabienne C; Springer, Wolfdieter; Dawson, Valina L; Shin, Joo-Ho; Dawson, Ted M

2017-01-24

Mutations in PTEN-induced putative kinase 1 (PINK1) and parkin cause autosomal-recessive Parkinson's disease through a common pathway involving mitochondrial quality control. Parkin inactivation leads to accumulation of the parkin interacting substrate (PARIS, ZNF746) that plays an important role in dopamine cell loss through repression of proliferator-activated receptor gamma coactivator-1-alpha (PGC-1α) promoter activity. Here, we show that PARIS links PINK1 and parkin in a common pathway that regulates dopaminergic neuron survival. PINK1 interacts with and phosphorylates serines 322 and 613 of PARIS to control its ubiquitination and clearance by parkin. PINK1 phosphorylation of PARIS alleviates PARIS toxicity, as well as repression of PGC-1α promoter activity. Conditional knockdown of PINK1 in adult mouse brains leads to a progressive loss of dopaminergic neurons in the substantia nigra that is dependent on PARIS. Altogether, these results uncover a function of PINK1 to direct parkin-PARIS-regulated PGC-1α expression and dopaminergic neuronal survival. Copyright © 2017 The Author(s). Published by Elsevier Inc. All rights reserved.

Improving transcriptome construction in non-model organisms: integrating manual and automated gene definition in Emiliania huxleyi.

PubMed

Feldmesser, Ester; Rosenwasser, Shilo; Vardi, Assaf; Ben-Dor, Shifra

2014-02-22

The advent of Next Generation Sequencing technologies and corresponding bioinformatics tools allows the definition of transcriptomes in non-model organisms. Non-model organisms are of great ecological and biotechnological significance, and consequently the understanding of their unique metabolic pathways is essential. Several methods that integrate de novo assembly with genome-based assembly have been proposed. Yet, there are many open challenges in defining genes, particularly where genomes are not available or incomplete. Despite the large numbers of transcriptome assemblies that have been performed, quality control of the transcript building process, particularly on the protein level, is rarely performed if ever. To test and improve the quality of the automated transcriptome reconstruction, we used manually defined and curated genes, several of them experimentally validated. Several approaches to transcript construction were utilized, based on the available data: a draft genome, high quality RNAseq reads, and ESTs. In order to maximize the contribution of the various data, we integrated methods including de novo and genome based assembly, as well as EST clustering. After each step a set of manually curated genes was used for quality assessment of the transcripts. The interplay between the automated pipeline and the quality control indicated which additional processes were required to improve the transcriptome reconstruction. We discovered that E. huxleyi has a very high percentage of non-canonical splice junctions, and relatively high rates of intron retention, which caused unique issues with the currently available tools. While individual tools missed genes and artificially joined overlapping transcripts, combining the results of several tools improved the completeness and quality considerably. The final collection, created from the integration of several quality control and improvement rounds, was compared to the manually defined set both on the DNA and protein levels, and resulted in an improvement of 20% versus any of the read-based approaches alone. To the best of our knowledge, this is the first time that an automated transcript definition is subjected to quality control using manually defined and curated genes and thereafter the process is improved. We recommend using a set of manually curated genes to troubleshoot transcriptome reconstruction.

Meeting the ambition of measuring the quality of hospitals' stroke care using routinely collected administrative data: a feasibility study.

PubMed

Palmer, William L; Bottle, Alex; Davie, Charlie; Vincent, Charles A; Aylin, Paul

2013-09-01

To examine the potential for using routinely collected administrative data to compare the quality and safety of stroke care at a hospital level, including evaluating any bias due to variations in coding practice. A retrospective cohort study of English hospitals' performance against six process and outcome indicators covering the acute care pathway. We used logistic regression to adjust the outcome measures for case mix. Hospitals in England. Stroke patients (ICD-10 I60-I64) admitted to English National Health Service public acute hospitals between April 2009 and March 2010, accounting for 91 936 admissions. The quality and safety were measured using six indicators spanning the hospital care pathway, from timely access to brain scans to emergency readmissions following discharge after stroke. There were 182 occurrences of hospitals performing statistically differently from the national average at the 99.8% significance level across the six indicators. Differences in coding practice appeared to only partially explain the variation. Hospital administrative data provide a practical and achievable method for evaluating aspects of stroke care across the acute pathway. However, without improvements in coding and further validation, it is unclear whether the cause of the variation is the quality of care or the result of different local care pathways and data coding accuracy.

CHIP protects against cardiac pressure overload through regulation of AMPK

PubMed Central

Schisler, Jonathan C.; Rubel, Carrie E.; Zhang, Chunlian; Lockyer, Pamela; Cyr, Douglas M.; Patterson, Cam

2013-01-01

Protein quality control and metabolic homeostasis are integral to maintaining cardiac function during stress; however, little is known about if or how these systems interact. Here we demonstrate that C terminus of HSC70-interacting protein (CHIP), a regulator of protein quality control, influences the metabolic response to pressure overload by direct regulation of the catalytic α subunit of AMPK. Induction of cardiac pressure overload in Chip–/– mice resulted in robust hypertrophy and decreased cardiac function and energy generation stemming from a failure to activate AMPK. Mechanistically, CHIP promoted LKB1-mediated phosphorylation of AMPK, increased the specific activity of AMPK, and was necessary and sufficient for stress-dependent activation of AMPK. CHIP-dependent effects on AMPK activity were accompanied by conformational changes specific to the α subunit, both in vitro and in vivo, identifying AMPK as the first physiological substrate for CHIP chaperone activity and establishing a link between cardiac proteolytic and metabolic pathways. PMID:23863712

USP8 regulates mitophagy by removing K6-linked ubiquitin conjugates from parkin

PubMed Central

Durcan, Thomas M; Tang, Matthew Y; Pérusse, Joëlle R; Dashti, Eman A; Aguileta, Miguel A; McLelland, Gian-Luca; Gros, Priti; Shaler, Thomas A; Faubert, Denis; Coulombe, Benoit; Fon, Edward A

2014-01-01

Mutations in the Park2 gene, encoding the E3 ubiquitin-ligase parkin, are responsible for a familial form of Parkinson's disease (PD). Parkin-mediated ubiquitination is critical for the efficient elimination of depolarized dysfunctional mitochondria by autophagy (mitophagy). As damaged mitochondria are a major source of toxic reactive oxygen species within the cell, this pathway is believed to be highly relevant to the pathogenesis of PD. Little is known about how parkin-mediated ubiquitination is regulated during mitophagy or about the nature of the ubiquitin conjugates involved. We report here that USP8/UBPY, a deubiquitinating enzyme not previously implicated in mitochondrial quality control, is critical for parkin-mediated mitophagy. USP8 preferentially removes non-canonical K6-linked ubiquitin chains from parkin, a process required for the efficient recruitment of parkin to depolarized mitochondria and for their subsequent elimination by mitophagy. This work uncovers a novel role for USP8-mediated deubiquitination of K6-linked ubiquitin conjugates from parkin in mitochondrial quality control. PMID:25216678

Ubiquitin and Parkinson's disease through the looking glass of genetics.

PubMed

Walden, Helen; Muqit, Miratul M K

2017-04-13

Biochemical alterations found in the brains of Parkinson's disease (PD) patients indicate that cellular stress is a major driver of dopaminergic neuronal loss. Oxidative stress, mitochondrial dysfunction, and ER stress lead to impairment of the homeostatic regulation of protein quality control pathways with a consequent increase in protein misfolding and aggregation and failure of the protein degradation machinery. Ubiquitin signalling plays a central role in protein quality control; however, prior to genetic advances, the detailed mechanisms of how impairment in the ubiquitin system was linked to PD remained mysterious. The discovery of mutations in the α-synuclein gene, which encodes the main protein misfolded in PD aggregates, together with mutations in genes encoding ubiquitin regulatory molecules, including PTEN-induced kinase 1 (PINK1), Parkin, and FBX07, has provided an opportunity to dissect out the molecular basis of ubiquitin signalling disruption in PD, and this knowledge will be critical for developing novel therapeutic strategies in PD that target the ubiquitin system. © 2017 The Author(s).

The usefulness of lean six sigma to the development of a clinical pathway for hip fractures.

PubMed

Niemeijer, Gerard C; Flikweert, Elvira; Trip, Albert; Does, Ronald J M M; Ahaus, Kees T B; Boot, Anja F; Wendt, Klaus W

2013-10-01

The objective of this study was to show the usefulness of lean six sigma (LSS) for the development of a multidisciplinary clinical pathway. A single centre, both retrospective and prospective, non-randomized controlled study design was used to identify the variables of a prolonged length of stay (LOS) for hip fractures in the elderly and to measure the effect of the process improvements--with the aim of improving efficiency of care and reducing the LOS. The project identified several variables influencing LOS, and interventions were designed to improve the process of care. Significant results were achieved by reducing both the average LOS by 4.2 days (-31%) and the average duration of surgery by 57 minutes (-36%). The average LOS of patients discharged to a nursing home reduced by 4.4 days. The findings of this study show a successful application of LSS methodology within the development of a clinical pathway. Further research is needed to explore the effect of the use of LSS methodology at clinical outcome and quality of life. © 2012 John Wiley & Sons Ltd.

Reducing signs of aging and increasing lifespan by drug synergy.

PubMed

Huang, Xinhe; Liu, Jun; Withers, Bradley R; Samide, Aaron J; Leggas, Markos; Dickson, Robert C

2013-08-01

Disease incidence rises rapidly with age and increases both human suffering and economic hardship while shortening life. Advances in understanding the signaling pathways and cellular processes that influence aging support the possibility of reducing the incidence of age-related diseases and increasing lifespan by pharmacological intervention. Here, we demonstrate a novel pharmacological strategy that both reduces signs of aging in the budding yeast Saccharomyces cerevisiae and generates a synergistic increase in lifespan. By combining a low dose of rapamycin, to reduce activity of the target of rapamycin complex 1 (TORC1) protein kinase, and myriocin, to reduce sphingolipid synthesis, we show enhancement of autophagy, genomic stability, mitochondrial function, and AMP kinase pathway activity. These processes are controlled by evolutionarily conserved signal transduction pathways that are vital for maintaining a healthy state and promoting a long life. Thus, our data show that it ought to be possible to find pharmacological approaches to generate a synergistic reduction in the incidence of human age-related diseases to improve health quality in the elderly and enhance lifespan. © 2013 John Wiley & Sons Ltd and the Anatomical Society.

Yeast chronological lifespan and proteotoxic stress: is autophagy good or bad?

PubMed

Sampaio-Marques, Belém; Felgueiras, Carolina; Silva, Alexandra; Rodrigues, Fernando; Ludovico, Paula

2011-10-01

Autophagy, a highly conserved proteolytic mechanism of quality control, is essential for the maintenance of metabolic and cellular homoeostasis and for an efficient cellular response to stress. Autophagy declines with aging and is believed to contribute to different aspects of the aging phenotype. The nutrient-sensing pathways PKA (protein kinase A), Sch9 and TOR (target of rapamycin), involved in the regulation of yeast lifespan, also converge on a common targeted process: autophagy. The molecular mechanisms underlying the regulation of autophagy and aging by these signalling pathways in yeast, with special attention to the TOR pathway, are discussed in the present paper. The question of whether or not autophagy could contribute to yeast cell death occurring during CLS (chronological lifespan) is discussed in the light of our findings obtained after autophagy activation promoted by proteotoxic stress. Autophagy progressively increases in cells expressing the aggregation-prone protein α-synuclein and seems to participate in the early cell death and shortening of CLS under these conditions, highlighting that autophagic activity should be maintained below physiological levels to exert its promising anti-aging effects.

Cbp80 is needed for the expression of piRNA components and piRNAs

PubMed Central

Colombo, Martino; Hernandez, Greco; Beuchle, Dirk; Berger, Fabienne; Peischl, Stephan; Bruggmann, Rémy

2017-01-01

Cap binding protein 80 (Cbp80) is the larger subunit of the nuclear cap-binding complex (nCBC), which is known to play important roles in nuclear mRNA processing, export, stability and quality control events. Reducing Cbp80 mRNA levels in the female germline revealed that Cbp80 is also involved in defending the germline against transposable elements. Combining such knockdown experiments with large scale sequencing of small RNAs further showed that Cbp80 is involved in the initial biogenesis of piRNAs as well as in the secondary biogenesis pathway, the ping-pong amplification cycle. We further found that Cbp80 knockdown not only led to the upregulation of transposons, but also to delocalization of Piwi, Aub and Ago3, key factors in the piRNA biosynthesis pathway. Furthermore, compared to controls, levels of Piwi and Aub were also reduced upon knock down of Cbp80. On the other hand, with the same treatment we could not detect significant changes in levels or subcellular distribution (nuage localization) of piRNA precursor transcripts. This shows that Cbp80 plays an important role in the production and localization of the protein components of the piRNA pathway and it seems to be less important for the production and export of the piRNA precursor transcripts. PMID:28746365

Linking microarray reporters with protein functions.

PubMed

Gaj, Stan; van Erk, Arie; van Haaften, Rachel I M; Evelo, Chris T A

2007-09-26

The analysis of microarray experiments requires accurate and up-to-date functional annotation of the microarray reporters to optimize the interpretation of the biological processes involved. Pathway visualization tools are used to connect gene expression data with existing biological pathways by using specific database identifiers that link reporters with elements in the pathways. This paper proposes a novel method that aims to improve microarray reporter annotation by BLASTing the original reporter sequences against a species-specific EMBL subset, that was derived from and crosslinked back to the highly curated UniProt database. The resulting alignments were filtered using high quality alignment criteria and further compared with the outcome of a more traditional approach, where reporter sequences were BLASTed against EnsEMBL followed by locating the corresponding protein (UniProt) entry for the high quality hits. Combining the results of both methods resulted in successful annotation of > 58% of all reporter sequences with UniProt IDs on two commercial array platforms, increasing the amount of Incyte reporters that could be coupled to Gene Ontology terms from 32.7% to 58.3% and to a local GenMAPP pathway from 9.6% to 16.7%. For Agilent, 35.3% of the total reporters are now linked towards GO nodes and 7.1% on local pathways. Our methods increased the annotation quality of microarray reporter sequences and allowed us to visualize more reporters using pathway visualization tools. Even in cases where the original reporter annotation showed the correct description the new identifiers often allowed improved pathway and Gene Ontology linking. These methods are freely available at http://www.bigcat.unimaas.nl/public/publications/Gaj_Annotation/.

Optimism on quality of life in Portuguese chronic patients: moderator/mediator?

PubMed

Vilhena, Estela; Pais-Ribeiro, José; Silva, Isabel; Pedro, Luísa; Meneses, Rute F; Cardoso, Helena; Silva, António Martins da; Mendonça, Denisa

2014-07-01

optimism is an important variable that has consistently been shown to affect adjustment to quality of life in chronic diseases. This study aims to clarify if dispositional optimism exerts a moderating or a mediating influence on the personality traits-quality of life association, in Portuguese chronic patients. multiple regression models were used to test the moderation and mediation effects of dispositional optimism in quality of life. A sample of 729 patients was recruited in Portugal's main hospitals and completed self-reported questionnaires assessing socio-demographic and clinical variables, personality, dispositional optimism, quality of life (QoL) and subjective well-being (SWB). the results of the regression models showed that dispositional optimism did not moderate the relationships between personality traits and quality of life. After controlling for gender, age, education level and severity of disease perception, the effects of personality traits on QoL and in SWB were mediated by dispositional optimism (partially and completely), except for the links between neuroticism/openness to experience and physical health. dispositional optimism is more likely to play a mediating, rather than a moderating role in personality traits-quality of life pathway in Portuguese chronic patients, suggesting that "the expectation that good things will happen" contributes to a better quality of life and subjective well-being.

Stormwater Management in Urban Areas of South Korea

NASA Astrophysics Data System (ADS)

Memon, S. A.; Raja, O. S.; Kandhro, B.; Salim, I.; Lee, C.-H.

2018-03-01

In early start of monitoring, a pathway for high runoff volumes and peak flows during rainfall period towards downstream of a waterbody was provided from storm sewer network, but later on it was realized to deal with stormwater quantity and quality to develop new approaches and management techniques. In early 90’s NPS pollution issue was highlighted in korea, but only limited studies were conceded out up to the year 2000, however reasonably huge numbers of studies were directed for environmental science. After the recognition of NPS, Ministry of Environment in 1998 has introduced NPS as a major contributor in total maximum daily load management system (TPLMS) and waterbodies impairment, which is one of the guidelines of widespread water improvement strategies for main rivers. It contains a number of agendas that intention is to improve, maintain or restore the water quality in national water systems. It can be potted that stormwater management has evolved during the decades as of understanding with its impacts and it has been evolved from focusing on flood control to now incorporating control for volume, erosion and water quality, which is theoretically based on a watershed concept.

Control of proliferation and cancer growth by the Hippo signaling pathway

PubMed Central

Ehmer, Ursula; Sage, Julien

2015-01-01

The control of cell division is essential for normal development and the maintenance of cellular homeostasis. Abnormal cell proliferation is associated with multiple pathological states, including cancer. While the Hippo/YAP signaling pathway was initially thought to control organ size and growth, increasing evidence indicates that this pathway also plays a major role in the control of proliferation independent of organ size control. In particular, accumulating evidence indicates that the Hippo/YAP signaling pathway functionally interacts with multiple other cellular pathways and serves as a central node in the regulation of cell division, especially in cancer cells. Here recent observations are highlighted that connect Hippo/YAP signaling to transcription, the basic cell cycle machinery, and the control of cell division. Furthermore, the oncogenic and tumor suppressive attributes of YAP/TAZ are reviewed which emphasizes the relevance of the Hippo pathway in cancer. PMID:26432795

Estimating environmental co-benefits of U.S. GHG reduction pathways using the GCAM-USA Integrated Assessment Model (A&WMA Presentation)

EPA Science Inventory

A variety of technological pathways lead to reduced greenhouse gas (GHG) emissions. However, different pathways can have substantially different impacts on other environmental endpoints, such as air quality and energy-related water demand. In this study we use the Global Change ...

The concentration-discharge slope as a tool for water quality management.

PubMed

Bieroza, M Z; Heathwaite, A L; Bechmann, M; Kyllmar, K; Jordan, P

2018-07-15

Recent technological breakthroughs of optical sensors and analysers have enabled matching the water quality measurement interval to the time scales of stream flow changes and led to an improved understanding of spatially and temporally heterogeneous sources and delivery pathways for many solutes and particulates. This new ability to match the chemograph with the hydrograph has promoted renewed interest in the concentration-discharge (c-q) relationship and its value in characterizing catchment storage, time lags and legacy effects for both weathering products and anthropogenic pollutants. In this paper we evaluated the stream c-q relationships for a number of water quality determinands (phosphorus, suspended sediments, nitrogen) in intensively managed agricultural catchments based on both high-frequency (sub-hourly) and long-term low-frequency (fortnightly-monthly) routine monitoring data. We used resampled high-frequency data to test the uncertainty in water quality parameters (e.g. mean, 95th percentile and load) derived from low-frequency sub-datasets. We showed that the uncertainty in water quality parameters increases with reduced sampling frequency as a function of the c-q slope. We also showed that different sources and delivery pathways control c-q relationship for different solutes and particulates. Secondly, we evaluated the variation in c-q slopes derived from the long-term low-frequency data for different determinands and catchments and showed strong chemostatic behaviour for phosphorus and nitrogen due to saturation and agricultural legacy effects. The c-q slope analysis can provide an effective tool to evaluate the current monitoring networks and the effectiveness of water management interventions. This research highlights how improved understanding of solute and particulate dynamics obtained with optical sensors and analysers can be used to understand patterns in long-term water quality time series, reduce the uncertainty in the monitoring data and to manage eutrophication in agricultural catchments. Copyright © 2018 Elsevier B.V. All rights reserved.

Determining if an mRNA is a Substrate of Nonsense-Mediated mRNA Decay in Saccharomyces cerevisiae.

PubMed

Johansson, Marcus J O

2017-01-01

Nonsense-mediated mRNA decay (NMD) is a conserved eukaryotic quality control mechanism which triggers decay of mRNAs harboring premature translation termination codons. In this chapter, I describe methods for monitoring the influence of NMD on mRNA abundance and decay rates in Saccharomyces cerevisiae. The descriptions include detailed methods for growing yeast cells, total RNA isolation, and Northern blotting. Although the chapter focuses on NMD, the methods can be easily adapted to assess the effect of other mRNA decay pathways.

Assessing national provision of care: variability in bariatric clinical care pathways.

PubMed

Telem, Dana A; Majid, Saniea F; Powers, Kinga; DeMaria, Eric; Morton, John; Jones, Daniel B

2017-02-01

The American Society for Metabolic and Bariatric Surgery (ASMBS) Quality Improvement and Patient Safety (QIPS) Committee hypothesized that collecting and sharing clinical pathways could provide a valuable resource to new and existing bariatric programs. To shed light on the variability in practice patterns across the country by analyzing pathways. United States Centers of Excellence METHODS: From June 2014 to April 2015, clinical pathways pertaining to preoperative, intraoperative, and postoperative management of bariatric patients were solicited from the ASMBS executive council (EC), QIPS committee members, and state chapter presidents. Pathways were de-identified and then analyzed based on predetermined metrics pertaining to preoperative, intraoperative, and postoperative care. Concordance and discordance were then analyzed. In total, 31 pathways were collected; response rate was 80% from the EC, 77% from the QIPS committee, and 21% from state chapter presidents. The number of pathways sent in ranged from 1 to 10 with a median of 3 pathways per individual or institution. The majority of pathways centered on perioperative care (80%). Binary assessment (presence or absence) of variables found a high concordance (defined by greater than 65% of pathways accounting for that parameter) in only 6 variables: nutritional evaluation, psychological evaluation, intraoperative venous thromboembolism (VTE) prophylaxis, utilization of antiemetics in the postoperative period, a dedicated pain pathway, and postoperative laboratory evaluation. There is considerable national variation in clinical pathways among practicing bariatric surgeons. Most pathways center on Metabolic and Bariatric Surgery Accredited Quality Improvement Program (MBSAQIP) accreditation parameters, patient satisfaction, or Surgical Care Improvement Protocol (SCIP) measures. These pathways provide a path toward standardization of improved care. Copyright © 2016. Published by Elsevier Inc.

DUQuE quality management measures: associations between quality management at hospital and pathway levels.

PubMed

Wagner, Cordula; Groene, Oliver; Thompson, Caroline A; Dersarkissian, Maral; Klazinga, Niek S; Arah, Onyebuchi A; Suñol, Rosa

2014-04-01

The assessment of integral quality management (QM) in a hospital requires measurement and monitoring from different perspectives and at various levels of care delivery. Within the DUQuE project (Deepening our Understanding of Quality improvement in Europe), seven measures for QM were developed. This study investigates the relationships between the various quality measures. It is a multi-level, cross-sectional, mixed-method study. As part of the DUQuE project, we invited a random sample of 74 hospitals in 7 countries. The quality managers of these hospitals were the main respondents. Furthermore, data of site visits of external surveyors assessing the participating hospitals were used. Three measures of QM at hospitals level focusing on integral systems (QMSI), compliance with the Plan-Do-Study-Act quality improvement cycle (QMCI) and implementation of clinical quality (CQII). Four measures of QM activities at care pathway level focusing on Specialized expertise and responsibility (SER), Evidence-based organization of pathways (EBOP), Patient safety strategies (PSS) and Clinical review (CR). Positive significant associations were found between the three hospitals level QM measures. Results of the relationships between levels were mixed and showed most associations between QMCI and department-level QM measures for all four types of departments. QMSI was associated with PSS in all types of departments. By using the seven measures of QM, it is possible to get a more comprehensive picture of the maturity of QM in hospitals, with regard to the different levels and across various types of hospital departments.

Automatically visualise and analyse data on pathways using PathVisioRPC from any programming environment.

PubMed

Bohler, Anwesha; Eijssen, Lars M T; van Iersel, Martijn P; Leemans, Christ; Willighagen, Egon L; Kutmon, Martina; Jaillard, Magali; Evelo, Chris T

2015-08-23

Biological pathways are descriptive diagrams of biological processes widely used for functional analysis of differentially expressed genes or proteins. Primary data analysis, such as quality control, normalisation, and statistical analysis, is often performed in scripting languages like R, Perl, and Python. Subsequent pathway analysis is usually performed using dedicated external applications. Workflows involving manual use of multiple environments are time consuming and error prone. Therefore, tools are needed that enable pathway analysis directly within the same scripting languages used for primary data analyses. Existing tools have limited capability in terms of available pathway content, pathway editing and visualisation options, and export file formats. Consequently, making the full-fledged pathway analysis tool PathVisio available from various scripting languages will benefit researchers. We developed PathVisioRPC, an XMLRPC interface for the pathway analysis software PathVisio. PathVisioRPC enables creating and editing biological pathways, visualising data on pathways, performing pathway statistics, and exporting results in several image formats in multiple programming environments. We demonstrate PathVisioRPC functionalities using examples in Python. Subsequently, we analyse a publicly available NCBI GEO gene expression dataset studying tumour bearing mice treated with cyclophosphamide in R. The R scripts demonstrate how calls to existing R packages for data processing and calls to PathVisioRPC can directly work together. To further support R users, we have created RPathVisio simplifying the use of PathVisioRPC in this environment. We have also created a pathway module for the microarray data analysis portal ArrayAnalysis.org that calls the PathVisioRPC interface to perform pathway analysis. This module allows users to use PathVisio functionality online without having to download and install the software and exemplifies how the PathVisioRPC interface can be used by data analysis pipelines for functional analysis of processed genomics data. PathVisioRPC enables data visualisation and pathway analysis directly from within various analytical environments used for preliminary analyses. It supports the use of existing pathways from WikiPathways or pathways created using the RPC itself. It also enables automation of tasks performed using PathVisio, making it useful to PathVisio users performing repeated visualisation and analysis tasks. PathVisioRPC is freely available for academic and commercial use at http://projects.bigcat.unimaas.nl/pathvisiorpc.

Divergent pathways to influence: Cognition and behavior differentially mediate the effects of optimism on physical and mental quality of life in Chinese university students.

PubMed

Ramsay, Jonathan E; Yang, Fang; Pang, Joyce S; Lai, Ching-Man; Ho, Roger Cm; Mak, Kwok-Kei

2015-07-01

Previous research has indicated that both cognitive and behavioral variables mediate the positive effect of optimism on quality of life; yet few attempts have been made to accommodate these constructs into a single explanatory framework. Adopting Fredrickson's broaden-and-build perspective, we examined the relationships between optimism, self-rated health, resilience, exercise, and quality of life in 365 Chinese university students using path analysis. For physical quality of life, a two-stage model, in which the effects of optimism were sequentially mediated by cognitive and behavioral variables, provided the best fit. A one-stage model, with full mediation by cognitive variables, provided the best fit for mental quality of life. This suggests that optimism influences physical and mental quality of life via different pathways. © The Author(s) 2013.

Dispositional optimism and sleep quality: a test of mediating pathways

PubMed Central

Cribbet, Matthew; Kent de Grey, Robert G.; Cronan, Sierra; Trettevik, Ryan; Smith, Timothy W.

2016-01-01

Dispositional optimism has been related to beneficial influences on physical health outcomes. However, its links to global sleep quality and the psychological mediators responsible for such associations are less studied. This study thus examined if trait optimism predicted global sleep quality, and if measures of subjective well-being were statistical mediators of such links. A community sample of 175 participants (93 men, 82 women) completed measures of trait optimism, depression, and life satisfaction. Global sleep quality was assessed using the Pittsburgh Sleep Quality Index. Results indicated that trait optimism was a strong predictor of better PSQI global sleep quality. Moreover, this association was mediated by depression and life satisfaction in both single and multiple mediator models. These results highlight the importance of optimism for the restorative process of sleep, as well as the utility of multiple mediator models in testing distinct psychological pathways. PMID:27592128

Dispositional optimism and sleep quality: a test of mediating pathways.

PubMed

Uchino, Bert N; Cribbet, Matthew; de Grey, Robert G Kent; Cronan, Sierra; Trettevik, Ryan; Smith, Timothy W

2017-04-01

Dispositional optimism has been related to beneficial influences on physical health outcomes. However, its links to global sleep quality and the psychological mediators responsible for such associations are less studied. This study thus examined if trait optimism predicted global sleep quality, and if measures of subjective well-being were statistical mediators of such links. A community sample of 175 participants (93 men, 82 women) completed measures of trait optimism, depression, and life satisfaction. Global sleep quality was assessed using the Pittsburgh Sleep Quality Index. Results indicated that trait optimism was a strong predictor of better PSQI global sleep quality. Moreover, this association was mediated by depression and life satisfaction in both single and multiple mediator models. These results highlight the importance of optimism for the restorative process of sleep, as well as the utility of multiple mediator models in testing distinct psychological pathways.

Construction of a controllable β-carotene biosynthetic pathway by decentralized assembly strategy in Saccharomyces cerevisiae.

PubMed

Xie, Wenping; Liu, Min; Lv, Xiaomei; Lu, Wenqiang; Gu, Jiali; Yu, Hongwei

2014-01-01

Saccharomyces cerevisiae is an important platform organism for the synthesis of a great number of natural products. However, the assembly of controllable and genetically stable heterogeneous biosynthetic pathways in S. cerevisiae still remains a significant challenge. Here, we present a strategy for reconstructing controllable multi-gene pathways by employing the GAL regulatory system. A set of marker recyclable integrative plasmids (pMRI) was designed for decentralized assembly of pathways. As proof-of-principle, a controllable β-carotene biosynthesis pathway (∼16 kb) was reconstructed and optimized by repeatedly using GAL10-GAL1 bidirectional promoters with high efficiency (80-100%). By controling the switch time of the pathway, production of 11 mg/g DCW of total carotenoids (72.57 mg/L) and 7.41 mg/g DCW of β-carotene was achieved in shake-flask culture. In addition, the engineered yeast strain exhibited high genetic stability after 20 generations of subculture. The results demonstrated a controllable and genetically stable biosynthetic pathway capable of increasing the yield of target products. Furthermore, the strategy presented in this study could be extended to construct other pathways in S. cerevisisae. © 2013 Wiley Periodicals, Inc.

Clinical- and cost-effectiveness of the STAR care pathway compared to usual care for patients with chronic pain after total knee replacement: study protocol for a UK randomised controlled trial.

PubMed

Wylde, Vikki; Bertram, Wendy; Beswick, Andrew D; Blom, Ashley W; Bruce, Julie; Burston, Amanda; Dennis, Jane; Garfield, Kirsty; Howells, Nicholas; Lane, Athene; McCabe, Candy; Moore, Andrew J; Noble, Sian; Peters, Tim J; Price, Andrew; Sanderson, Emily; Toms, Andrew D; Walsh, David A; White, Simon; Gooberman-Hill, Rachael

2018-02-21

Approximately 20% of patients experience chronic pain after total knee replacement. There is little evidence for effective interventions for the management of this pain, and current healthcare provision is patchy and inconsistent. Given the complexity of this condition, multimodal and individualised interventions matched to pain characteristics are needed. We have undertaken a comprehensive programme of work to develop a care pathway for patients with chronic pain after total knee replacement. This protocol describes the design of a randomised controlled trial to evaluate the clinical- and cost-effectiveness of a complex intervention care pathway compared with usual care. This is a pragmatic two-armed, open, multi-centred randomised controlled trial conducted within secondary care in the UK. Patients will be screened at 2 months after total knee replacement and 381 patients with chronic pain at 3 months postoperatively will be recruited. Recruitment processes will be optimised through qualitative research during a 6-month internal pilot phase. Patients are randomised using a 2:1 intervention:control allocation ratio. All participants receive usual care as provided by their hospital. The intervention comprises an assessment clinic appointment at 3 months postoperatively with an Extended Scope Practitioner and up to six telephone follow-up calls over 12 months. In the assessment clinic, a standardised protocol is followed to identify potential underlying causes for the chronic pain and enable appropriate onward referrals to existing services for targeted and individualised treatment. Outcomes are assessed by questionnaires at 6 and 12 months after randomisation. The co-primary outcomes are pain severity and pain interference assessed using the Brief Pain Inventory at 12 months after randomisation. Secondary outcomes relate to resource use, function, neuropathic pain, mental well-being, use of pain medications, satisfaction with pain relief, pain frequency, capability, health-related quality of life and bodily pain. After trial completion, up to 30 patients in the intervention group will be interviewed about their experiences of the care pathway. If shown to be clinically and cost-effective, this care pathway intervention could improve the management of chronic pain after total knee replacement. ISRCTN registry ( ISRCTN92545361 ), prospectively registered on 30 August 2016.

The human immunodeficiency virus antigen Nef forms protein bodies in leaves of transgenic tobacco when fused to zeolin

PubMed Central

de Virgilio, Maddalena; Bellucci, Michele; Mainieri, Davide; Rossi, Marika; Benvenuto, Eugenio; Arcioni, Sergio; Vitale, Alessandro

2008-01-01

Protein bodies (PB) are stable polymers naturally formed by certain seed storage proteins within the endoplasmic reticulum (ER). The human immunodeficiency virus negative factor (Nef) protein, a potential antigen for the development of an anti-viral vaccine, is highly unstable when introduced into the plant secretory pathway, probably because of folding defects in the ER environment. The aim of this study was to promote the formation of Nef-containing PB in tobacco (Nicotiana tabacum) leaves by fusing the Nef sequence to the N-terminal domains of the maize storage protein γ-zein or to the chimeric protein zeolin (which efficiently forms PB and is composed of the vacuolar storage protein phaseolin fused to the N-terminal domains of γ-zein). Protein blots and pulse–chase indicate that fusions between Nef and the same γ-zein domains present in zeolin are degraded by ER quality control. Consistently, a mutated zeolin, in which wild-type phaseolin was substituted with a defective version known to be degraded by ER quality control, is unstable in plant cells. Fusion of Nef to the entire zeolin sequence instead allows the formation of PB detectable by electron microscopy and subcellular fractionation, leading to zeolin–Nef accumulation higher than 1% of total soluble protein, consistently reproduced in independent transgenic plants. It is concluded that zeolin, but not its γ-zein portion, has a positive dominant effect over ER quality control degradation. These results provide insights into the requirements for PB formation and avoidance of quality-control degradation, and indicate a strategy for enhancing foreign protein accumulation in plants. PMID:18540021

Nonsense-Mediated Decay in Genetic Disease: Friend or Foe?

PubMed Central

Miller, Jake N.; Pearce, David A.

2014-01-01

Eukaryotic cells utilize various RNA quality control mechanisms to ensure high fidelity of gene expression, thus protecting against the accumulation of nonfunctional RNA and the subsequent production of abnormal peptides. Messenger RNAs (mRNAs) are largely responsible for protein production, and mRNA quality control is particularly important for protecting the cell against the downstream effects of genetic mutations. Nonsense-mediated decay (NMD) is an evolutionarily conserved mRNA quality control system in all eukaryotes that degrades transcripts containing premature termination codons (PTCs). By degrading these aberrant transcripts, NMD acts to prevent the production of truncated proteins that could otherwise harm the cell through various insults, such as dominant negative effects or the ER stress response. Although NMD functions to protect the cell against the deleterious effects of aberrant mRNA, there is a growing body of evidence that mutation-, codon-, gene-, cell-, and tissue-specific differences in NMD efficiency can alter the underlying pathology of genetic disease. In addition, the protective role that NMD plays in genetic disease can undermine current therapeutic strategies aimed at increasing the production of full-length functional protein from genes harboring nonsense mutations. Here, we review the normal function of this RNA surveillance pathway and how it is regulated, provide current evidence for the role that it plays in modulating genetic disease phenotypes, and how NMD can be used as a therapeutic target. PMID:25485595

Protein Kinase A Regulates Molecular Chaperone Transcription and Protein Aggregation

PubMed Central

Prince, Thomas; Calderwood, Stuart K.

2011-01-01

Heat shock factor 1 (HSF1) regulates one of the major pathways of protein quality control and is essential for deterrence of protein-folding disorders, particularly in neuronal cells. However, HSF1 activity declines with age, a change that may open the door to progression of neurodegenerative disorders such as Huntington's disease. We have investigated mechanisms of HSF1 regulation that may become compromised with age. HSF1 binds stably to the catalytic domain of protein kinase A (PKAcα) and becomes phosphorylated on at least one regulatory serine residue (S320). We show here that PKA is essential for effective transcription of HSP genes by HSF1. PKA triggers a cascade involving HSF1 binding to the histone acetylase p300 and positive translation elongation factor 1 (p-TEFb) and phosphorylation of the c-terminal domain of RNA polymerase II, a key mechanism in the downstream steps of HSF1-mediated transcription. This cascade appears to play a key role in protein quality control in neuronal cells expressing aggregation-prone proteins with long poly-glutamine (poly-Q) tracts. Such proteins formed inclusion bodies that could be resolved by HSF1 activation during heat shock. Resolution of the inclusions was inhibited by knockdown of HSF1, PKAcα, or the pTEFb component CDK9, indicating a key role for the HSF1-PKA cascade in protein quality control. PMID:22216146

How Parkinsonian Toxins Dysregulate the Autophagy Machinery

PubMed Central

Dagda, Ruben K.; Das Banerjee, Tania; Janda, Elzbieta

2013-01-01

Since their discovery, Parkinsonian toxins (6-hydroxydopamine, MPP+, paraquat, and rotenone) have been widely employed as in vivo and in vitro chemical models of Parkinson’s disease (PD). Alterations in mitochondrial homeostasis, protein quality control pathways, and more recently, autophagy/mitophagy have been implicated in neurotoxin models of PD. Here, we highlight the molecular mechanisms by which different PD toxins dysregulate autophagy/mitophagy and how alterations of these pathways play beneficial or detrimental roles in dopamine neurons. The convergent and divergent effects of PD toxins on mitochondrial function and autophagy/mitophagy are also discussed in this review. Furthermore, we propose new diagnostic tools and discuss how pharmacological modulators of autophagy/mitophagy can be developed as disease-modifying treatments for PD. Finally, we discuss the critical need to identify endogenous and synthetic forms of PD toxins and develop efficient health preventive programs to mitigate the risk of developing PD. PMID:24217228

Autophagy as a Therapeutic Target in Cardiovascular Disease

PubMed Central

Nemchenko, Andriy; Chiong, Mario; Turer, Aslan; Lavandero, Sergio; Hill, Joseph A.

2011-01-01

The epidemic of heart failure continues apace, and development of novel therapies with clinical efficacy has lagged. Now, important insights into the molecular circuitry of cardiovascular autophagy have raised the prospect that this cellular pathway of protein quality control may be a target of clinical relevance. Whereas basal levels of autophagy are required for cell survival, excessive levels – or perhaps distinct forms of autophagic flux – contribute to disease pathogenesis. Our challenge will be to distinguish mechanisms that drive adaptive versus maladaptive autophagy and to manipulate those pathways for therapeutic gain. Recent evidence suggests this may be possible. Here, we review the fundamental biology of autophagy and its role in a variety of forms of cardiovascular disease. We discuss ways in which this evolutionarily conserved catabolic mechanism can be manipulated, discuss studies presently underway in heart disease, and provide our perspective on where this exciting field may lead in the future. PMID:21723289

Substrate recognition and catalysis by GH47 α-mannosidases involved in Asn-linked glycan maturation in the mammalian secretory pathway

DOE Office of Scientific and Technical Information (OSTI.GOV)

Xiang, Yong; Karaveg, Khanita; Moremen, Kelley W.

2016-11-17

Asn-linked glycosylation of newly synthesized polypeptides occurs in the endoplasmic reticulum of eukaryotic cells. Glycan structures are trimmed and remodeled as they transit the secretory pathway, and processing intermediates play various roles as ligands for folding chaperones and signals for quality control and intracellular transport. Key steps for the generation of these trimmed intermediates are catalyzed by glycoside hydrolase family 47 (GH47) α-mannosidases that selectively cleave α1,2-linked mannose residues. Despite the sequence and structural similarities among the GH47 enzymes, the molecular basis for residue-specific cleavage remains obscure. The present studies reveal enzyme–substrate complex structures for two related GH47 α-mannosidases andmore » provide insights into how these enzymes recognize the same substrates differently and catalyze the complementary glycan trimming reactions necessary for glycan maturation.« less

Molecular cues for development and regeneration of salivary glands

PubMed Central

Liu, Fei; Wang, Songlin

2015-01-01

The hypofunction of salivary glands caused by Sjögren’s Syndrome or radiotherapy for head and neck cancer significantly compromises the quality of life of millions patients. Currently no curative treatment is available for the irreversible hyposalivation, whereas regenerative strategies targeting salivary stem/progenitor cells are promising. However, the success of these strategies is constrained by the lack of insights on the molecular cues of salivary gland regeneration. Recent advances in the molecular controls of salivary gland morphogenesis provided valuable clues for identifying potential regenerative cues. A complicated network of signaling molecules between epithelia, mesenchyme, endothelia, extracellular matrix and innervating nerves orchestrate the salivary gland organogenesis. Here we discuss the roles of several cross-talking intercellular signaling pathways, i.e., FGF, Wnt, Hedgehog, Eda, Notch, Chrm1/HB-EGF and Laminin/Integrin pathways, in the development of salivary glands and their potentials to promote salivary regeneration. PMID:24189993

WGA-Alexa conjugates for axonal tracing

PubMed Central

Levy, Sabrina L.; White, Joshua J.; Lackey, Elizabeth P.; Schwartz, Lindsey; Sillitoe, Roy V.

2017-01-01

Anatomical labeling approaches are essential for understanding brain organization. Among these approaches are various methods of performing tract tracing. However, a major hurdle to overcome when marking neurons in vivo is visibility. Poor visibility makes it challenging to image a desired neuronal pathway so that it can be easily differentiated from a closely neighboring pathway. As a result, it becomes impossible to analyze individual projections or their connections. The tracer that is chosen for a given purpose has a major influence on the quality of the tracing. Here, we describe the wheat germ agglutinin (WGA) tracer conjugated to Alexa fluorophores for reliable high-resolution tracing of central nervous system projections. Using the mouse cerebellum as a model system, we implement WGA-Alexa tracing for marking and mapping neural circuits that control motor function. We also show its utility for marking localized regions of the cerebellum after performing single-unit extracellular recordings in vivo. PMID:28398642

Emergency ultrasound-based algorithms for diagnosing blunt abdominal trauma.

PubMed

Stengel, Dirk; Bauwens, Kai; Rademacher, Grit; Ekkernkamp, Axel; Güthoff, Claas

2013-07-31

Ultrasonography is regarded as the tool of choice for early diagnostic investigations in patients with suspected blunt abdominal trauma. Although its sensitivity is too low for definite exclusion of abdominal organ injury, proponents of ultrasound argue that ultrasound-based clinical pathways enhance the speed of primary trauma assessment, reduce the number of computed tomography scans and cut costs. To assess the effects of trauma algorithms that include ultrasound examinations in patients with suspected blunt abdominal trauma. We searched the Cochrane Injuries Group's Specialised Register, CENTRAL (The Cochrane Library), MEDLINE (OvidSP), EMBASE (OvidSP), CINAHL (EBSCO), publishers' databases, controlled trials registers and the Internet. Bibliographies of identified articles and conference abstracts were searched for further elligible studies. Trial authors were contacted for further information and individual patient data. The searches were updated in February 2013. randomised controlled trials (RCTs) and quasi-randomised trials (qRCTs). patients with blunt torso, abdominal or multiple trauma undergoing diagnostic investigations for abdominal organ injury. diagnostic algorithms comprising emergency ultrasonography (US). diagnostic algorithms without ultrasound examinations (for example, primary computed tomography [CT] or diagnostic peritoneal lavage [DPL]). mortality, use of CT and DPL, cost-effectiveness, laparotomy and negative laparotomy rates, delayed diagnoses, and quality of life. Two authors independently selected trials for inclusion, assessed methodological quality and extracted data. Where possible, data were pooled and relative risks (RRs), risk differences (RDs) and weighted mean differences, each with 95% confidence intervals (CIs), were calculated by fixed- or random-effects modelling, as appropriate. We identified four studies meeting our inclusion criteria. Overall, trials were of moderate methodological quality. Few trial authors responded to our written inquiries seeking to resolve controversial issues and to obtain individual patient data. We pooled mortality data from three trials involving 1254 patients; relative risk in favour of the US arm was 1.00 (95% CI 0.50 to 2.00). US-based pathways significantly reduced the number of CT scans (random-effects RD -0.52, 95% CI -0.83 to -0.21), but the meaning of this result is unclear. Given the low sensitivity of ultrasound, the reduction in CT scans may either translate to a number needed to treat or number needed to harm of two. There is currently insufficient evidence from RCTs to justify promotion of ultrasound-based clinical pathways in diagnosing patients with suspected blunt abdominal trauma.

Control of Organ Growth by Patterning and Hippo Signaling in Drosophila

PubMed Central

Irvine, Kenneth D.; Harvey, Kieran F.

2015-01-01

Control of organ size is of fundamental importance and is controlled by genetic, environmental, and mechanical factors. Studies in many species have pointed to the existence of both organ-extrinsic and -intrinsic size-control mechanisms, which ultimately must coordinate to regulate organ size. Here, we discuss organ size control by organ patterning and the Hippo pathway, which both act in an organ-intrinsic fashion. The influence of morphogens and other patterning molecules couples growth and patterning, whereas emerging evidence suggests that the Hippo pathway controls growth in response to mechanical stimuli and signals emanating from cell–cell interactions. Several points of cross talk have been reported between signaling pathways that control organ patterning and the Hippo pathway, both at the level of membrane receptors and transcriptional regulators. However, despite substantial progress in the past decade, key questions in the growth-control field remain, including precisely how and when organ patterning and the Hippo pathway communicate to control size, and whether these communication mechanisms are organ specific or general. In addition, elucidating mechanisms by which organ-intrinsic cues, such as patterning factors and the Hippo pathway, interface with extrinsic cues, such as hormones to control organ size, remain unresolved. PMID:26032720

Estimating changes in urban ozone concentrations due to life cycle emissions from hydrogen transportation systems

NASA Astrophysics Data System (ADS)

Wang, Guihua; Ogden, Joan M.; Chang, Daniel P. Y.

Hydrogen has been proposed as a low polluting alternative transportation fuel that could help improve urban air quality. This paper examines the potential impact of introducing a hydrogen-based transportation system on urban ambient ozone concentrations. This paper considers two scenarios, where significant numbers of new hydrogen vehicles are added to a constant number of gasoline vehicles. In our scenarios hydrogen fuel cell vehicles (HFCVs) are introduced in Sacramento, California at market penetrations of 9% and 20%. From a life cycle analysis (LCA) perspective, considering all the emissions involved in producing, transporting, and using hydrogen, this research compares three hypothetical natural gas to hydrogen pathways: (1) on-site hydrogen production; (2) central hydrogen production with pipeline delivery; and (3) central hydrogen production with liquid hydrogen truck delivery. Using a regression model, this research shows that the daily maximum temperature correlates well with atmospheric ozone formation. However, increases in initial VOC and NO x concentrations do not necessarily increase the peak ozone concentration, and may even cause it to decrease. It is found that ozone formation is generally limited by NO x in the summer and is mostly limited by VOC in the fall in Sacramento. Of the three hydrogen pathways, the truck delivery pathway contributes the most to ozone precursor emissions. Ozone precursor emissions from the truck pathway at 9% market penetration can cause additional 3-h average VOC (or NO x) concentrations up to approximately 0.05% (or 1%) of current pollution levels, and at 20% market penetration up to approximately 0.1% (or 2%) of current pollution levels. However, all of the hydrogen pathways would result in very small (either negative or positive) changes in ozone air quality. In some cases they will result in worse ozone air quality (mostly in July, August, and September), and in some cases they will result in better ozone air quality (mostly in October). The truck pathway tends to cause a much wider fluctuation in degradation or improvement of ozone air quality: percentage changes in peak ozone concentrations are approximately -0.01% to 0.04% for the assumed 9% market penetration, and approximately -0.03% to 0.1% for the 20% market penetration. Moreover, the 20% on-site pathway occasionally results in a decrease of about -0.1% of baseline ozone pollution. Compared to the current ambient pollution level, all three hydrogen pathways are unlikely to cause a serious ozone problem for market penetration levels of HFCVs in the 9-20% range.

The air quality and health co-benefits of alternative post-2020 pathways for achieving peak carbon targets in Jiangsu, China

NASA Astrophysics Data System (ADS)

Liu, M.; Bi, J.; Huang, Y.; Kinney, P. L.

2016-12-01

Jiangsu, which has three national low-carbon pilot cities, is set to be a model province in China for achieving peak carbon targets before 2030. However, according to local planning of responding to climate change, carbon emissions are projected to keep going up before 2020 even the strictest measures are implemented. In other words, innovative measures must be in action after 2020. This work aimed at assessing the air quality and health co-benefits of alternative post-2020 measures to help remove barriers of policy implementation through tying it to local incentives for air quality improvement. To achieve the aim, we select 2010 as baseline year and develop Bussiness As Usual (BAU) and Traditional Carbon Reduction (TCR) scenarios before 2020. Under BAU, only existing climate and air pollution control policies are considered; under TCR, potential climate policies in local planning and existing air pollution control policies are considered. After 2020, integrated gasification combined cycle (IGCC) plant with carbon capture and storage (CCS) technology and large-scale substitution of renewable energy seem to be two promising pathways for achieving peak carbon targets. Therefore, two additional scenarios (TCR-IGCC and TCR-SRE) are set after 2020. Based on the projections of future energy balances and industrial productions, we estimate the pollutant emissions and simulate PM2.5 and ozone concentrations by 2017, 2020, 2030 and 2050 using CMAQ. Then using health impact assessment approach, the premature deaths are estimated and monetized. Results show that the carbon peak in Jiangsu will be achieved before 2030 only under TCR-IGCC and TCR-SRE scenarios. Under three policy scenarios, Jiangsu's carbon emission control targets would have substantial effects on primary air pollutant emissions far beyond those we estimate would be needed to meet the PM2.5 concentration targets in 2017. Compared with IGCC with CCS, large-scale substitutions of renewable energy bring comparable pollutant emission reductions but more health benefits because it reduces more emissions from traffic sources which are more harmful to health. However, large-scale substitution of renewable energy posed challenges on energy supply capacity, which need to be seriously considered in future policy decision.

Linking microarray reporters with protein functions

PubMed Central

Gaj, Stan; van Erk, Arie; van Haaften, Rachel IM; Evelo, Chris TA

2007-01-01

Background The analysis of microarray experiments requires accurate and up-to-date functional annotation of the microarray reporters to optimize the interpretation of the biological processes involved. Pathway visualization tools are used to connect gene expression data with existing biological pathways by using specific database identifiers that link reporters with elements in the pathways. Results This paper proposes a novel method that aims to improve microarray reporter annotation by BLASTing the original reporter sequences against a species-specific EMBL subset, that was derived from and crosslinked back to the highly curated UniProt database. The resulting alignments were filtered using high quality alignment criteria and further compared with the outcome of a more traditional approach, where reporter sequences were BLASTed against EnsEMBL followed by locating the corresponding protein (UniProt) entry for the high quality hits. Combining the results of both methods resulted in successful annotation of > 58% of all reporter sequences with UniProt IDs on two commercial array platforms, increasing the amount of Incyte reporters that could be coupled to Gene Ontology terms from 32.7% to 58.3% and to a local GenMAPP pathway from 9.6% to 16.7%. For Agilent, 35.3% of the total reporters are now linked towards GO nodes and 7.1% on local pathways. Conclusion Our methods increased the annotation quality of microarray reporter sequences and allowed us to visualize more reporters using pathway visualization tools. Even in cases where the original reporter annotation showed the correct description the new identifiers often allowed improved pathway and Gene Ontology linking. These methods are freely available at http://www.bigcat.unimaas.nl/public/publications/Gaj_Annotation/. PMID:17897448

Spermidine coupled with exercise rescues skeletal muscle atrophy from D-gal-induced aging rats through enhanced autophagy and reduced apoptosis via AMPK-FOXO3a signal pathway

PubMed Central

Fan, Jingjing; Yang, Xiaoqi; Li, Jie; Shu, Ziyang; Dai, Jun; Liu, Xingran; Li, Biao; Jia, Shaohui; Kou, Xianjuan; Yang, Yi; Chen, Ning

2017-01-01

The quality control of skeletal muscle is a continuous requirement throughout the lifetime, although its functions and quality present as a declining trend during aging process. Dysfunctional or deficient autophagy and excessive apoptosis may contribute to the atrophy of senescent skeletal muscle. Spermidine, as a natural polyamine, can be involved in important cellular functions for lifespan extension and stress resistance in several model organisms through activating autophagy. Similarly, cellular autophagic responses to exercise have also been extensively investigated. In the present study, in order to confirm the mitigation or amelioration of skeletal muscle atrophy in aging rats through spermidine coupled with exercise intervention and explore corresponding mechanisms, the rat model with aging-related atrophy of skeletal muscle was established by intraperitoneal injection of D-galactose (D-gal) (200 mg/kgd), and model rats were subjected to the intervention with spermidine (5 mg/kgd) or swimming (60 min/d, 5 d/wk) or combination for 42 days. Spermidine coupled with exercise could attenuate D-gal-induced aging-related atrophy of skeletal muscle through induced autophagy and reduced apoptosis with characteristics of more autophagosomes, activated mitophagy, enhanced mitochondrial quality, alleviated cell shrinkage, and less swollen mitochondria under transmission scanning microscopic observation. Meanwhile, spermidine coupled with exercise could induce autophagy through activating AMPK-FOXO3a signal pathway with characterization of increased Beclin1 and LC3-II/LC3-I ratio, up-regulated anti-apoptotic Bcl-2, down-regulated pro-apoptotic Bax and caspase-3, as well as activated AMPK and FOXO3a. Therefore, spermidine combined with exercise can execute the prevention or treatment of D-gal-induced aging-related skeletal muscle atrophy through enhanced autophagy and reduced apoptosis mediated by AMPK-FOXO3a signal pathway. PMID:28407698

Environmental control of branching in petunia.

PubMed

Drummond, Revel S M; Janssen, Bart J; Luo, Zhiwei; Oplaat, Carla; Ledger, Susan E; Wohlers, Mark W; Snowden, Kimberley C

2015-06-01

Plants alter their development in response to changes in their environment. This responsiveness has proven to be a successful evolutionary trait. Here, we tested the hypothesis that two key environmental factors, light and nutrition, are integrated within the axillary bud to promote or suppress the growth of the bud into a branch. Using petunia (Petunia hybrida) as a model for vegetative branching, we manipulated both light quality (as crowding and the red-to-far-red light ratio) and phosphate availability, such that the axillary bud at node 7 varied from deeply dormant to rapidly growing. In conjunction with the phenotypic characterization, we also monitored the state of the strigolactone (SL) pathway by quantifying SL-related gene transcripts. Mutants in the SL pathway inhibit but do not abolish the branching response to these environmental signals, and neither signal is dominant over the other, suggesting that the regulation of branching in response to the environment is complex. We have isolated three new putatively SL-related TCP (for Teosinte branched1, Cycloidia, and Proliferating cell factor) genes from petunia, and have identified that these TCP-type transcription factors may have roles in the SL signaling pathway both before and after the reception of the SL signal at the bud. We show that the abundance of the receptor transcript is regulated by light quality, such that axillary buds growing in added far-red light have greatly increased receptor transcript abundance. This suggests a mechanism whereby the impact of any SL signal reaching an axillary bud is modulated by the responsiveness of these cells to the signal. © 2015 American Society of Plant Biologists. All Rights Reserved.

Environmental Control of Branching in Petunia1[OPEN

PubMed Central

Oplaat, Carla; Wohlers, Mark W.

2015-01-01

Plants alter their development in response to changes in their environment. This responsiveness has proven to be a successful evolutionary trait. Here, we tested the hypothesis that two key environmental factors, light and nutrition, are integrated within the axillary bud to promote or suppress the growth of the bud into a branch. Using petunia (Petunia hybrida) as a model for vegetative branching, we manipulated both light quality (as crowding and the red-to-far-red light ratio) and phosphate availability, such that the axillary bud at node 7 varied from deeply dormant to rapidly growing. In conjunction with the phenotypic characterization, we also monitored the state of the strigolactone (SL) pathway by quantifying SL-related gene transcripts. Mutants in the SL pathway inhibit but do not abolish the branching response to these environmental signals, and neither signal is dominant over the other, suggesting that the regulation of branching in response to the environment is complex. We have isolated three new putatively SL-related TCP (for Teosinte branched1, Cycloidia, and Proliferating cell factor) genes from petunia, and have identified that these TCP-type transcription factors may have roles in the SL signaling pathway both before and after the reception of the SL signal at the bud. We show that the abundance of the receptor transcript is regulated by light quality, such that axillary buds growing in added far-red light have greatly increased receptor transcript abundance. This suggests a mechanism whereby the impact of any SL signal reaching an axillary bud is modulated by the responsiveness of these cells to the signal. PMID:25911529

Misfolded Polyglutamine, Polyalanine, and Superoxide Dismutase 1 Aggregate via Distinct Pathways in the Cell*

PubMed Central

Polling, Saskia; Mok, Yee-Foong; Ramdzan, Yasmin M.; Turner, Bradley J.; Yerbury, Justin J.; Hill, Andrew F.; Hatters, Danny M.

2014-01-01

Protein aggregation into intracellular inclusions is a key feature of many neurodegenerative disorders. A common theme has emerged that inappropriate self-aggregation of misfolded or mutant polypeptide sequences is detrimental to cell health. Yet protein quality control mechanisms may also deliberately cluster them together into distinct inclusion subtypes, including the insoluble protein deposit (IPOD) and the juxtanuclear quality control (JUNQ). Here we investigated how the intrinsic oligomeric state of three model systems of disease-relevant mutant protein and peptide sequences relates to the IPOD and JUNQ patterns of aggregation using sedimentation velocity analysis. Two of the models (polyalanine (37A) and superoxide dismutase 1 (SOD1) mutants A4V and G85R) accumulated into the same JUNQ-like inclusion whereas the other, polyglutamine (72Q), formed spatially distinct IPOD-like inclusions. Using flow cytometry pulse shape analysis (PulSA) to separate cells with inclusions from those without revealed the SOD1 mutants and 37A to have abruptly altered oligomeric states with respect to the nonaggregating forms, regardless of whether cells had inclusions or not, whereas 72Q was almost exclusively monomeric until inclusions formed. We propose that mutations leading to JUNQ inclusions induce a constitutively “misfolded” state exposing hydrophobic side chains that attract and ultimately overextend protein quality capacity, which leads to aggregation into JUNQ inclusions. Poly(Q) is not misfolded in this same sense due to universal polar side chains, but is highly prone to forming amyloid fibrils that we propose invoke a different engagement mechanism with quality control. PMID:24425868

Misfolded polyglutamine, polyalanine, and superoxide dismutase 1 aggregate via distinct pathways in the cell.

PubMed

Polling, Saskia; Mok, Yee-Foong; Ramdzan, Yasmin M; Turner, Bradley J; Yerbury, Justin J; Hill, Andrew F; Hatters, Danny M

2014-03-07

Protein aggregation into intracellular inclusions is a key feature of many neurodegenerative disorders. A common theme has emerged that inappropriate self-aggregation of misfolded or mutant polypeptide sequences is detrimental to cell health. Yet protein quality control mechanisms may also deliberately cluster them together into distinct inclusion subtypes, including the insoluble protein deposit (IPOD) and the juxtanuclear quality control (JUNQ). Here we investigated how the intrinsic oligomeric state of three model systems of disease-relevant mutant protein and peptide sequences relates to the IPOD and JUNQ patterns of aggregation using sedimentation velocity analysis. Two of the models (polyalanine (37A) and superoxide dismutase 1 (SOD1) mutants A4V and G85R) accumulated into the same JUNQ-like inclusion whereas the other, polyglutamine (72Q), formed spatially distinct IPOD-like inclusions. Using flow cytometry pulse shape analysis (PulSA) to separate cells with inclusions from those without revealed the SOD1 mutants and 37A to have abruptly altered oligomeric states with respect to the nonaggregating forms, regardless of whether cells had inclusions or not, whereas 72Q was almost exclusively monomeric until inclusions formed. We propose that mutations leading to JUNQ inclusions induce a constitutively "misfolded" state exposing hydrophobic side chains that attract and ultimately overextend protein quality capacity, which leads to aggregation into JUNQ inclusions. Poly(Q) is not misfolded in this same sense due to universal polar side chains, but is highly prone to forming amyloid fibrils that we propose invoke a different engagement mechanism with quality control.

Diel Metagenomics and Metatranscriptomics of Elkhorn Slough Hypersaline Microbial Mat

NASA Astrophysics Data System (ADS)

Lee, J.; Detweiler, A. M.; Everroad, R. C.; Bebout, L. E.; Weber, P. K.; Pett-Ridge, J.; Bebout, B.

2014-12-01

To understand the variation in gene expression associated with the daytime oxygenic phototrophic and nighttime fermentation regimes seen in hypersaline microbial mats, a contiguous mat piece was subjected to sampling at regular intervals over a 24-hour diel period. Additionally, to understand the impact of sulfate reduction on biohydrogen consumption, molybdate was added to a parallel experiment in the same run. 4 metagenome and 12 metatranscriptome Illumina HiSeq lanes were completed over day / night, and control / molybdate experiments. Preliminary comparative examination of noon and midnight metatranscriptomic samples mapped using bowtie2 to reference genomes has revealed several notable results about the dominant mat-building cyanobacterium Microcoleus chthonoplastes PCC 7420. Dominant cyanobacterium M. chthonoplastes PCC 7420 shows expression in several pathways for nitrogen scavenging, including nitrogen fixation. Reads mapped to M. chthonoplastes PCC 7420 shows expression of two starch storage and utilization pathways, one as a starch-trehalose-maltose-glucose pathway, another through UDP-glucose-cellulose-β-1,4 glucan-glucose pathway. The overall trend of gene expression was primarily light driven up-regulation followed by down-regulation in dark, while much of the remaining expression profile appears to be constitutive. Co-assembly of quality-controlled reads from 4 metagenomes was performed using Ray Meta with progressively smaller K-mer sizes, with bins identified and filtered using principal component analysis of coverages from all libraries and a %GC filter, followed by reassembly of the remaining co-assembly reads and binned reads. Despite having relatively similar abundance profiles in each metagenome, this binning approach was able to distinctly resolve bins from dominant taxa, but also sulfate reducing bacteria that are desired for understanding molybdate inhibition. Bins generated from this iterative assembly process will be used for downstream mapping of transcriptomic reads as well as isolation efforts for Cyanobacteria-associated bacteria.

Ready, Steady, Go! Program, Italy: a Program Impact Pathways (PIP) analysis.

PubMed

Veracini, Giordana; Leonardi, Elisabetta; Girotti, Rita; Thrasher, Erika Willumsen

2014-09-01

Ready, Steady, Go! promotes proper nutrition and physical activity among people of all ages in targeted neighborhoods and encourages social integration and children's participation in decisions that affect their lives. It also seeks to involve parents in activities so that they can influence their children's attitudes toward lifestyles and personal development. This partnership has reached 70,000 Italian children and adults with new opportunities for physical activities and social experiences that help them improve nutritional behaviors while having fun with their peers. To assess the Ready, Steady, Go! Program logic and to identify Critical Quality Control Points (CCPs) and a core suite of impact indicators based on a Program Impact Pathways (PIP) analysis. The PIP analysis team reviewed the key activities and processes that form Ready, Steady, Go! and then identified key CCPs for the project. The findings were presented at the Healthy Lifestyles Program Evaluation Workshop held in Granada, Spain, 13-14 September 2013, under the auspices of the Mondelēz International Foundation. The PIP analysis confirmed that Ready, Steady, Go! has a structure that is likely to support the primary aims of the program. The CCPs identified are training of teachers in healthy lifestyles, teachers' active participation in the program, access to remodeled and well-equipped sports and recreational centers, participation of parents and grandparents, and involvement of local institutions and networks. A suite of impact indicators for changes in healthy lifestyle knowledge, attitudes, and behavior was identified. Project staff are now more aware of the importance of carefully monitoring the CCPs and have decided to conduct quarterly PIP-informed quality control evaluations.

Regulation of mitochondrial biogenesis and its intersection with inflammatory responses.

PubMed

Cherry, Anne D; Piantadosi, Claude A

2015-04-20

Mitochondria play a vital role in cellular homeostasis and are susceptible to damage from inflammatory mediators released by the host defense. Cellular recovery depends, in part, on mitochondrial quality control programs, including mitochondrial biogenesis. Early-phase inflammatory mediator proteins interact with PRRs to activate NF-κB-, MAPK-, and PKB/Akt-dependent pathways, resulting in increased expression or activity of coactivators and transcription factors (e.g., PGC-1α, NRF-1, NRF-2, and Nfe2l2) that regulate mitochondrial biogenesis. Inflammatory upregulation of NOS2-induced NO causes mitochondrial dysfunction, but NO is also a signaling molecule upregulating mitochondrial biogenesis via PGC-1α, participating in Nfe2l2-mediated antioxidant gene expression and modulating inflammation. NO and reactive oxygen species generated by the host inflammatory response induce the redox-sensitive HO-1/CO system, causing simultaneous induction of mitochondrial biogenesis and antioxidant gene expression. Recent evidence suggests that mitochondrial biogenesis and mitophagy are coupled through redox pathways; for instance, parkin, which regulates mitophagy in chronic inflammation, may also modulate mitochondrial biogenesis and is upregulated through NF-κB. Further research on parkin in acute inflammation is ongoing. This highlights certain common features of the host response to acute and chronic inflammation, but caution is warranted in extrapolating findings across inflammatory conditions. Inflammatory mitochondrial dysfunction and oxidative stress initiate further inflammatory responses through DAMP/PRR interactions and by inflammasome activation, stimulating mitophagy. A deeper understanding of mitochondrial quality control programs' impact on intracellular inflammatory signaling will improve our approach to the restoration of mitochondrial homeostasis in the resolution of acute inflammation.

A user-friendly workflow for analysis of Illumina gene expression bead array data available at the arrayanalysis.org portal.

PubMed

Eijssen, Lars M T; Goelela, Varshna S; Kelder, Thomas; Adriaens, Michiel E; Evelo, Chris T; Radonjic, Marijana

2015-06-30

Illumina whole-genome expression bead arrays are a widely used platform for transcriptomics. Most of the tools available for the analysis of the resulting data are not easily applicable by less experienced users. ArrayAnalysis.org provides researchers with an easy-to-use and comprehensive interface to the functionality of R and Bioconductor packages for microarray data analysis. As a modular open source project, it allows developers to contribute modules that provide support for additional types of data or extend workflows. To enable data analysis of Illumina bead arrays for a broad user community, we have developed a module for ArrayAnalysis.org that provides a free and user-friendly web interface for quality control and pre-processing for these arrays. This module can be used together with existing modules for statistical and pathway analysis to provide a full workflow for Illumina gene expression data analysis. The module accepts data exported from Illumina's GenomeStudio, and provides the user with quality control plots and normalized data. The outputs are directly linked to the existing statistics module of ArrayAnalysis.org, but can also be downloaded for further downstream analysis in third-party tools. The Illumina bead arrays analysis module is available at http://www.arrayanalysis.org . A user guide, a tutorial demonstrating the analysis of an example dataset, and R scripts are available. The module can be used as a starting point for statistical evaluation and pathway analysis provided on the website or to generate processed input data for a broad range of applications in life sciences research.

Toxicogenomics: the challenges and opportunities to identify biomarkers, signatures and thresholds to support mode-of-action.

PubMed

Currie, Richard A

2012-08-15

Toxicogenomics (TGx) can be defined as the application of "omics" techniques to toxicology and risk assessment. By identifying molecular changes associated with toxicity, TGx data might assist hazard identification and investigate causes. Early technical challenges were evaluated and addressed by consortia (e.g. ISLI/HESI and the Microarray Quality Control consortium), which demonstrated that TGx gave reliable and reproducible information. The MAQC also produced "best practice on signature generation" after conducting an extensive evaluation of different methods on common datasets. Two findings of note were the need for methods that control batch variability, and that the predictive ability of a signature changes in concert with the variability of the endpoint. The key challenge remaining is data interpretation, because TGx can identify molecular changes that are causal, associated with or incidental to toxicity. Application of Bradford Hill's tests for causation, which are used to build mode of action (MOA) arguments, can produce reasonable hypotheses linking altered pathways to phenotypic changes. However, challenges in interpretation still remain: are all pathway changes equal, which are most important and plausibly linked to toxicity? Therefore the expert judgement of the toxicologist is still needed. There are theoretical reasons why consistent alterations across a metabolic pathway are important, but similar changes in signalling pathways may not alter information flow. At the molecular level thresholds may be due to the inherent properties of the regulatory network, for example switch-like behaviours from some network motifs (e.g. positive feedback) in the perturbed pathway leading to the toxicity. The application of systems biology methods to TGx data can generate hypotheses that explain why a threshold response exists. However, are we adequately trained to make these judgments? There is a need for collaborative efforts between regulators, industry and academia to properly define how these technologies can be applied using appropriate case-studies. Copyright © 2012 Elsevier B.V. All rights reserved.

Cell wall, cell membrane, and volatile metabolism are altered by antioxidant treatment, temperature shifts, and peel necrosis during apple fruit storage.

PubMed

Leisso, Rachel; Buchanan, David; Lee, Jinwook; Mattheis, James; Rudell, David

2013-02-13

The transition from cold storage to ambient temperature alters apple quality through accelerated softening, flavor and color changes, and development of physiological peel disorders, such as superficial scald, in susceptible cultivars. To reveal global metabolism associated with this transition, the 'Granny Smith' peel metabolome was evaluated during storage of 6 months and shelf life periods. Treatment with the antioxidant diphenylamine (DPA) reduced scald, creating a metabolic contrast with untreated fruit, which developed superficial scald. Superficial scald symptoms developed on control fruit after 120 days of storage, and symptoms progressed following transition to ambient-temperature shelf life. The metabolic profile of control and DPA-treated fruit was divergent after 30 days of cold storage due to differing levels of α-farnesene oxidation products, methyl esters, phytosterols, and other compounds potentially associated with chloroplast integrity and oxidative stress response. Hierarchical cluster analysis revealed coregulation within the volatile synthesis pathway including control of the availability of methyl, propyl, ethyl, acetyl, and butyl alcohol and/or acid moieties for ester biosynthesis. Overall, the application of metabolomics techniques lends new insight into physiological processes leading to cell death and ripening processes that affect fruit flavor, appearance, and overall quality.

Bromelain has significant clinical benefits after extraction of the third molar during chemotherapy in patients with hematologic tumor.

PubMed

Tan, Yi; Li, Ping

2018-03-01

The purpose of this study was to investigate the application of bromelain in the treatment of pain, swelling, and limited mouth opening in patients with hematologic tumor after extraction of the third molar during chemotherapy. We recruited 72 patients with hematologic tumor who were treated by oral and maxillofacial surgery in our hospital, and third molar extraction was performed under local anesthesia. After extraction, patients in the control group were treated with cold - hot compress and patients in the experimental group were treated by oral administration of bromelain. One, three, and seven days after extraction, pain, swelling, and mouth opening in the experimental group improved compared to the control group. Additionally, the levels of IL-25 and TNF-α in the experimental group were significantly lower than in the control group, suggesting less inflammatory response. On the other hand, EGFR and β-FGF were significantly higher in the experimental group, supporting the activation of tissue repair pathways. Quality of life scores were significantly better in the experimental group. Overall, bromelain improves the quality of life, alleviates pain, swelling, and mouth opening, and effectively prevent postoperative complications in patients with hematologic tumors after third molar extraction during chemotherapy.

Pathways Between Discrimination and Quality of Life in Patients with Type 2 Diabetes

PubMed Central

Achuko, Obinna; Walker, Rebekah J.; Campbell, Jennifer A.; Dawson, Aprill Z.

2016-01-01

Abstract Background: Discrimination is a social determinant that has been linked to poor physical and mental health outcomes. This study aimed to examine the pathway whereby discrimination influences quality of life in patients with type 2 diabetes. Subjects and Methods: Six hundred fifteen patients were recruited from two adult primary care clinics in the southeastern United States. Measures included perceived discrimination, perceived stress, social support, and social cohesion and were based on a theoretical model for the pathways by which perceived discrimination influences mental and physical health. Quality of life was measured using the SF-12 questionnaire. Results: The final model [χ2(106) = 157.35, P = 0.009, R2 = 0.99, root mean square error of approximation = 0.03, comparative fit index = 0.99] indicates direct effects of higher perceived stress (r = −1.02, P < 0.05) and lower social support (r = 0.36, P < 0.001) significantly related to decreased mental health component score (MCS) of quality of life. Discrimination and social cohesion were not significantly directly related to MCS. However, higher discrimination (r = 0.47, P < 0.001), higher social cohesion (r = 0.14, P < 0.05), and lower social support (r = −0.43, P < 0.001) were significantly directly related to increased stress. No significant paths were found for the physical component score of quality of life. Conclusions: Perceived discrimination was significantly associated with stress and served as a pathway to influence the mental health component of quality of life (MCS). Social support had a direct and an indirect effect on MCS through a negative association with stress. These results suggest that future interventions should be developed to decrease stress and increase social support surrounding discrimination to improve the MCS of quality of life in patients with diabetes. PMID:26866351

Pathways Between Discrimination and Quality of Life in Patients with Type 2 Diabetes.

PubMed

Achuko, Obinna; Walker, Rebekah J; Campbell, Jennifer A; Dawson, Aprill Z; Egede, Leonard E

2016-03-01

Discrimination is a social determinant that has been linked to poor physical and mental health outcomes. This study aimed to examine the pathway whereby discrimination influences quality of life in patients with type 2 diabetes. Six hundred fifteen patients were recruited from two adult primary care clinics in the southeastern United States. Measures included perceived discrimination, perceived stress, social support, and social cohesion and were based on a theoretical model for the pathways by which perceived discrimination influences mental and physical health. Quality of life was measured using the SF-12 questionnaire. The final model [χ(2)(106) = 157.35, P = 0.009, R(2) = 0.99, root mean square error of approximation = 0.03, comparative fit index = 0.99] indicates direct effects of higher perceived stress (r = -1.02, P < 0.05) and lower social support (r = 0.36, P < 0.001) significantly related to decreased mental health component score (MCS) of quality of life. Discrimination and social cohesion were not significantly directly related to MCS. However, higher discrimination (r = 0.47, P < 0.001), higher social cohesion (r = 0.14, P < 0.05), and lower social support (r = -0.43, P < 0.001) were significantly directly related to increased stress. No significant paths were found for the physical component score of quality of life. Perceived discrimination was significantly associated with stress and served as a pathway to influence the mental health component of quality of life (MCS). Social support had a direct and an indirect effect on MCS through a negative association with stress. These results suggest that future interventions should be developed to decrease stress and increase social support surrounding discrimination to improve the MCS of quality of life in patients with diabetes.

Transcriptomics Analysis on Excellent Meat Quality Traits of Skeletal Muscles of the Chinese Indigenous Min Pig Compared with the Large White Breed

PubMed Central

Liu, Yingzi; Yang, Xiuqin; Jing, Xiaoyan; He, Xinmiao; Wang, Liang; Liu, Yang; Liu, Di

2017-01-01

The Min pig (Sus scrofa) is a well-known indigenous breed in China. One of its main advantages over European breeds is its high meat quality. Additionally, different cuts of pig also show some different traits of meat quality. To explore the underlying mechanism responsible for the differences of meat quality between different breeds or cuts, the longissimus dorsi muscle (LM) and the biceps femoris muscle (BF) from Min and Large White pigs were investigated using transcriptome analysis. The gene expression profiling identified 1371 differentially expressed genes (DEGs) between LM muscles from Min and Large White pigs, and 114 DEGs between LM and BF muscles from the same Min pigs. Gene Ontology (GO) enrichment of biological functions and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that the gene products were mainly involved in the IRS1/Akt/FoxO1 signaling pathway, adenosine 5′-monophosphate-activated protein kinase (AMPK) cascade effects, lipid metabolism and amino acid metabolism pathway. Such pathways contributed to fatty acid metabolism, intramuscular fat deposition, and skeletal muscle growth in Min pig. These results give an insight into the mechanisms underlying the formation of skeletal muscle and provide candidate genes for improving meat quality. It will contribute to improving meat quality of pigs through molecular breeding. PMID:29271915

Critical review on non-operative management of adolescent idiopathic scoliosis.

PubMed

Wong, M S; Liu, W C

2003-12-01

There are a number of different non-operative interventions which aim to control moderate adolescent idiopathic scoliosis (AIS) from progression. Clinicians may find difficulties in the selection of appropriate interventions for AIS. A comprehensive literature review was carried out to study all contemporary non-operative interventions, it was noted that rigid spinal orthoses apparently give more curve control; however, it would compromise the patient's quality of life via those inevitable factors--physical constraint, poor acceptance and psychological disturbance. There is a trend to develop more effective, acceptable and user-friendly interventions. Under such an aspiration, the theories and clinical evidence of different interventions should be developed along the clinical pathway of early intervention with reliable indicators/predictors, patient's active participation, dynamic control mechanism, holistic psychological and psychosocial considerations, and effective and long-lasting outcome.

Analysis of alternative pathways for reducing nitrogen oxide emissions.

PubMed

Loughlin, Daniel H; Kaufman, Katherine R; Lenox, Carol S; Hubbell, Bryan J

2015-09-01

Strategies for reducing tropospheric ozone (O3) typically include modifying combustion processes to reduce the formation of nitrogen oxides (NOx) and applying control devices that remove NOx from the exhaust gases of power plants, industrial sources and vehicles. For portions of the U.S., these traditional controls may not be sufficient to achieve the National Ambient Air Quality Standard for ozone. We apply the MARKet ALlocation (MARKAL) energy system model in a sensitivity analysis to explore whether additional NOx reductions can be achieved through extensive electrification of passenger vehicles, adoption of energy efficiency and conservation measures within buildings, and deployment of wind and solar power in the electric sector. Nationally and for each region of the country, we estimate the NOx implications of these measures. Energy efficiency and renewable electricity are shown to reduce NOx beyond traditional controls. Wide-spread light duty vehicle electrification produces varied results, with NOx increasing in some regions and decreasing in others. However, combining vehicle electrification with renewable electricity reduces NOx in all regions. State governments are charged with developing plans that demonstrate how air quality standards will be met and maintained. The results presented here provide an indication of the national and regional NOx reductions available beyond traditional controls via extensive adoption of energy efficiency, renewable electricity, and vehicle electrification.

Clinical Pathways and the Patient Perspective in the Pursuit of Value-Based Oncology Care.

PubMed

Ersek, Jennifer L; Nadler, Eric; Freeman-Daily, Janet; Mazharuddin, Samir; Kim, Edward S

2017-01-01

The art of practicing oncology has evolved substantially in the past 5 years. As more and more diagnostic tests, biomarker-directed therapies, and immunotherapies make their way to the oncology marketplace, oncologists will find it increasingly difficult to keep up with the many therapeutic options. Additionally, the cost of cancer care seems to be increasing. Clinical pathways are a systematic way to organize and display detailed, evidence-based treatment options and assist the practitioner with best practice. When selecting which treatment regimens to include on a clinical pathway, considerations must include the efficacy and safety, as well as costs, of the therapy. Pathway treatment regimens must be continually assessed and modified to ensure that the most up-to-date, high-quality options are incorporated. Value-based models, such as the ASCO Value Framework, can assist providers in presenting economic evaluations of clinical pathway treatment options to patients, thus allowing the patient to decide the overall value of each treatment regimen. Although oncologists and pathway developers can decide which treatment regimens to include on a clinical pathway based on the efficacy of the treatment, assessment of the value of that treatment regimen ultimately lies with the patient. Patient definitions of value will be an important component to enhancing current value-based oncology care models and incorporating new, high-quality, value-based therapeutics into oncology clinical pathways.

Evaluating the Quality of Colorectal Cancer Care across the Interface of Healthcare Sectors

PubMed Central

Ludt, Sabine; Urban, Elisabeth; Eckardt, Jörg; Wache, Stefanie; Broge, Björn; Kaufmann-Kolle, Petra; Heller, Günther; Miksch, Antje; Glassen, Katharina; Hermann, Katja; Bölter, Regine; Ose, Dominik; Campbell, Stephen M.; Wensing, Michel; Szecsenyi, Joachim

2013-01-01

Background Colorectal cancer (CRC) has a high prevalence in western countries. Diagnosis and treatment of CRC is complex and requires multidisciplinary collaboration across the interface of health care sectors. In Germany, a new nationwide established program aims to provide quality information of healthcare delivery across different sectors. Within this context, this study describes the development of a set of quality indicators charting the whole pathway of CRC-care including data specifications that are necessary to operationalize these indicators before practice testing. Methods Indicators were developed following a systematic 10 step modified ‘RAND/UCLA Appropriateness Method’ which involved a multidisciplinary panel of thirteen participants. For each indicator in the final set, data specifications relating to sources of quality information, data collection procedures, analysis and feedback were described. Results The final indicator set included 52 indicators covering diagnostic procedures (11 indicators), therapeutic management (28 indicators) and follow-up (6 indicators). In addition, 7 indicators represented patient perspectives. Primary surgical tumor resection and pre-operative radiation (rectum carcinoma only) were perceived as most useful tracer procedures initiating quality data collection. To assess the quality of CRC care across sectors, various data sources were identified: medical records, administrative inpatient and outpatient data, sickness-funds billing code systems and patient survey. Conclusion In Germany, a set of 52 quality indicators, covering necessary aspects across the interfaces and pathways relevant to CRC-care has been developed. Combining different sectors and sources of health care in quality assessment is an innovative and challenging approach but reflects better the reality of the patient pathway and experience of CRC-care. PMID:23658684

Exposure to bisphenol A (BPA) in Wistar rats reduces sperm quality with disruption of ERK signal pathway.

PubMed

Li, Juan; Mao, Rui; Zhou, Qin; Ding, Ling; Tao, Jin; Ran, Mao-Mei; Gao, Er-Sheng; Yuan, Wei; Wang, Jin-Tao; Hou, Li-Fang

2016-01-01

Bisphenol A (BPA) is an estrogenic environmental toxin widely used in the production of plastics and ubiquitous human exposure to this chemical has been proposed to be a potential risk to human health. Exposure to BPA can negatively impact sperm quality. However, the mechanism remains largely unknown. The objectives of this study were to assess the role of BPA on sperm quality and explore the possible mechanisms. The Wistar male rats (aged 28 days) were administered BPA by oral gavage for 28 days at dose of 50, 100 and 200 mg/kg/day; meanwhile, the negative control with corn oil (0 mg/kg/day BPA) and positive control with E2 at the dose of 100 μg/kg/day. The sperm density, sperm activity and sperm survival rate were analyzed byCASA system, and the sperm abnormality rate was analyzed by improved Papanicolaou stained. The protein expression levels of Src/p-Src, ERK1/2, p-ERK1/2 and CREB/p-CREB were detected by Western bolt. The results showed that the body weight gain, testes weight, testis coefficient, sperm density, sperm activity, sperm survival rate and protein expression levels of p-ERK1, p-ERK2 and p-CREB decreased, but the sperm abnormality rate increased with increasing BPA concentrations. There were positive correlations between sperm density, sperm activity and sperm survival rate with protein expression levels of p-ERK1, p-ERK2 and p-CREB, and negative correlations between sperm abnormality rate with the protein expression levels of p-ERK1, p-ERK2 and p-CREB. Results from the structural equation model demonstrated that BPA retained a significant negative effect to p-ERK, whereas p-ERK retained a significant positive effect to sperm quality and acted as the mediate variable. This study provides a novel insight regarding the potential role of p-ERK1 and p-ERK2 protein kinase on reproductive toxicity of BPA. The adverse effects of BPA on adult male sperm quality may be through the induction of the disruption of ERK signal pathway. However, additional research is needed to confirm our findings and to further test the suggested potential mechanisms.

Care pathways for organ donation after brain death: guidance from available literature?

PubMed

Hoste, Pieter; Vanhaecht, Kris; Ferdinande, Patrick; Rogiers, Xavier; Eeckloo, Kristof; Blot, Stijn; Hoste, Eric; Vogelaers, Dirk; Vandewoude, Koenraad

2016-10-01

A discussion of the literature concerning the impact of care pathways in the complex and by definition multidisciplinary process of organ donation following brain death. Enhancing the quality and safety of organs for transplantation has become a central concern for governmental and professional organizations. At the local hospital level, a donor coordinator can use a range of interventions to improve the donation and procurement process. Care pathways have been proven to represent an effective intervention in several settings for optimizing processes and outcomes. A discussion paper. A systematic review of the Medline, CINAHL, EMBASE and The Cochrane Library databases was conducted for articles published until June 2015, using the keywords donation after brain death and care pathways. Each paper was reviewed to investigate the effects of existing care pathways for donation after brain death. An additional search for unpublished information was conducted. Although literature supports care pathways as an effective intervention in several settings, few studies have explored its use and effectiveness for complex care processes such as donation after brain death. Nurses should be aware of their role in the donation process. Care pathways have the potential to support them, but their effectiveness has been insufficiently explored. Further research should focus on the development and standardization of the clinical content of a care pathway for donation after brain death and the identification of quality indicators. These should be used in a prospective effectiveness assessment of the proposed pathway. © 2016 John Wiley & Sons Ltd.

Impact of Care Pathway-Based Approach on Outcomes in a Specialist Intellectual Disability Inpatient Unit

ERIC Educational Resources Information Center

Devapriam, John; Alexander, Regi; Gumber, Rohit; Pither, Judith; Gangadharan, Satheesh

2014-01-01

Specialist intellectual disability inpatient units have come under increased scrutiny, leading to questions about the quality of service provision in this sector. A care pathway-based approach was implemented in such a unit and its impact on outcome variables was measured. The care pathway-based approach resulted in the turnover of more patients,…

Leading High School Transformation for College and Career Success: A Guide for Developing a System of Linked Learning Pathways

ERIC Educational Resources Information Center

Stearns, Roman

2014-01-01

This ConnectEd Guide for Developing a System of Linked Learning Pathways will introduce school district leaders and their community partners to Linked Learning and a system of quality pathways that can transform high schools, instructional practice, and the student experience. Not intended to be prescriptive, this document can and should be…

A proposed clinical research support career pathway for noninvestigators.

PubMed

Smith, Sheree; Gullick, Janice; Ballard, Jacqueline; Perry, Lin

2018-06-01

To discuss the international experience of clinical research support for noninvestigator roles and to propose a new pathway for Australia, to promote a sustainable research support workforce capable of delivering high-quality clinical research. Noninvestigator research support roles are currently characterized by an ad hoc approach to training, with limited role delineation and perceived professional isolation with implications for study completion rates and participant safety. A focused approach to developing and implementing research support pathways has improved patient recruitment, study completion, job satisfaction, and research governance. The Queensland and New South Wales state-based Nurses' Awards, the Australian Qualifications Framework, and a University Professional (Research) Staff Award. Research nurses in the clinical environment improve study coordination, adherence to study protocol, patient safety, and clinical care. A career pathway that guides education and outlines position descriptions and skill sets would enhance development of the research support workforce. This pathway could contribute to changing the patient outcomes through coordination and study completion of high-quality research. A wide consultative approach is required to determine a cost-effective and feasible approach to implementation and evaluation of the proposed pathway. © 2018 John Wiley & Sons Australia, Ltd.

Implementation of a Nurse Driven Pathway to Reduce Incidence of Hospital Acquired Pressure Injuries in the Pediatric Intensive Care Setting.

PubMed

Rowe, Angela D; McCarty, Karen; Huett, Amy

2018-03-13

A large, freestanding pediatric hospital in the southern United States saw a 117% increase in reported hospital acquired pressure injuries (HAPI) between 2013 and 2015, with the intensive care units being the units of highest occurrence. Design and Methods A quality improvement project was designed and implemented to assist with pressure injury prevention. Literature review confirmed that pediatric HAPIs are a challenge and that usage of bundles and user-friendly guidelines/pathways can help eliminate barriers to prevention. The aim of this quality improvement project had two aims. First, to reduce HAPI incidence in the PICU by 10%. Second, to increase consistent usage of pressure injury prevention strategies as evidenced by a 10% increase in pressure injury bundle compliance. The third aim was to identify if there are differences in percentage of interventions implemented between two different groups of patients. Donabedian's model of Structure, Process, and Outcomes guided the development and implementation of this quality improvement project. Interventions focused on risk assessment subscale scores have the opportunity to mitigate specific risk factors and improve pressure injury prevention. Through implementation of the nurse driven pathway there was as 57% decrease in reported HAPIs in the PICU as well as a 66% increase in pressure ulcer prevention bundle compliance. Implementation of the nurse driven pressure injury prevention pathway was successful. There was a significant increase in bundle compliance for pressure ulcer prevention and a decrease in reported HAPIs. The pathway developed and implemented for this quality improvement project could be adapted to other populations and care settings to provide guidance across the continuum. Copyright © 2018 Elsevier Inc. All rights reserved.

Maternal buffering beyond glucocorticoids: impact of early life stress on corticolimbic circuits that control infant responses to novelty

PubMed Central

Howell, Brittany R.; McMurray, Matthew S.; Guzman, Dora B.; Nair, Govind; Shi, Yundi; McCormack, Kai M.; Hu, Xiaoping; Styner, Martin A.; Sanchez, Mar M.

2017-01-01

Maternal presence has a potent buffering effect on infant fear and stress responses in primates. We previously reported that maternal presence is not effective in buffering the endocrine stress response in infant rhesus monkeys reared by maltreating mothers. We have also reported that maltreating mothers show low maternal responsiveness and permissiveness/secure-base behavior. Although still not understood, it is possible that this maternal buffering effect is mediated, at least partially, through deactivation of amygdala response circuits when mothers are present. Here we studied rhesus monkey infants that differed in the quality of early maternal care to investigate how this early experience modulated maternal buffering effects on behavioral responses to novelty during the weaning period. We also examined the relationship between these behavioral responses and structural connectivity in one of the underlying regulatory neural circuits: amygdala-prefrontal pathways. Our findings suggest that infant exploration in a novel situation is predicted by maternal responsiveness and structural integrity of amygdala-prefrontal white matter depending on maternal presence (positive relationships when mother is absent). These results provide evidence that maternal buffering of infant behavioral inhibition is dependent on the quality of maternal care and structural connectivity of neural pathways that are sensitive to early life stress. PMID:27295326

Best practice in the management of clinical coding services: Insights from a project in the Republic of Ireland, Part 2.

PubMed

Reid, Beth A; Ridoutt, Lee; O'Connor, Paul; Murphy, Deirdre

2017-09-01

This is the second of two articles about best practice in the management of coding services. The best practice project was part of a year-long project conducted in the Republic of Ireland to review the quality of the Hospital Inpatient Enquiry data for its use in activity-based funding. The four methods used to address the best practice aspect of the project were described in detail in Part 1. The results included in this article are those relating to the coding manager's background, preparation and style, clinical coder (CC) workforce adequacy, the CC workforce structure and career pathway, and the physical and psychological work environment for the clinical coding service. Examples of best practice were found in the study hospitals but there were also areas for improvement. Coding managers would benefit from greater support in the form of increased opportunities for management training and a better method for calculating CC workforce numbers. A career pathway is needed for CCs to progress from entry to expert CC, mentor, manager and quality controller. Most hospitals could benefit from investment in infrastructure that places CCs in a physical environment that tells them they are an important part of the hospital and their work is valued.

The water quality of the LOCAR Pang and Lambourn catchments

NASA Astrophysics Data System (ADS)

Neal, C.; Jarvie, H. P.; Wade, A. J.; Neal, M.; Wyatt, R.; Wickham, H.; Hill, L.; Hewitt, N.

The water quality of the Pang and Lambourn, tributaries of the River Thames, in south-eastern England, is described in relation to spatial and temporal dimensions. The river waters are supplied mainly from Chalk-fed aquifer sources and are, therefore, of a calcium-bicarbonate type. The major, minor and trace element chemistry of the rivers is controlled by a combination of atmospheric and pollutant inputs from agriculture and sewage sources superimposed on a background water quality signal linked to geological sources. Water quality does not vary greatly over time or space. However, in detail, there are differences in water quality between the Pang and Lambourn and between sites along the Pang and the Lambourn. These differences reflect hydrological processes, water flow pathways and water quality input fluxes. The Pang’s pattern of water quality change is more variable than that of the Lambourn. The flow hydrograph also shows both a cyclical and "uniform pattern" characteristic of aquifer drainage with, superimposed, a series of "flashier" spiked responses characteristic of karstic systems. The Lambourn, in contrast, shows simpler features without the "flashier" responses. The results are discussed in relation to the newly developed UK community programme LOCAR dealing with Lowland Catchment Research. A descriptive and box model structure is provided to describe the key features of water quality variations in relation to soil, unsaturated and groundwater flows and storage both away from and close to the river.

[Education for patients with fibromyalgia. A systematic review of randomised clinical trials].

PubMed

Elizagaray-Garcia, Ignacio; Muriente-Gonzalez, Jorge; Gil-Martinez, Alfonso

2016-01-16

To analyse the effectiveness of education about pain, quality of life and functionality in patients with fibromyalgia. The search for articles was carried out in electronic databases. Eligibility criteria were: controlled randomised clinical trials (RCT), published in English and Spanish, that had been conducted on patients with fibromyalgia, in which the therapeutic procedure was based on patient education. Two independent reviewers analysed the methodological quality using the PEDro scale. Five RCT were selected, of which four offered good methodological quality. In three of the studies, patient education, in combination with another intervention based on therapeutic exercise, improved the outcomes in the variables assessing pain and quality of life as compared with the same procedures performed separately. Moreover, an RCT with a high quality methodology showed that patient education activated inhibitory neural pathways capable of lowering the level of pain. The quantitative analysis yields strong-moderate evidence that patient education, in combination with other therapeutic exercise procedures, offers positive results in the variables pain, quality of life and functionality. Patient education in itself has not proved to be effective for pain, quality of life or functionality in patients with fibromyalgia. There is strong evidence, however, of the effectiveness of combining patient education with exercise and active strategies for coping with pain, quality of life and functionality in the short, medium and long term in patients with fibromyalgia.

Computer animation in teaching science: Effectiveness in teaching retrograde motion to 9th graders

NASA Astrophysics Data System (ADS)

Klenk, Kristin Elmstrom

The purpose of this study is to determine whether an instructional approach which includes computer animations is more effective than a traditional textbook-only approach in helping ninth grade students learn an abstract concept, in this case planetary retrograde motion. This investigation uses a quasi-experimental design with convenient sampling. The independent variable is the type of instruction provided to students; traditional text-based instruction (control group) compared to traditional instruction which also includes the viewing of 4 computer animations (treatment). Two conditions of the treatment examine the relative advantage of the order of the presentation of the animations and text-based instruction, as well as the quality of understanding and the retention of the learning over time. The dependent variable is student achievement which is measured using an instrument designed specifically for this study. Comparison of the independent variable to the dependent variable based upon the results from a Repeated Measure Factorial Design in ANOVA indicates that the treatment is an effective instructional technique. The posttest1 mean score of the treatment groups was significantly greater than the posttest1 mean score of the control group. Further posthoc tests indicate that there was no significant difference between the two treatments (1 and 2); read/animation versus animation/read. However, there was a significant difference in the mean score depending on the pathway, students enrolled in the A pathway achieved a significantly higher mean score after the treatment than students in the B pathway. The A pathway (n = 185) represent the larger heterogeneous population of students as compared to the B pathway (n=16) which includes students with lower cognitive abilities and special needs. When all of the students are included in the analysis the results indicate that students do not retain their understanding of the concept. However, when the students in the B pathway are removed from the data set the analysis changes, the posttest1 and posttest2 means are not significantly different. Students in the A pathway did retain their understanding of the concept and were able to demonstrate it on the assessment. A detailed item analysis of the multiple choice question suggest that students in the B pathway were much more likely to guess on the multiple choice questions than students in the A pathway who show no evidence of guessing. The outcome of this study suggests that an instructional approach with includes viewing computer animations is an effective strategy for teaching and learning an abstract concept in a ninth grade Earth Science classroom.

Topological analysis of metabolic control.

PubMed

Sen, A K

1990-12-01

A topological approach is presented for the analysis of control and regulation in metabolic pathways. In this approach, the control structure of a metabolic pathway is represented by a weighted directed graph. From an inspection of the topology of the graph, the control coefficients of the enzymes are evaluated in a heuristic manner in terms of the enzyme elasticities. The major advantage of the topological approach is that it provides a visual framework for (1) calculating the control coefficients of the enzymes, (2) analyzing the cause-effect relationships of the individual enzymes, (3) assessing the relative importance of the enzymes in metabolic regulation, and (4) simplifying the structure of a given pathway, from a regulatory viewpoint. Results are obtained for (a) an unbranched pathway in the absence of feedback the feedforward regulation and (b) an unbranched pathway with feedback inhibition. Our formulation is based on the metabolic control theory of Kacser and Burns (1973) and Heinrich and Rapoport (1974).

Network inference reveals novel connections in pathways regulating growth and defense in the yeast salt response.

PubMed

MacGilvray, Matthew E; Shishkova, Evgenia; Chasman, Deborah; Place, Michael; Gitter, Anthony; Coon, Joshua J; Gasch, Audrey P

2018-05-01

Cells respond to stressful conditions by coordinating a complex, multi-faceted response that spans many levels of physiology. Much of the response is coordinated by changes in protein phosphorylation. Although the regulators of transcriptome changes during stress are well characterized in Saccharomyces cerevisiae, the upstream regulatory network controlling protein phosphorylation is less well dissected. Here, we developed a computational approach to infer the signaling network that regulates phosphorylation changes in response to salt stress. We developed an approach to link predicted regulators to groups of likely co-regulated phospho-peptides responding to stress, thereby creating new edges in a background protein interaction network. We then use integer linear programming (ILP) to integrate wild type and mutant phospho-proteomic data and predict the network controlling stress-activated phospho-proteomic changes. The network we inferred predicted new regulatory connections between stress-activated and growth-regulating pathways and suggested mechanisms coordinating metabolism, cell-cycle progression, and growth during stress. We confirmed several network predictions with co-immunoprecipitations coupled with mass-spectrometry protein identification and mutant phospho-proteomic analysis. Results show that the cAMP-phosphodiesterase Pde2 physically interacts with many stress-regulated transcription factors targeted by PKA, and that reduced phosphorylation of those factors during stress requires the Rck2 kinase that we show physically interacts with Pde2. Together, our work shows how a high-quality computational network model can facilitate discovery of new pathway interactions during osmotic stress.

Genetic Analyses of Interferon Pathway-Related Genes Reveals Multiple New Loci Associated with Systemic Lupus Erythematosus (SLE)

PubMed Central

Ramos, Paula S.; Williams, Adrienne H.; Ziegler, Julie T.; Comeau, Mary E.; Guy, Richard T.; Lessard, Christopher J.; Li, He; Edberg, Jeffrey C.; Zidovetzki, Raphael; Criswell, Lindsey A.; Gaffney, Patrick M.; Graham, Deborah Cunninghame; Graham, Robert R.; Kelly, Jennifer A.; Kaufman, Kenneth M.; Brown, Elizabeth E.; Alarcón, Graciela S.; Petri, Michelle A.; Reveille, John D.; McGwin, Gerald; Vilá, Luis M.; Ramsey-Goldman, Rosalind; Jacob, Chaim O.; Vyse, Timothy J.; Tsao, Betty P.; Harley, John B.; Kimberly, Robert P.; Alarcón-Riquelme, Marta E.; Langefeld, Carl D.; Moser, Kathy L.

2011-01-01

Objective The overexpression of interferon (IFN)-inducible genes is a prominent feature of SLE, serves as a marker for active and more severe disease, and is also observed in other autoimmune and inflammatory conditions. The genetic variations responsible for sustained activation of IFN responsive genes are unknown. Methods We systematically evaluated association of SLE with a total of 1,754 IFN-pathway related genes, including IFN-inducible genes known to be differentially expressed in SLE patients and their direct regulators. We performed a three-stage design where two cohorts (total n=939 SLE cases, 3,398 controls) were analyzed independently and jointly for association with SLE, and the results were adjusted for the number of comparisons. Results A total of 16,137 SNPs passed all quality control filters of which 316 demonstrated replicated association with SLE in both cohorts. Nine variants were further genotyped for confirmation in an average of 1,316 independent SLE cases and 3,215 independent controls. Association with SLE was confirmed for several genes, including the transmembrane receptor CD44 (rs507230, P = 3.98×10−12), cytokine pleiotrophin (PTN) (rs919581, P = 5.38×10−04), the heat-shock DNAJA1 (rs10971259, P = 6.31×10−03), and the nuclear import protein karyopherin alpha 1 (KPNA1) (rs6810306, P = 4.91×10−02). Conclusion This study expands the number of candidate genes associated with SLE and highlights the potential of pathway-based approaches for gene discovery. Identification of the causal alleles will help elucidate the molecular mechanisms responsible for activation of the IFN system in SLE. PMID:21437871

Process and product development in the manufacturing of molecular therapeutics.

PubMed

Atkinson, E M; Christensen, J R

1999-08-01

In the development of molecular therapies, a great deal of attention has focused on tissue targets, gene delivery vectors, and expression cassettes. In order to become an approved therapy, however, a molecular therapeutic has to pass down the same product registration pathway as any other biological product. Moving from research into industrial production requires careful attention to regulatory, manufacturing and quality concerns. Early work on developing and characterizing robust and scaleable manufacturing processes will ultimately be rewarded by ease of implementation as the product is successful in clinical trials. Regulatory agencies require solid process and product characterization studies to demonstrate control and understanding of the molecular therapeutic. As the gene therapy industry matures, standards will continue to rise, creating an industry that is capable of producing safe, high-quality and effective therapies for many of the world's most difficult disease targets.

Protein degradation and dynamic tRNA thiolation fine-tune translation at elevated temperatures.

PubMed

Tyagi, Kshitiz; Pedrioli, Patrick G A

2015-05-19

Maintenance of protein quality control has implications in various processes such as neurodegeneration and ageing. To investigate how environmental insults affect this process, we analysed the proteome of yeast continuously exposed to mild heat stress. In agreement with previous transcriptomics studies, amongst the most marked changes, we found up-regulation of cytoprotective factors; a shift from oxidative phosphorylation to fermentation; and down-regulation of translation. Importantly, we also identified a novel, post-translationally controlled, component of the heat shock response. The abundance of Ncs2p and Ncs6p, two members of the URM1 pathway responsible for the thiolation of wobble uridines in cytoplasmic tRNAs tK(UUU), tQ(UUG) and tE(UUC), is down-regulated in a proteasomal dependent fashion. Using random forests we show that this results in differential translation of transcripts with a biased content for the corresponding codons. We propose that the role of this pathway in promoting catabolic and inhibiting anabolic processes, affords cells with additional time and resources needed to attain proper protein folding under periods of stress. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

Pathways to Healing: Person-centered Responses to Complementary Services

PubMed Central

Bertrand, Sharon W.; Fermon, Barbara; Coleman, Julie Foley

2014-01-01

Objectives: This research study assessed perceived changes in quality-of-life measures related to participation in complementary services consisting of a variety of nontraditional therapies and/or programs at Pathways: A Health Crisis Resource Center in Minneapolis, Minnesota. Design: Survey data were used to assess perceived changes participants ascribed to their experience with complementary services at Pathways. Quantitative data analysis was conducted using participant demographics together with participant ratings of items from the “Self-Assessment of Change” (SAC) measure developed at the University of Arizona, Tucson. Qualitative data analysis was conducted on written responses to an additional survey question: “To what extent has your participation at Pathways influenced your healing process?” Setting/Location: Pathways offers a variety of services, including one-to-one sessions using nontraditional healing therapies, support groups, educational classes, and practice groups such as yoga and meditation for those facing serious health challenges. These services are offered free of charge through community financial support using volunteer practitioners. Participants: People (126) diagnosed with serious health challenges who used Pathways services from 2007 through 2009. Interventions: Participation in self-selected Pathways services. Measures: Responses to items on the SAC measure plus written responses to the question, “To what extent has your participation at Pathways influenced your healing process?” Results: Quantitative findings: Participants reported experiencing significant changes across all components of the SAC measure. Qualitative findings: Responses to the open-ended survey question identified perspectives on the culture of Pathways and a shift in participants' perceptions of well-being based on their experience of Pathways services. Conclusions: Participation in services provided by the Pathways organization improved perceptions of quality of life and well-being and led to more active involvement in the experience of a healing process. PMID:24753990

Comparative Transcriptome Analysis of Cultivated and Wild Watermelon during Fruit Development

PubMed Central

Guo, Shaogui; Sun, Honghe; Zhang, Haiying; Liu, Jingan; Ren, Yi; Gong, Guoyi; Jiao, Chen; Zheng, Yi; Yang, Wencai; Fei, Zhangjun; Xu, Yong

2015-01-01

Watermelon [Citrullus lanatus (Thunb.) Matsum. & Nakai] is an important vegetable crop world-wide. Watermelon fruit quality is a complex trait determined by various factors such as sugar content, flesh color and flesh texture. Fruit quality and developmental process of cultivated and wild watermelon are highly different. To systematically understand the molecular basis of these differences, we compared transcriptome profiles of fruit tissues of cultivated watermelon 97103 and wild watermelon PI296341-FR. We identified 2,452, 826 and 322 differentially expressed genes in cultivated flesh, cultivated mesocarp and wild flesh, respectively, during fruit development. Gene ontology enrichment analysis of these genes indicated that biological processes and metabolic pathways related to fruit quality such as sweetness and flavor were significantly changed only in the flesh of 97103 during fruit development, while those related to abiotic stress response were changed mainly in the flesh of PI296341-FR. Our comparative transcriptome profiling analysis identified critical genes potentially involved in controlling fruit quality traits including α-galactosidase, invertase, UDP-galactose/glucose pyrophosphorylase and sugar transporter genes involved in the determination of fruit sugar content, phytoene synthase, β-carotene hydroxylase, 9-cis-epoxycarotenoid dioxygenase and carotenoid cleavage dioxygenase genes involved in carotenoid metabolism, and 4-coumarate:coenzyme A ligase, cellulose synthase, pectinesterase, pectinesterase inhibitor, polygalacturonase inhibitor and α-mannosidase genes involved in the regulation of flesh texture. In addition, we found that genes in the ethylene biosynthesis and signaling pathway including ACC oxidase, ethylene receptor and ethylene responsive factor showed highly ripening-associated expression patterns, indicating a possible role of ethylene in fruit development and ripening of watermelon, a non-climacteric fruit. Our analysis provides novel insights into watermelon fruit quality and ripening biology. Furthermore, the comparative expression profile data we developed provides a valuable resource to accelerate functional studies in watermelon and facilitate watermelon crop improvement. PMID:26079257

Energy balance and obesity: what are the main drivers?

PubMed

Romieu, Isabelle; Dossus, Laure; Barquera, Simón; Blottière, Hervé M; Franks, Paul W; Gunter, Marc; Hwalla, Nahla; Hursting, Stephen D; Leitzmann, Michael; Margetts, Barrie; Nishida, Chizuru; Potischman, Nancy; Seidell, Jacob; Stepien, Magdalena; Wang, Youfa; Westerterp, Klaas; Winichagoon, Pattanee; Wiseman, Martin; Willett, Walter C

2017-03-01

The aim of this paper is to review the evidence of the association between energy balance and obesity. In December 2015, the International Agency for Research on Cancer (IARC), Lyon, France convened a Working Group of international experts to review the evidence regarding energy balance and obesity, with a focus on Low and Middle Income Countries (LMIC). The global epidemic of obesity and the double burden, in LMICs, of malnutrition (coexistence of undernutrition and overnutrition) are both related to poor quality diet and unbalanced energy intake. Dietary patterns consistent with a traditional Mediterranean diet and other measures of diet quality can contribute to long-term weight control. Limiting consumption of sugar-sweetened beverages has a particularly important role in weight control. Genetic factors alone cannot explain the global epidemic of obesity. However, genetic, epigenetic factors and the microbiota could influence individual responses to diet and physical activity. Energy intake that exceeds energy expenditure is the main driver of weight gain. The quality of the diet may exert its effect on energy balance through complex hormonal and neurological pathways that influence satiety and possibly through other mechanisms. The food environment, marketing of unhealthy foods and urbanization, and reduction in sedentary behaviors and physical activity play important roles. Most of the evidence comes from High Income Countries and more research is needed in LMICs.

Regulators of Mitochondrial Quality Control Differs in Subcutaneous Fat of Metabolically Healthy and Unhealthy Obese Monkeys

PubMed Central

Kavanagh, Kylie; Davis, Ashley T; Peters, Diane E; Le Grand, Andre; Bharadwaj, Manish S; Molina, Anthony JA

2016-01-01

Objectives Obesity exists with and without accompanying cardiometabolic disease, termed metabolically unhealthy obesity (MUO) and healthy obesity respectively (MHO). Underlying differences in the ability of subcutaneous (SQ) fat to respond to nutrient excess is emerging as a key pathway. We aimed to document the first spontaneous animal model of MHO and MUO and differences in SQ adipose tissue. Methods Vervet monkeys (Chlorocebus aethiops; n=171) were screened for Metabolic Syndrome. A subset of MHO and MUO monkeys (n=6/group) had SQ fat biopsies collected for histologic evaluations and examination of key mitochondrial proteins. Results Obesity was seen in 20% of monkeys, and within this population, 31% were healthy which mirrors human prevalence estimates. MUO monkeys had more than 60% lower adiponectin concentrations despite similar fat cell size, uncoupling protein 3, and activated macrophage abundance. However, alternatively activated/anti-inflammatory macrophages were 70% lower. Deficiencies of 50% or more in mitochondrial quality control regulators, and selected mitochondrial fission and fusion markers were observed in the SQ fat of MUO monkeys despite comparable mitochondrial content. Conclusions We characterized a novel and translatable spontaneously obese animal model of healthy and unhealthy obesity, occurring independently of dietary factors. Differences in mitochondrial quality and inflammatory cell populations of subcutaneous fat may underpin divergent metabolic health. PMID:28236433

Regulators of mitochondrial quality control differ in subcutaneous fat of metabolically healthy and unhealthy obese monkeys.

PubMed

Kavanagh, Kylie; Davis, Ashley T; Peters, Diane E; LeGrand, Andre C; Bharadwaj, Manish S; Molina, Anthony J A

2017-04-01

Obesity exists with and without accompanying cardiometabolic disease, termed metabolically unhealthy obesity (MUO) and healthy obesity (MHO), respectively. Underlying differences in the ability of subcutaneous (SQ) fat to respond to nutrient excess are emerging as a key pathway. This study aimed to document the first spontaneous animal model of MHO and MUO and differences in SQ adipose tissue. Vervet monkeys (Chlorocebus aethiops; N = 171) were screened for metabolic syndrome. A subset of MHO and MUO monkeys (n = 6/group) had SQ fat biopsies collected for histological evaluations and examination of key mitochondrial proteins. Obesity was seen in 20% of monkeys, and within this population, 31% were healthy, which mirrors human prevalence estimates. MUO monkeys had more than 60% lower adiponectin concentrations despite similar fat cell size, uncoupling protein 3, and activated macrophage abundance. However, alternatively activated/anti-inflammatory macrophages were 70% lower. Deficiencies of 50% or more in mitochondrial quality control regulators and selected mitochondrial fission and fusion markers were observed in the SQ fat of MUO monkeys despite comparable mitochondrial content. A novel and translatable spontaneously obese animal model of MHO and MUO, occurring independently of dietary factors, was characterized. Differences in mitochondrial quality and inflammatory cell populations of subcutaneous fat may underpin divergent metabolic health. © 2017 The Obesity Society.

2% Crisaborole topical ointment for the treatment of mild-to-moderate atopic dermatitis.

PubMed

Cheape, Alice C; Murrell, Dedee F

2017-05-01

Crisaborole 2% topical ointment is an anti-inflammatory, non-steroidal phosphodiesterase 4 inhibitor which is currently under investigation for its potential role in the treatment of atopic dermatitis and psoriasis. Areas covered: So far, 7 trials have been completed in atopic dermatitis. The 2% strength appeared to be the superior dosing regimen. Pruritus improved significantly within one week. The improvements in objective efficacy assessments in crisaborole-treated patients were also statistically significant compared to the vehicle. Expert commentary: Crisaborole has several key features in its mode of action which distinguish it from existing treatments for atopic dermatitis (AD), notably its activity against the phosphodiesterase E4 (PDE4) pathway, regulating cyclic AMP (cAMP) levels. This is less immunosuppressive than other pathways and has no effect on skin thinning. The pathway interrupts the itch sensation (pruritus) which means that the itch-scratch cycle, the bane in the life of patients with AD, is interrupted, usually as early as a few days into treatment. Hence, with the promising safety profile demonstrated, early treatment of mild to moderate AD patients might help to control AD better and improve quality of life for patients.

Engineering of protein folding and secretion-strategies to overcome bottlenecks for efficient production of recombinant proteins.

PubMed

Delic, Marizela; Göngrich, Rebecca; Mattanovich, Diethard; Gasser, Brigitte

2014-07-20

Recombinant protein production has developed into a huge market with enormous positive implications for human health and for the future direction of a biobased economy. Limitations in the economic and technical feasibility of production processes are often related to bottlenecks of in vivo protein folding. Based on cell biological knowledge, some major bottlenecks have been overcome by the overexpression of molecular chaperones and other folding related proteins, or by the deletion of deleterious pathways that may lead to misfolding, mistargeting, or degradation. While important success could be achieved by this strategy, the list of reported unsuccessful cases is disappointingly long and obviously dependent on the recombinant protein to be produced. Singular engineering of protein folding steps may not lead to desired results if the pathway suffers from several limitations. In particular, the connection between folding quality control and proteolytic degradation needs further attention. Based on recent understanding that multiple steps in the folding and secretion pathways limit productivity, synergistic combinations of the cell engineering approaches mentioned earlier need to be explored. In addition, systems biology-based whole cell analysis that also takes energy and redox metabolism into consideration will broaden the knowledge base for future rational engineering strategies.

Systems biology: a new tool for farm animal science.

PubMed

Hollung, Kristin; Timperio, Anna M; Olivan, Mamen; Kemp, Caroline; Coto-Montes, Ana; Sierra, Veronica; Zolla, Lello

2014-03-01

It is rapidly emerging that the tender meat phenotype is affected by an enormous amount of variables, not only tied to genetics (livestock breeding selection), but also to extrinsic factors, such as feeding conditions, physical activity, rearing environment, administration of hormonal growth promotants, pre-slaughter handling and stress. Proteomics has been widely accepted by meat scientists over the last years and is now commonly used to shed light on the postmortem processes involved in meat tenderization. This review discusses the latest findings with the use of proteomics and systems biology to study the different biochemical pathways postmortem aiming at understanding the concerted action of different molecular mechanisms responsible for meat quality. The conversion of muscle to meat postmortem can be described as a sequence of events involving molecular pathways controlled by a complex interplay of many factors. Among the different pathways emerging are the influence of apoptosis and lately also the role of autophagy in muscle postmortem development. This review thus, focus on how systems-wide integrated investigations (metabolomics, transcriptomics, interactomics, phosphoproteomics, mathematical modeling), which have emerged as complementary tools to proteomics, have helped establishing a few milestones in our understanding of the events leading from muscle to meat conversion.

Parent-Child Interaction, Self-Regulation, and Obesity Prevention in Early Childhood.

PubMed

Anderson, Sarah E; Keim, Sarah A

2016-06-01

This paper describes the epidemiologic evidence linking parent-child relationships, self-regulation, and weight status with a focus on early childhood. The emotional quality of parent-child interactions may influence children's risk for obesity through multiple pathways. Prospective studies linking observer ratings of young children's self-regulation, particularly inhibitory control, to future weight status are discussed. Although findings are preliminary, promoting positive relationships between parents/caregivers and young children holds promise as a component of efforts to prevent childhood obesity. Multi-disciplinary collaborations between researchers with training in developmental science and child health should be encouraged.

Mitochondrial quality control: Easy come, easy go

PubMed Central

Stotland, Aleksandr; Gottlieb, Roberta A.

2015-01-01

“Friends come and go but enemies accumulate.”Arthur Bloch Mitochondrial networks in eukaryotic cells are maintained via regular cycles of degradation and biogenesis. These complex processes function in concert with one another to eliminate dysfunctional mitochondria in a specific and targeted manner and coordinate the biogenesis of new organelles. This review covers the two aspects of mitochondrial turnover, focusing on the main pathways and mechanisms involved. The review also summarizes the current methods and techniques for analyzing mitochondrial turnover in vivo and in vitro, from the whole animal proteome level to the level of single organelle. PMID:25596427

Improving the effectiveness of psychological interventions for depression and anxiety in the cardiac rehabilitation pathway using group-based metacognitive therapy (PATHWAY Group MCT): study protocol for a randomised controlled trial.

PubMed

Wells, Adrian; McNicol, Kirsten; Reeves, David; Salmon, Peter; Davies, Linda; Heagerty, Anthony; Doherty, Patrick; McPhillips, Rebecca; Anderson, Rebecca; Faija, Cintia; Capobianco, Lora; Morley, Helen; Gaffney, Hannah; Shields, Gemma; Fisher, Peter

2018-04-03

Anxiety and depression are prevalent among cardiac rehabilitation patients but pharmacological and psychological treatments have limited effectiveness in this group. Furthermore, psychological interventions have not been systematically integrated into cardiac rehabilitation services despite being a strategic priority for the UK National Health Service. A promising new treatment, metacognitive therapy, may be well-suited to the needs of cardiac rehabilitation patients and has the potential to improve outcomes. It is based on the metacognitive model, which proposes that a thinking style dominated by rumination, worry and threat monitoring maintains emotional distress. Metacognitive therapy is highly effective at reducing this thinking style and alleviating anxiety and depression in mental health settings. This trial aims to evaluate the effectiveness and cost-effectiveness of group-based metacognitive therapy for cardiac rehabilitation patients with elevated anxiety and/or depressive symptoms. The PATHWAY Group-MCT trial is a multicentre, two-arm, single-blind, randomised controlled trial comparing the clinical- and cost-effectiveness of group-based metacognitive therapy plus usual cardiac rehabilitation to usual cardiac rehabilitation alone. Cardiac rehabilitation patients (target sample n = 332) with elevated anxiety and/or depressive symptoms will be recruited across five UK National Health Service Trusts. Participants randomised to the intervention arm will receive six weekly sessions of group-based metacognitive therapy delivered by either cardiac rehabilitation professionals or research nurses. The intervention and control groups will both be offered the usual cardiac rehabilitation programme within their Trust. The primary outcome is severity of anxiety and depressive symptoms at 4-month follow-up measured by the Hospital Anxiety and Depression Scale total score. Secondary outcomes are severity of anxiety/depression at 12-month follow-up, health-related quality of life, severity of post-traumatic stress symptoms and strength of metacognitive beliefs at 4- and 12-month follow-up. Qualitative interviews will help to develop an account of barriers and enablers to the effectiveness of the intervention. This trial will evaluate the effectiveness and cost-effectiveness of group-based metacognitive therapy in alleviating anxiety and depression in cardiac rehabilitation patients. The therapy, if effective, offers the potential to improve psychological wellbeing and quality of life in this large group of patients. UK Clinical Trials Gateway, ISRCTN74643496 , Registered on 8 April 2015.

Molecular evolution of multiple-level control of heme biosynthesis pathway in animal kingdom.

PubMed

Tzou, Wen-Shyong; Chu, Ying; Lin, Tzung-Yi; Hu, Chin-Hwa; Pai, Tun-Wen; Liu, Hsin-Fu; Lin, Han-Jia; Cases, Ildeofonso; Rojas, Ana; Sanchez, Mayka; You, Zong-Ye; Hsu, Ming-Wei

2014-01-01

Adaptation of enzymes in a metabolic pathway can occur not only through changes in amino acid sequences but also through variations in transcriptional activation, mRNA splicing and mRNA translation. The heme biosynthesis pathway, a linear pathway comprised of eight consecutive enzymes in animals, provides researchers with ample information for multiple types of evolutionary analyses performed with respect to the position of each enzyme in the pathway. Through bioinformatics analysis, we found that the protein-coding sequences of all enzymes in this pathway are under strong purifying selection, from cnidarians to mammals. However, loose evolutionary constraints are observed for enzymes in which self-catalysis occurs. Through comparative genomics, we found that in animals, the first intron of the enzyme-encoding genes has been co-opted for transcriptional activation of the genes in this pathway. Organisms sense the cellular content of iron, and through iron-responsive elements in the 5' untranslated regions of mRNAs and the intron-exon boundary regions of pathway genes, translational inhibition and exon choice in enzymes may be enabled, respectively. Pathway product (heme)-mediated negative feedback control can affect the transport of pathway enzymes into the mitochondria as well as the ubiquitin-mediated stability of enzymes. Remarkably, the positions of these controls on pathway activity are not ubiquitous but are biased towards the enzymes in the upstream portion of the pathway. We revealed that multiple-level controls on the activity of the heme biosynthesis pathway depend on the linear depth of the enzymes in the pathway, indicating a new strategy for discovering the molecular constraints that shape the evolution of a metabolic pathway.

Molecular chaperones and photoreceptor function

PubMed Central

Kosmaoglou, Maria; Schwarz, Nele; Bett, John S.; Cheetham, Michael E.

2008-01-01

Molecular chaperones facilitate and regulate protein conformational change within cells. This encompasses many fundamental cellular processes: including the correct folding of nascent chains; protein transport and translocation; signal transduction and protein quality control. Chaperones are, therefore, important in several forms of human disease, including neurodegeneration. Within the retina, the highly specialized photoreceptor cell presents a fascinating paradigm to investigate the specialization of molecular chaperone function and reveals unique chaperone requirements essential to photoreceptor function. Mutations in several photoreceptor proteins lead to protein misfolding mediated neurodegeneration. The best characterized of these are mutations in the molecular light sensor, rhodopsin, which cause autosomal dominant retinitis pigmentosa. Rhodopsin biogenesis is likely to require chaperones, while rhodopsin misfolding involves molecular chaperones in quality control and the cellular response to protein aggregation. Furthermore, the specialization of components of the chaperone machinery to photoreceptor specific roles has been revealed by the identification of mutations in molecular chaperones that cause inherited retinal dysfunction and degeneration. These chaperones are involved in several important cellular pathways and further illuminate the essential and diverse roles of molecular chaperones. PMID:18490186

RNA Surveillance: Molecular Approaches in Transcript Quality Control and their Implications in Clinical Diseases

PubMed Central

Moraes, Karen CM

2010-01-01

Production of mature mRNAs that encode functional proteins involves highly complex pathways of synthesis, processing and surveillance. At numerous steps during the maturation process, the mRNA transcript undergoes scrutiny by cellular quality control machinery. This extensive RNA surveillance ensures that only correctly processed mature mRNAs are translated and precludes production of aberrant transcripts that could encode mutant or possibly deleterious proteins. Recent advances in elucidating the molecular mechanisms of mRNA processing have demonstrated the existence of an integrated network of events, and have revealed that a variety of human diseases are caused by disturbances in the well-coordinated molecular equilibrium of these events. From a medical perspective, both loss and gain of function are relevant, and a considerable number of different diseases exemplify the importance of the mechanistic function of RNA surveillance in a cell. Here, mechanistic hallmarks of mRNA processing steps are reviewed, highlighting the medical relevance of their deregulation and how the understanding of such mechanisms can contribute to the development of therapeutic strategies. PMID:19829759

α-Melanocyte-stimulating hormone ameliorates ocular surface dysfunctions and lesions in a scopolamine-induced dry eye model via PKA-CREB and MEK-Erk pathways.

PubMed

Ru, Yusha; Huang, Yue; Liu, Huijuan; Du, Juan; Meng, Zhu; Dou, Zexia; Liu, Xun; Wei, Rui Hua; Zhang, Yan; Zhao, Shaozhen

2015-12-21

Dry eye is a highly prevalent, chronic, and multifactorial disease that compromises quality of life and generates socioeconomic burdens. The pathogenic factors of dry eye disease (DED) include tear secretion abnormalities, tear film instability, and ocular surface inflammation. An effective intervention targeting the pathogenic factors is needed to control this disease. Here we applied α-Melanocyte-stimulating hormone (α-MSH) twice a day to the ocular surface of a scopolamine-induced dry eye rat model. The results showed that α-MSH at different doses ameliorated tear secretion, tear film stability, and corneal integrity, and corrected overexpression of proinflammatory factors, TNF-α, IL-1β, and IFN-γ, in ocular surface of the dry eye rats. Moreover, α-MSH, at 10(-4) μg/μl, maintained corneal morphology, inhibited apoptosis, and restored the number and size of conjunctival goblet cells in the dry eye rats. Mechanistically, α-MSH activated both PKA-CREB and MEK-Erk pathways in the dry eye corneas and conjunctivas; pharmacological blockade of either pathway abolished α-MSH's protective effects, suggesting that both pathways are necessary for α-MSH's protection under dry eye condition. The peliotropic protective functions and explicit signaling mechanism of α-MSH warrant translation of the α-MSH-containing eye drop into a novel and effective intervention to DED.

α-Melanocyte-stimulating hormone ameliorates ocular surface dysfunctions and lesions in a scopolamine-induced dry eye model via PKA-CREB and MEK-Erk pathways

PubMed Central

Ru, Yusha; Huang, Yue; Liu, Huijuan; Du, Juan; Meng, Zhu; Dou, Zexia; Liu, Xun; Wei, Rui Hua; Zhang, Yan; Zhao, Shaozhen

2015-01-01

Dry eye is a highly prevalent, chronic, and multifactorial disease that compromises quality of life and generates socioeconomic burdens. The pathogenic factors of dry eye disease (DED) include tear secretion abnormalities, tear film instability, and ocular surface inflammation. An effective intervention targeting the pathogenic factors is needed to control this disease. Here we applied α-Melanocyte-stimulating hormone (α-MSH) twice a day to the ocular surface of a scopolamine-induced dry eye rat model. The results showed that α-MSH at different doses ameliorated tear secretion, tear film stability, and corneal integrity, and corrected overexpression of proinflammatory factors, TNF-α, IL-1β, and IFN-γ, in ocular surface of the dry eye rats. Moreover, α-MSH, at 10−4 μg/μl, maintained corneal morphology, inhibited apoptosis, and restored the number and size of conjunctival goblet cells in the dry eye rats. Mechanistically, α-MSH activated both PKA-CREB and MEK-Erk pathways in the dry eye corneas and conjunctivas; pharmacological blockade of either pathway abolished α-MSH’s protective effects, suggesting that both pathways are necessary for α-MSH’s protection under dry eye condition. The peliotropic protective functions and explicit signaling mechanism of α-MSH warrant translation of the α-MSH-containing eye drop into a novel and effective intervention to DED. PMID:26685899

Dietary phytochemicals for possible preventive and therapeutic option of uterine fibroids: Signaling pathways as target.

PubMed

Islam, Md Soriful; Segars, James H; Castellucci, Mario; Ciarmela, Pasquapina

2017-02-01

A growing interest has emerged on dietary phytochemicals to control diverse pathological conditions. Unfortunately, dietary phytochemical research in uterine fibroids is still under construction. Uterine fibroids/leiomyomas are benign tumors developing from the myometrium of the uterus in premenopausal women. They may occur in more than 70% of women, and approximately 25% of women show clinically significant symptoms. These include heavy and prolonged menstrual bleeding, pelvic pressure (urinary frequency, incontinence, and difficulty with urination), pelvic pain, pelvic mass, infertility, and reproductive dysfunction. Due to lack of medical treatments surgery has been definitive choice for fibroid management. Moreover, surgery negatively affects women's quality of life, and its associated cost appears to be expensive. The molecular mechanism of fibroids development and growth is not fully elucidated. However, accumulated evidence shows that several signaling pathways, including Smad 2/3, PI3K/AKT/mTOR, ERK 1/2 and β-catenin are involved in the leiomyoma pathogenesis, indicating that they could serve as targets for prevention and/or treatment of this tumor. Therefore, in this review, we discuss the involvement of signaling pathways in leiomyoma development and growth, and introduce some potential dietary phytochemicals that could modulate those signaling pathways. Copyright © 2016 Institute of Pharmacology, Polish Academy of Sciences. Published by Elsevier Urban & Partner Sp. z o.o. All rights reserved.

Crossroads of Wnt and Hippo in epithelial tissues.

PubMed

Bernascone, Ilenia; Martin-Belmonte, Fernando

2013-08-01

Epithelial tissues undergo constant growth and differentiation during embryonic development and to replace damaged tissue in adult organs. These processes are governed by different signaling pathways that ultimately control the expression of genes associated with cell proliferation, patterning, and death. One essential pathway is Wnt, which controls tubulogenesis in several epithelial organs. Recently, Wnt has been closely linked to other signaling pathways, such as Hippo, that orchestrate proliferation and apoptosis to control organ size. There is evidence that epithelial cell junctions may sequester the transcription factors that act downstream of these signaling pathways, which would represent an important aspect of their functional regulation and their influence on cell behavior. Here, we review the transcriptional control exerted by the Wnt and Hippo signaling pathways during epithelial growth, patterning, and differentiation and recent advances in understanding of the regulation and crosstalk of these pathways in epithelial tissues. Copyright © 2013 Elsevier Ltd. All rights reserved.

Critical Roles of the Direct GABAergic Pallido-cortical Pathway in Controlling Absence Seizures

PubMed Central

Li, Min; Ma, Tao; Wu, Shengdun; Ma, Jingling; Cui, Yan; Xia, Yang; Xu, Peng; Yao, Dezhong

2015-01-01

The basal ganglia (BG), serving as an intermediate bridge between the cerebral cortex and thalamus, are believed to play crucial roles in controlling absence seizure activities generated by the pathological corticothalamic system. Inspired by recent experiments, here we systematically investigate the contribution of a novel identified GABAergic pallido-cortical pathway, projecting from the globus pallidus externa (GPe) in the BG to the cerebral cortex, to the control of absence seizures. By computational modelling, we find that both increasing the activation of GPe neurons and enhancing the coupling strength of the inhibitory pallido-cortical pathway can suppress the bilaterally synchronous 2–4 Hz spike and wave discharges (SWDs) during absence seizures. Appropriate tuning of several GPe-related pathways may also trigger the SWD suppression, through modulating the activation level of GPe neurons. Furthermore, we show that the previously discovered bidirectional control of absence seizures due to the competition between other two BG output pathways also exists in our established model. Importantly, such bidirectional control is shaped by the coupling strength of this direct GABAergic pallido-cortical pathway. Our work suggests that the novel identified pallido-cortical pathway has a functional role in controlling absence seizures and the presented results might provide testable hypotheses for future experimental studies. PMID:26496656

Pathway-based outlier method reveals heterogeneous genomic structure of autism in blood transcriptome

PubMed Central

2013-01-01

Background Decades of research strongly suggest that the genetic etiology of autism spectrum disorders (ASDs) is heterogeneous. However, most published studies focus on group differences between cases and controls. In contrast, we hypothesized that the heterogeneity of the disorder could be characterized by identifying pathways for which individuals are outliers rather than pathways representative of shared group differences of the ASD diagnosis. Methods Two previously published blood gene expression data sets – the Translational Genetics Research Institute (TGen) dataset (70 cases and 60 unrelated controls) and the Simons Simplex Consortium (Simons) dataset (221 probands and 191 unaffected family members) – were analyzed. All individuals of each dataset were projected to biological pathways, and each sample’s Mahalanobis distance from a pooled centroid was calculated to compare the number of case and control outliers for each pathway. Results Analysis of a set of blood gene expression profiles from 70 ASD and 60 unrelated controls revealed three pathways whose outliers were significantly overrepresented in the ASD cases: neuron development including axonogenesis and neurite development (29% of ASD, 3% of control), nitric oxide signaling (29%, 3%), and skeletal development (27%, 3%). Overall, 50% of cases and 8% of controls were outliers in one of these three pathways, which could not be identified using group comparison or gene-level outlier methods. In an independently collected data set consisting of 221 ASD and 191 unaffected family members, outliers in the neurogenesis pathway were heavily biased towards cases (20.8% of ASD, 12.0% of control). Interestingly, neurogenesis outliers were more common among unaffected family members (Simons) than unrelated controls (TGen), but the statistical significance of this effect was marginal (Chi squared P < 0.09). Conclusions Unlike group difference approaches, our analysis identified the samples within the case and control groups that manifested each expression signal, and showed that outlier groups were distinct for each implicated pathway. Moreover, our results suggest that by seeking heterogeneity, pathway-based outlier analysis can reveal expression signals that are not apparent when considering only shared group differences. PMID:24063311

Exercise Therapy in Juvenile Idiopathic Arthritis: A Systematic Review and Meta-Analysis.

PubMed

Kuntze, Gregor; Nesbitt, Colleen; Whittaker, Jackie L; Nettel-Aguirre, Alberto; Toomey, Clodagh; Esau, Shane; Doyle-Baker, Patricia K; Shank, Jena; Brooks, Julia; Benseler, Susanne; Emery, Carolyn A

2018-01-01

To conduct a systematic review to evaluate the efficacy of exercise interventions in improving outcomes across domains of functioning and disability in children and adolescents with juvenile idiopathic arthritis (JIA). Seven electronic databases were systematically searched up to November 16, 2016. Original data, analytic prospective design, physical therapy-led exercise intervention evaluation, children and adolescents with JIA, and assessment of functional, structural, activity, participation, or quality of life outcomes. Two authors screened search results, and discrepancies were resolved by consensus. Of 5037 potentially relevant studies, 9 randomized controlled trials and 1 cohort study were included and scored. Study quality (Downs and Black quality assessment tool) and level of evidence (Oxford Centre of Evidence-Based Medicine model) were assessed and meta-analysis conducted where appropriate. Alternatively, a descriptive summary approach was chosen. All randomized controlled trials were moderate-quality intervention studies (level 2b evidence; median Downs and Black score, 20 out of 32; range, 15-27). Interventions included aquatic, strengthening, proprioceptive, aerobic, and Pilates exercises. Pediatric activity capacity (Child Health Assessment Questionnaire) improved with exercise (mean difference, .45; 95% confidence interval, .05-.76). Furthermore, descriptive summaries indicated improved activity capacity, body function and structure (pain and muscle strength), and quality of life outcomes. Exercise therapy appears to be well tolerated and beneficial across clinically relevant outcomes in patients with JIA. The paucity of high-quality evidence and study heterogeneity limited the ability to provide conclusive, generalizing evidence for the efficacy of exercise therapy and to provide specific recommendations for clinical practice at this time. Future research evaluating exercise program implementation using validated outcomes and detailed adherence and safety assessment is needed to optimize clinical decision pathways in patients with JIA. Copyright © 2016 American Congress of Rehabilitation Medicine. Published by Elsevier Inc. All rights reserved.

Is sense of coherence a pathway for improving the quality of life of patients who grow up with chronic diseases? A hypothesis.

PubMed

Moons, Philip; Norekvål, Tone M

2006-03-01

A recent study indicated that the quality of life in adult patients with congenital heart disease was better than that of their healthy counterparts. A possible explanation for this is that these patients have a stronger sense of coherence than do their healthy counterparts. This enhanced sense of coherence develops in childhood through the successful application of generalized resistance resources. Here, we advance the hypothesis that sense of coherence may be a potential pathway for improving the quality of life in patients who grow up with a chronic health condition. This hypothesis needs to be tested in long-term longitudinal studies. If such studies can confirm the hypothesis, SOC can be an important target for interventions in childhood to improve patients' quality of life during adulthood.

Poorly controlled postoperative pain: prevalence, consequences, and prevention

PubMed Central

Gan, Tong J

2017-01-01

This review provides an overview of the clinical issue of poorly controlled postoperative pain and therapeutic approaches that may help to address this common unresolved health-care challenge. Postoperative pain is not adequately managed in greater than 80% of patients in the US, although rates vary depending on such factors as type of surgery performed, analgesic/anesthetic intervention used, and time elapsed after surgery. Poorly controlled acute postoperative pain is associated with increased morbidity, functional and quality-of-life impairment, delayed recovery time, prolonged duration of opioid use, and higher health-care costs. In addition, the presence and intensity of acute pain during or after surgery is predictive of the development of chronic pain. More effective analgesic/anesthetic measures in the perioperative period are needed to prevent the progression to persistent pain. Although clinical findings are inconsistent, some studies of local anesthetics and nonopioid analgesics have suggested potential benefits as preventive interventions. Conventional opioids remain the standard of care for the management of acute postoperative pain; however, the risk of opioid-related adverse events can limit optimal dosing for analgesia, leading to poorly controlled acute postoperative pain. Several new opioids have been developed that modulate μ-receptor activity by selectively engaging intracellular pathways associated with analgesia and not those associated with adverse events, creating a wider therapeutic window than unselective conventional opioids. In clinical studies, oliceridine (TRV130), a novel μ-receptor G-protein pathway-selective modulator, produced rapid postoperative analgesia with reduced prevalence of adverse events versus morphine. PMID:29026331

Poorly controlled postoperative pain: prevalence, consequences, and prevention.

PubMed

Gan, Tong J

2017-01-01

This review provides an overview of the clinical issue of poorly controlled postoperative pain and therapeutic approaches that may help to address this common unresolved health-care challenge. Postoperative pain is not adequately managed in greater than 80% of patients in the US, although rates vary depending on such factors as type of surgery performed, analgesic/anesthetic intervention used, and time elapsed after surgery. Poorly controlled acute postoperative pain is associated with increased morbidity, functional and quality-of-life impairment, delayed recovery time, prolonged duration of opioid use, and higher health-care costs. In addition, the presence and intensity of acute pain during or after surgery is predictive of the development of chronic pain. More effective analgesic/anesthetic measures in the perioperative period are needed to prevent the progression to persistent pain. Although clinical findings are inconsistent, some studies of local anesthetics and nonopioid analgesics have suggested potential benefits as preventive interventions. Conventional opioids remain the standard of care for the management of acute postoperative pain; however, the risk of opioid-related adverse events can limit optimal dosing for analgesia, leading to poorly controlled acute postoperative pain. Several new opioids have been developed that modulate μ-receptor activity by selectively engaging intracellular pathways associated with analgesia and not those associated with adverse events, creating a wider therapeutic window than unselective conventional opioids. In clinical studies, oliceridine (TRV130), a novel μ-receptor G-protein pathway-selective modulator, produced rapid postoperative analgesia with reduced prevalence of adverse events versus morphine.

Deepening our understanding of quality improvement in Europe (DUQuE): overview of a study of hospital quality management in seven countries.

PubMed

Secanell, Mariona; Groene, Oliver; Arah, Onyebuchi A; Lopez, Maria Andrée; Kutryba, Basia; Pfaff, Holger; Klazinga, Niek; Wagner, Cordula; Kristensen, Solvejg; Bartels, Paul Daniel; Garel, Pascal; Bruneau, Charles; Escoval, Ana; França, Margarida; Mora, Nuria; Suñol, Rosa

2014-04-01

This paper provides an overview of the DUQuE (Deepening our Understanding of Quality Improvement in Europe) project, the first study across multiple countries of the European Union (EU) to assess relationships between quality management and patient outcomes at EU level. The paper describes the conceptual framework and methods applied, highlighting the novel features of this study. DUQuE was designed as a multi-level cross-sectional study with data collection at hospital, pathway, professional and patient level in eight countries. We aimed to collect data for the assessment of hospital-wide constructs from up to 30 randomly selected hospitals in each country, and additional data at pathway and patient level in 12 of these 30. A comprehensive conceptual framework was developed to account for the multiple levels that influence hospital performance and patient outcomes. We assessed hospital-specific constructs (organizational culture and professional involvement), clinical pathway constructs (the organization of care processes for acute myocardial infarction, stroke, hip fracture and deliveries), patient-specific processes and outcomes (clinical effectiveness, patient safety and patient experience) and external constructs that could modify hospital quality (external assessment and perceived external pressure). Data was gathered from 188 hospitals in 7 participating countries. The overall participation and response rate were between 75% and 100% for the assessed measures. This is the first study assessing relation between quality management and patient outcomes at EU level. The study involved a large number of respondents and achieved high response rates. This work will serve to develop guidance in how to assess quality management and makes recommendations on the best ways to improve quality in healthcare for hospital stakeholders, payers, researchers, and policy makers throughout the EU.

Overview of Global/Regional Models Used to Evaluate Tropospheric Ozone in North America

NASA Technical Reports Server (NTRS)

Johnson, Matthew S.

2015-01-01

Ozone (O3) is an important greenhouse gas, toxic pollutant, and plays a major role in atmospheric chemistry. Tropospheric O3 which resides in the planetary boundary layer (PBL) is highly reactive and has a lifetime on the order of days, however, O3 in the free troposphere and stratosphere has a lifetime on the order of weeks or months. Modeling O3 mixing ratios at and above the surface is difficult due to the multiple formation/destruction processes and transport pathways that cause large spatio-temporal variability in O3 mixing ratios. This talk will summarize in detail the global/regional models that are commonly used to simulate/predict O3 mixing ratios in the United States. The major models which will be focused on are the: 1) Community Multi-scale Air Quality Model (CMAQ), 2) Comprehensive Air Quality Model with Extensions (CAMx), 3) Goddard Earth Observing System with Chemistry (GEOS-Chem), 4) Real Time Air Quality Modeling System (RAQMS), 5) Weather Research and Forecasting/Chemistry (WRF-Chem) model, National Center for Atmospheric Research (NCAR)'s Model for OZone And Related chemical Tracers (MOZART), and 7) Geophysical Fluid Dynamics Laboratory (GFDL) AM3 model. I will discuss the major modeling components which impact O3 mixing ratio calculations in each model and the similarities/differences between these models. This presentation is vital to the 2nd Annual Tropospheric Ozone Lidar Network (TOLNet) Conference as it will provide an overview of tools, which can be used in conjunction with TOLNet data, to evaluate the complex chemistry and transport pathways controlling tropospheric O3 mixing ratios.

Mining pathway associations for disease-related pathway activity analysis based on gene expression and methylation data.

PubMed

Lee, Hyeonjeong; Shin, Miyoung

2017-01-01

The problem of discovering genetic markers as disease signatures is of great significance for the successful diagnosis, treatment, and prognosis of complex diseases. Even if many earlier studies worked on identifying disease markers from a variety of biological resources, they mostly focused on the markers of genes or gene-sets (i.e., pathways). However, these markers may not be enough to explain biological interactions between genetic variables that are related to diseases. Thus, in this study, our aim is to investigate distinctive associations among active pathways (i.e., pathway-sets) shown each in case and control samples which can be observed from gene expression and/or methylation data. The pathway-sets are obtained by identifying a set of associated pathways that are often active together over a significant number of class samples. For this purpose, gene expression or methylation profiles are first analyzed to identify significant (active) pathways via gene-set enrichment analysis. Then, regarding these active pathways, an association rule mining approach is applied to examine interesting pathway-sets in each class of samples (case or control). By doing so, the sets of associated pathways often working together in activity profiles are finally chosen as our distinctive signature of each class. The identified pathway-sets are aggregated into a pathway activity network (PAN), which facilitates the visualization of differential pathway associations between case and control samples. From our experiments with two publicly available datasets, we could find interesting PAN structures as the distinctive signatures of breast cancer and uterine leiomyoma cancer, respectively. Our pathway-set markers were shown to be superior or very comparable to other genetic markers (such as genes or gene-sets) in disease classification. Furthermore, the PAN structure, which can be constructed from the identified markers of pathway-sets, could provide deeper insights into distinctive associations between pathway activities in case and control samples.

Why is intelligence correlated with semen quality?: Biochemical pathways common to sperm and neuron function and their vulnerability to pleiotropic mutations.

PubMed

Pierce, Arand; Miller, Geoffrey; Arden, Rosalind; Gottfredson, Linda S

2009-09-01

We recently found positive correlations between human general intelligence and three key indices of semen quality, and hypothesized that these correlations arise through a phenotype-wide 'general fitness factor' reflecting overall mutation load. In this addendum we consider some of the biochemical pathways that may act as targets for pleiotropic mutations that disrupt both neuron function and sperm function in parallel. We focus especially on the inter-related roles of polyunsaturated fatty acids, exocytosis and receptor signaling.

Redundancy control in pathway databases (ReCiPa): an application for improving gene-set enrichment analysis in Omics studies and "Big data" biology.

PubMed

Vivar, Juan C; Pemu, Priscilla; McPherson, Ruth; Ghosh, Sujoy

2013-08-01

Abstract Unparalleled technological advances have fueled an explosive growth in the scope and scale of biological data and have propelled life sciences into the realm of "Big Data" that cannot be managed or analyzed by conventional approaches. Big Data in the life sciences are driven primarily via a diverse collection of 'omics'-based technologies, including genomics, proteomics, metabolomics, transcriptomics, metagenomics, and lipidomics. Gene-set enrichment analysis is a powerful approach for interrogating large 'omics' datasets, leading to the identification of biological mechanisms associated with observed outcomes. While several factors influence the results from such analysis, the impact from the contents of pathway databases is often under-appreciated. Pathway databases often contain variously named pathways that overlap with one another to varying degrees. Ignoring such redundancies during pathway analysis can lead to the designation of several pathways as being significant due to high content-similarity, rather than truly independent biological mechanisms. Statistically, such dependencies also result in correlated p values and overdispersion, leading to biased results. We investigated the level of redundancies in multiple pathway databases and observed large discrepancies in the nature and extent of pathway overlap. This prompted us to develop the application, ReCiPa (Redundancy Control in Pathway Databases), to control redundancies in pathway databases based on user-defined thresholds. Analysis of genomic and genetic datasets, using ReCiPa-generated overlap-controlled versions of KEGG and Reactome pathways, led to a reduction in redundancy among the top-scoring gene-sets and allowed for the inclusion of additional gene-sets representing possibly novel biological mechanisms. Using obesity as an example, bioinformatic analysis further demonstrated that gene-sets identified from overlap-controlled pathway databases show stronger evidence of prior association to obesity compared to pathways identified from the original databases.

Neural pathways for colorectal control, relevance to spinal cord injury and treatment: a narrative review.

PubMed

Callaghan, Brid; Furness, John B; Pustovit, Ruslan V

2018-03-01

Narrative review. The purpose is to review the organisation of the nerve pathways that control defecation and to relate this knowledge to the deficits in colorectal function after SCI. A literature review was conducted to identify salient features of defecation control pathways and the functional consequences of damage to these pathways in SCI. The control pathways for defecation have separate pontine centres under cortical control that influence defecation. The pontine centres connect, separately, with autonomic preganglionic neurons of the spinal defecation centres and somatic motor neurons of Onuf's nucleus in the sacral spinal cord. Organised propulsive motor patterns can be generated by stimulation of the spinal defecation centres. Activation of the somatic neurons contracts the external sphincter. The analysis aids in interpreting the consequences of SCI and predicts therapeutic strategies. Analysis of the bowel control circuits identifies sites at which bowel function may be modulated after SCI. Colokinetic drugs that elicit propulsive contractions of the colorectum may provide valuable augmentation of non-pharmacological bowel management procedures.

The pathways of high school science teachers and policy efforts to alter the pipeline

NASA Astrophysics Data System (ADS)

Sass, Tim

2012-03-01

There is currently much interest in improving the quality of science education in K-12 schools and encouraging more students, particularly minorities and women, to pursue careers in STEM fields. Two interrelated issues are at the forefront: the quality of science teachers and the supply of science teachers. Education research in general finds that the single most important school-based factor affecting student achievement is teacher quality. While there is little evidence that teacher credentials matter for student achievement in the lower grades, there is at least some evidence that content knowledge is an important determinant of teacher quality in middle and secondary schools. However, little is known about the pre-service preparation of high school science teachers and how the training of science teachers affects their performance in the classroom. While there are many efforts underway to increase the supply of science teachers, little is known about the supply of science teachers from different pathways and the factors that lead science teachers to leave the profession. In this presentation I discuss recent work on the supply of teachers from alternative pathways, focusing on high school science teachers. I also summarize the literature on teacher quality and attrition, emphasizing the current state of knowledge on secondary school teachers. Finally, I present current policy initiatives and discuss the likelihood of their success given current research findings.

Engineering Emergency: African Americans and Hispanics Lack Pathways to Engineering. Vital Signs: Reports on the Condition of STEM Learning in the U.S.

ERIC Educational Resources Information Center

Change the Equation, 2014

2014-01-01

A quality education that leads to good jobs offers a reliable pathway to economic security, yet the first step on that pathway remains inaccessible to far too many Americans, especially Americans of color. Nowhere is this inequity more apparent than in engineering. On average, people with engineering bachelor's degrees earn higher salaries than…

Design and evaluation of a wireless electronic health records system for field care in mass casualty settings.

PubMed

Lenert, L A; Kirsh, D; Griswold, W G; Buono, C; Lyon, J; Rao, R; Chan, T C

2011-01-01

There is growing interest in the use of technology to enhance the tracking and quality of clinical information available for patients in disaster settings. This paper describes the design and evaluation of the Wireless Internet Information System for Medical Response in Disasters (WIISARD). WIISARD combined advanced networking technology with electronic triage tags that reported victims' position and recorded medical information, with wireless pulse-oximeters that monitored patient vital signs, and a wireless electronic medical record (EMR) for disaster care. The EMR system included WiFi handheld devices with barcode scanners (used by front-line responders) and computer tablets with role-tailored software (used by managers of the triage, treatment, transport and medical communications teams). An additional software system provided situational awareness for the incident commander. The WIISARD system was evaluated in a large-scale simulation exercise designed for training first responders. A randomized trial was overlaid on this exercise with 100 simulated victims, 50 in a control pathway (paper-based), and 50 in completely electronic WIISARD pathway. All patients in the electronic pathway were cared for within the WIISARD system without paper-based workarounds. WIISARD reduced the rate of the missing and/or duplicated patient identifiers (0% vs 47%, p<0.001). The total time of the field was nearly identical (38:20 vs 38:23, IQR 26:53-1:05:32 vs 18:55-57:22). Overall, the results of WIISARD show that wireless EMR systems for care of the victims of disasters would be complex to develop but potentially feasible to build and deploy, and likely to improve the quality of information available for the delivery of care during disasters.

Design and evaluation of a wireless electronic health records system for field care in mass casualty settings

PubMed Central

Kirsh, D; Griswold, W G; Buono, C; Lyon, J; Rao, R; Chan, T C

2011-01-01

Background There is growing interest in the use of technology to enhance the tracking and quality of clinical information available for patients in disaster settings. This paper describes the design and evaluation of the Wireless Internet Information System for Medical Response in Disasters (WIISARD). Materials and methods WIISARD combined advanced networking technology with electronic triage tags that reported victims' position and recorded medical information, with wireless pulse-oximeters that monitored patient vital signs, and a wireless electronic medical record (EMR) for disaster care. The EMR system included WiFi handheld devices with barcode scanners (used by front-line responders) and computer tablets with role-tailored software (used by managers of the triage, treatment, transport and medical communications teams). An additional software system provided situational awareness for the incident commander. The WIISARD system was evaluated in a large-scale simulation exercise designed for training first responders. A randomized trial was overlaid on this exercise with 100 simulated victims, 50 in a control pathway (paper-based), and 50 in completely electronic WIISARD pathway. All patients in the electronic pathway were cared for within the WIISARD system without paper-based workarounds. Results WIISARD reduced the rate of the missing and/or duplicated patient identifiers (0% vs 47%, p<0.001). The total time of the field was nearly identical (38:20 vs 38:23, IQR 26:53–1:05:32 vs 18:55–57:22). Conclusion Overall, the results of WIISARD show that wireless EMR systems for care of the victims of disasters would be complex to develop but potentially feasible to build and deploy, and likely to improve the quality of information available for the delivery of care during disasters. PMID:21709162

Descending motor pathways and the spinal motor system - Limbic and non-limbic components

NASA Technical Reports Server (NTRS)

Holstege, Gert

1991-01-01

Research on descending motor pathways to caudal brainstem and spinal cord in the spinal motor system is reviewed. Particular attention is given to somatic and autonomic motoneurons in the spinal cord and brainstem, local projections to motoneurons, bulbospinal interneurons projecting to motoneurons, descending pathways of somatic motor control systems, and descending pathways involved in limbic motor control systems.

MDRC Research on Career Pathways. Issue Brief

ERIC Educational Resources Information Center

Kazis, Richard

2016-01-01

As postsecondary credentials have become increasingly important to accessing higher-quality employment, a growing number of education and workforce programs are implementing "career pathways" approaches to help both youth and adults prepare for further education and better jobs. In recent years, the Manpower Demonstration Research…

Identity dynamics and peer relationship quality in adolescents with a chronic disease: the sample case of congenital heart disease.

PubMed

Rassart, Jessica; Luyckx, Koen; Apers, Silke; Goossens, Eva; Moons, Philip

2012-10-01

Identity formation has been found to relate to psychosocial and disease-specific functioning in chronically ill adolescents. Therefore, examining antecedent factors of identity formation in this population is needed. The main goal of the present longitudinal study was to examine how peer relationship quality influenced identity formation in adolescents with congenital heart disease (CHD). Adolescents with CHD were selected from the database of pediatric and congenital cardiology of the University Hospitals Leuven. A total of 429 adolescents (14-18 years) with CHD participated at time 1; 401 were matched on gender and age with community controls recruited at secondary schools. Adolescents completed questionnaires on identity and peer relationship quality. Nine months later, at time 2, 382 patients again completed these questionnaires. Adolescents with CHD were generally found to be as competent as controls in addressing the task of identity formation. Moreover, the importance of peer relationships for identity formation was demonstrated. Supportive peer relationships positively influenced the process of identifying with the identity commitments made. Furthermore, such relationships protected adolescents from getting stuck in the exploration process. Finally, reciprocal pathways were uncovered; a maladaptive exploration process was also found to negatively affect peer relationships. The present study found peer relationship quality to be an important antecedent factor of identity formation in adolescents with CHD. Future research should investigate how changes in peer relationships and identity relate to well-being in these patients.

Neuronal and behavioural modulations by pathway-selective optogenetic stimulation of the primate oculomotor system

PubMed Central

Inoue, Ken-ichi; Takada, Masahiko; Matsumoto, Masayuki

2015-01-01

Optogenetics enables temporally and spatially precise control of neuronal activity in vivo. One of the key advantages of optogenetics is that it can be used to control the activity of targeted neural pathways that connect specific brain regions. While such pathway-selective optogenetic control is a popular tool in rodents, attempts at modulating behaviour using pathway-selective optogenetics have not yet been successful in primates. Here we develop a methodology for pathway-selective optogenetics in macaque monkeys, focusing on the pathway from the frontal eye field (FEF) to the superior colliculus (SC), part of the complex oculomotor network. We find that the optogenetic stimulation of FEF projections to the SC modulates SC neuron activity and is sufficient to evoke saccadic eye movements towards the response field corresponding to the stimulation site. Thus, our results demonstrate the feasibility of using pathway-selective optogenetics to elucidate neural network function in primates. PMID:26387804

Neuronal and behavioural modulations by pathway-selective optogenetic stimulation of the primate oculomotor system.

PubMed

Inoue, Ken-ichi; Takada, Masahiko; Matsumoto, Masayuki

2015-09-21

Optogenetics enables temporally and spatially precise control of neuronal activity in vivo. One of the key advantages of optogenetics is that it can be used to control the activity of targeted neural pathways that connect specific brain regions. While such pathway-selective optogenetic control is a popular tool in rodents, attempts at modulating behaviour using pathway-selective optogenetics have not yet been successful in primates. Here we develop a methodology for pathway-selective optogenetics in macaque monkeys, focusing on the pathway from the frontal eye field (FEF) to the superior colliculus (SC), part of the complex oculomotor network. We find that the optogenetic stimulation of FEF projections to the SC modulates SC neuron activity and is sufficient to evoke saccadic eye movements towards the response field corresponding to the stimulation site. Thus, our results demonstrate the feasibility of using pathway-selective optogenetics to elucidate neural network function in primates.

Identification of Differentially Expressed Genes and Pathways for Myofiber Characteristics in Soleus Muscles between Chicken Breeds Differing in Meat Quality.

PubMed

Du, Y F; Ding, Q L; Li, Y M; Fang, W R

2017-04-03

In the modern chicken industry, fast-growing broilers have undergone strong artificial selection for muscle growth, which has led to remarkable phenotypic variations compared with slow-growing chickens. However, the molecular mechanism underlying these phenotypes differences remains unknown. In this study, a systematic identification of candidate genes and new pathways related to myofiber development and composition in chicken Soleus muscle (SOL) has been made using gene expression profiles of two distinct breeds: Qingyuan partridge (QY), a slow-growing Chinese breed possessing high meat quality and Cobb 500 (CB), a commercial fast-growing broiler line. Agilent cDNA microarray analyses were conducted to determine gene expression profiles of soleus muscle sampled at sexual maturity age of QY (112 d) and CB (42 d). The 1318 genes with at least 2-fold differences were identified (P < 0.05, FDR <0.05, FC ≥ 2) in SOL muscles of QY and CB chickens. Differentially expressed genes (DEGs) related to muscle development, energy metabolism or lipid metabolism processes were examined further in each breed based on Gene Ontology (GO) analysis, and 11 genes involved in these processes were selected for further validation studies by qRT-PCR. In addition, based on KEGG pathway analysis of DEGs in both QY and CB chickens, it was found that in addition to pathways affecting myogenic fibre-type development and differentiation (pathways for Hedgehog & Calcium signaling), energy metabolism (Phosphatidylinositol signaling system, VEGF signaling pathway, Purine metabolism, Pyrimidine metabolism) were also enriched and might form a network with pathways related to muscle metabolism to influence the development of myofibers. This study is the first stage in the understanding of molecular mechanisms underlying variations in poultry meat quality. Large scale analyses are now required to validate the role of the genes identified and ultimately to find molecular markers that can be used for selection or to optimize rearing practices.

Prospective associations of social isolation and loneliness with poor sleep quality in older adults.

PubMed

Yu, Bin; Steptoe, Andrew; Niu, Kaijun; Ku, Po-Wen; Chen, Li-Jung

2018-03-01

There is evidence for negative associations between social isolation and loneliness and sleep quality in older adults. However, it is unclear to what extent these two factors independently affect sleep quality. This study examined the simultaneous associations of social isolation and loneliness with sleep quality in a longitudinal study of older adults. Data were analyzed from the Social Environment and Biomarkers of Aging Study in Taiwan collected in 2000 and 2006, involving a cohort of 639 participants (mean age = 66.14, SD 7.26). Poisson regression models were conducted to examine the association of social isolation and/or loneliness with sleep quality at follow-up after adjusting for multiple confounding variables. Univariate analysis showed that sleep quality was inversely associated with both social isolation and loneliness. After demographic, health, cognitive factors, and depressive symptoms were controlled in multivariable analysis, social isolation at the baseline still predicted poor sleep quality 6 years later (incident rate ratio, IRR 1.14; 95% CI 1.04-1.24; p < 0.01), while the association between loneliness and sleep quality was no longer significant (IRR 1.08; 95% CI 0.94-1.23; p = 0.27). The results were unchanged when participants who had poor sleep quality at the baseline were excluded from the analysis. These findings confirm an adverse effect of social isolation on the sleep quality of older adults, but indicate that this effect is independent of loneliness. Social isolation and loneliness seem to have distinct pathways in affecting the sleep quality of older adults.

The Pathway Tools software.

PubMed

Karp, Peter D; Paley, Suzanne; Romero, Pedro

2002-01-01

Bioinformatics requires reusable software tools for creating model-organism databases (MODs). The Pathway Tools is a reusable, production-quality software environment for creating a type of MOD called a Pathway/Genome Database (PGDB). A PGDB such as EcoCyc (see http://ecocyc.org) integrates our evolving understanding of the genes, proteins, metabolic network, and genetic network of an organism. This paper provides an overview of the four main components of the Pathway Tools: The PathoLogic component supports creation of new PGDBs from the annotated genome of an organism. The Pathway/Genome Navigator provides query, visualization, and Web-publishing services for PGDBs. The Pathway/Genome Editors support interactive updating of PGDBs. The Pathway Tools ontology defines the schema of PGDBs. The Pathway Tools makes use of the Ocelot object database system for data management services for PGDBs. The Pathway Tools has been used to build PGDBs for 13 organisms within SRI and by external users.

Trypanosoma cruzi Calreticulin Is a Lectin That Binds Monoglucosylated Oligosaccharides but Not Protein Moieties of Glycoproteins

PubMed Central

Labriola, Carlos; Cazzulo, Juan J.; Parodi, Armando J.

1999-01-01

Trypanosoma cruzi is a protozoan parasite that belongs to an early branch in evolution. Although it lacks several features of the pathway of protein N-glycosylation and oligosaccharide processing present in the endoplasmic reticulum of higher eukaryotes, it displays UDP-Glc:glycoprotein glucosyltransferase and glucosidase II activities. It is herewith reported that this protozoan also expresses a calreticulin-like molecule, the third component of the quality control of glycoprotein folding. No calnexin-encoding gene was detected. Recombinant T. cruzi calreticulin specifically recognized free monoglucosylated high-mannose-type oligosaccharides. Addition of anti-calreticulin serum to extracts obtained from cells pulse–chased with [35S]Met plus [35S]Cys immunoprecipitated two proteins that were identified as calreticulin and the lysosomal proteinase cruzipain (a major soluble glycoprotein). The latter but not the former protein disappeared from immunoprecipitates upon chasing cells. Contrary to what happens in mammalian cells, addition of the glucosidase II inhibitor 1-deoxynojirimycin promoted calreticulin–cruzipain interaction. This result is consistent with the known pathway of protein N-glycosylation and oligosaccharide processing occurring in T. cruzi. A treatment of the calreticulin-cruzipain complexes with endo-β-N-acetylglucosaminidase H either before or after addition of anti-calreticulin serum completely disrupted calreticulin–cruzipain interaction. In addition, mature monoglucosylated but not unglucosylated cruzipain isolated from lysosomes was found to interact with recombinant calreticulin. It was concluded that the quality control of glycoprotein folding appeared early in evolution, and that T. cruzi calreticulin binds monoglucosylated oligosaccharides but not the protein moiety of cruzipain. Furthermore, evidence is presented indicating that glucosyltransferase glucosylated cruzipain at its last folding stages. PMID:10233151

Trypanosoma cruzi calreticulin is a lectin that binds monoglucosylated oligosaccharides but not protein moieties of glycoproteins.

PubMed

Labriola, C; Cazzulo, J J; Parodi, A J

1999-05-01

Trypanosoma cruzi is a protozoan parasite that belongs to an early branch in evolution. Although it lacks several features of the pathway of protein N-glycosylation and oligosaccharide processing present in the endoplasmic reticulum of higher eukaryotes, it displays UDP-Glc:glycoprotein glucosyltransferase and glucosidase II activities. It is herewith reported that this protozoan also expresses a calreticulin-like molecule, the third component of the quality control of glycoprotein folding. No calnexin-encoding gene was detected. Recombinant T. cruzi calreticulin specifically recognized free monoglucosylated high-mannose-type oligosaccharides. Addition of anti-calreticulin serum to extracts obtained from cells pulse-chased with [35S]Met plus [35S]Cys immunoprecipitated two proteins that were identified as calreticulin and the lysosomal proteinase cruzipain (a major soluble glycoprotein). The latter but not the former protein disappeared from immunoprecipitates upon chasing cells. Contrary to what happens in mammalian cells, addition of the glucosidase II inhibitor 1-deoxynojirimycin promoted calreticulin-cruzipain interaction. This result is consistent with the known pathway of protein N-glycosylation and oligosaccharide processing occurring in T. cruzi. A treatment of the calreticulin-cruzipain complexes with endo-beta-N-acetylglucosaminidase H either before or after addition of anti-calreticulin serum completely disrupted calreticulin-cruzipain interaction. In addition, mature monoglucosylated but not unglucosylated cruzipain isolated from lysosomes was found to interact with recombinant calreticulin. It was concluded that the quality control of glycoprotein folding appeared early in evolution, and that T. cruzi calreticulin binds monoglucosylated oligosaccharides but not the protein moiety of cruzipain. Furthermore, evidence is presented indicating that glucosyltransferase glucosylated cruzipain at its last folding stages.

The de-ubiquitinating enzyme ataxin-3 does not modulate disease progression in a knock-in mouse model of Huntington disease.

PubMed

Zeng, Li; Tallaksen-Greene, Sara J; Wang, Bo; Albin, Roger L; Paulson, Henry L

2013-01-01

Ataxin-3 is a deubiquitinating enzyme (DUB) that participates in ubiquitin-dependent protein quality control pathways and, based on studies in model systems, may be neuroprotective against toxic polyglutamine proteins such as the Huntington's disease (HD) protein, huntingtin (htt). HD is one of at least nine polyglutamine neurodegenerative diseases in which disease-causing proteins accumulate in ubiquitin-positive inclusions within neurons. In studies crossing mice null for ataxin-3 to an established HD knock-in mouse model (HdhQ200), we tested whether loss of ataxin-3 alters disease progression, perhaps by impairing the clearance of mutant htt or the ubiquitination of inclusions. While loss of ataxin-3 mildly exacerbated age-dependent motor deficits, it did not alter inclusion formation, ubiquitination of inclusions or levels of mutant or normal htt. Ataxin-3, itself a polyglutamine-containing protein with multiple ubiquitin binding domains, was not observed to localize to htt inclusions. Changes in neurotransmitter receptor binding known to occur in HD knock-in mice also were not altered by the loss of ataxin-3, although we unexpectedly observed increased GABAA receptor binding in the striatum of HdhQ200 mice, which has not previously been noted. Finally, we confirmed that CNS levels of hsp70 are decreased in HD mice as has been reported in other HD mouse models, regardless of the presence or absence of ataxin-3. We conclude that while ataxin-3 may participate in protein quality control pathways, it does not critically regulate the handling of mutant htt or contribute to major features of disease pathogenesis in HD.

Parenting in Infancy and Self-Regulation in Preschool: An Investigation of the Role of Attachment History

PubMed Central

Birmingham, R.S.; Bub, K.L.; Vaughn, B.E.

2017-01-01

Parenting and attachment are critical in the emergence of self-regulation (SR) in preschool. However, most studies use general indexes of parenting quality, failing to explore the unique contributions of sensitivity and home quality to SR. Further, the nature of the interplay between parenting and attachment history is not well understood. Using a sample of 938 children from The NICHD Study of Early Child Care and Youth Development, a series of structural equation models were fit to determine whether sensitivity and home quality concurrently predicted SR at 54 months, and whether attachment mediated or moderated these pathways. Results suggest that both sensitivity and home quality uniquely predict SR. Further, these early parenting variables were each indirectly associated with SR through children's attachment history. That is, higher levels of sensitivity and home quality predicted secure attachment history, which, along with parenting, predicted more advanced SR skills at 54 months. No moderated pathways emerged, suggesting attachment history may be best conceptualized as a mediating mechanism. PMID:27894211

IL-1β Signaling Promotes CNS-Intrinsic Immune Control of West Nile Virus Infection

PubMed Central

Ramos, Hilario J.; Lanteri, Marion C.; Blahnik, Gabriele; Negash, Amina; Suthar, Mehul S.; Brassil, Margaret M.; Sodhi, Khushbu; Treuting, Piper M.; Busch, Michael P.; Norris, Philip J.; Gale, Michael

2012-01-01

West Nile virus (WNV) is an emerging flavivirus capable of infecting the central nervous system (CNS) and mediating neuronal cell death and tissue destruction. The processes that promote inflammation and encephalitis within the CNS are important for control of WNV disease but, how inflammatory signaling pathways operate to control CNS infection is not defined. Here, we identify IL-1β signaling and the NLRP3 inflammasome as key host restriction factors involved in viral control and CNS disease associated with WNV infection. Individuals presenting with acute WNV infection displayed elevated levels of IL-1β in their plasma over the course of infection, suggesting a role for IL-1β in WNV immunity. Indeed, we found that in a mouse model of infection, WNV induced the acute production of IL-1β in vivo, and that animals lacking the IL-1 receptor or components involved in inflammasome signaling complex exhibited increased susceptibility to WNV pathogenesis. This outcome associated with increased accumulation of virus within the CNS but not peripheral tissues and was further associated with altered kinetics and magnitude of inflammation, reduced quality of the effector CD8+ T cell response and reduced anti-viral activity within the CNS. Importantly, we found that WNV infection triggers production of IL-1β from cortical neurons. Furthermore, we found that IL-1β signaling synergizes with type I IFN to suppress WNV replication in neurons, thus implicating antiviral activity of IL-1β within neurons and control of virus replication within the CNS. Our studies thus define the NLRP3 inflammasome pathway and IL-1β signaling as key features controlling WNV infection and immunity in the CNS, and reveal a novel role for IL-1β in antiviral action that restricts virus replication in neurons. PMID:23209411

RESRAD model presentation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yu, C.; Faillace, E.; Chen, S.Y.

RESRAD was one of the multimedia models selected by the US Nuclear Regulatory Commission (NRC) to include in its workshop on radiation dose modeling and demonstration of compliance with the radiological criteria for license termination. This paper is a summary of the presentation made at the workshop and focuses on the 10 questions the NRC distributed to all participants prior to the workshop. The code selection criteria, which were solicited by the NRC, for demonstrating compliance with the license termination rule are also included. Among the RESRAD family of codes, RESRAD and RESRAD-BUILD are designed for evaluating radiological contamination inmore » soils and in buildings. Many documents have been published to support the use of these codes. This paper focuses on these two codes. The pathways considered, the databases and parameters used, quality control and quality assurance, benchmarking, verification and validation of these codes, and capabilities as well as limitations of these codes are discussed in detail.« less

sbv IMPROVER: Modern Approach to Systems Biology.

PubMed

Guryanova, Svetlana; Guryanova, Anna

2017-01-01

The increasing amount and variety of data in biosciences call for innovative methods of visualization, scientific verification, and pathway analysis. Novel approaches to biological networks and research quality control are important because of their role in development of new products, improvement, and acceleration of existing health policies and research for novel ways of solving scientific challenges. One such approach is sbv IMPROVER. It is a platform that uses crowdsourcing and verification to create biological networks with easy public access. It contains 120 networks built in Biological Expression Language (BEL) to interpret data from PubMed articles with high-quality verification available for free on the CBN database. Computable, human-readable biological networks with a structured syntax are a powerful way of representing biological information generated from high-density data. This article presents sbv IMPROVER, a crowd-verification approach for the visualization and expansion of biological networks.

The genetic aspects of berries: from field to health.

PubMed

Mazzoni, Luca; Perez-Lopez, Patricia; Giampieri, Francesca; Alvarez-Suarez, Jose M; Gasparrini, Massimiliano; Forbes-Hernandez, Tamara Y; Quiles, Jose L; Mezzetti, Bruno; Battino, Maurizio

2016-01-30

Berries are a relevant source of micronutrients and nonessential phytochemicals, such as polyphenol compounds, that play a synergistic and cumulative role in human health promotion. Several systematic analyses showed that berry phenolics are able to detoxify reactive oxygen and nitrogen species, blocking their production, to intervene in the cell cycle, participating in the transduction and expression of genes involved in apoptosis, and to repair oxidative DNA damage. As a consequence, the improvement of the nutritional quality of berries has become a new quality target of breeding and biotechnological strategies, to control or to increase the content of specific health-related compounds in fruits. This work reviews, on the basis of the in vitro and in vivo evidence, the main berries' phytochemical compounds and their possible mechanisms of action on pathways involved in several type of diseases, with particular attention to cancer, inflammation, neurodegeneration, diabetes and cardiovascular diseases. © 2015 Society of Chemical Industry.

Integrating Hospital Administrative Data to Improve Health Care Efficiency and Outcomes: “The Socrates Story”

PubMed Central

Lawrence, Justin; Delaney, Conor P.

2013-01-01

Evaluation of health care outcomes has become increasingly important as we strive to improve quality and efficiency while controlling cost. Many groups feel that analysis of large datasets will be useful in optimizing resource utilization; however, the ideal blend of clinical and administrative data points has not been developed. Hospitals and health care systems have several tools to measure cost and resource utilization, but the data are often housed in disparate systems that are not integrated and do not permit multisystem analysis. Systems Outcomes and Clinical Resources AdministraTive Efficiency Software (SOCRATES) is a novel data merging, warehousing, analysis, and reporting technology, which brings together disparate hospital administrative systems generating automated or customizable risk-adjusted reports. Used in combination with standardized enhanced care pathways, SOCRATES offers a mechanism to improve the quality and efficiency of care, with the ability to measure real-time changes in outcomes. PMID:24436649

Integrating hospital administrative data to improve health care efficiency and outcomes: "the socrates story".

PubMed

Lawrence, Justin; Delaney, Conor P

2013-03-01

Evaluation of health care outcomes has become increasingly important as we strive to improve quality and efficiency while controlling cost. Many groups feel that analysis of large datasets will be useful in optimizing resource utilization; however, the ideal blend of clinical and administrative data points has not been developed. Hospitals and health care systems have several tools to measure cost and resource utilization, but the data are often housed in disparate systems that are not integrated and do not permit multisystem analysis. Systems Outcomes and Clinical Resources AdministraTive Efficiency Software (SOCRATES) is a novel data merging, warehousing, analysis, and reporting technology, which brings together disparate hospital administrative systems generating automated or customizable risk-adjusted reports. Used in combination with standardized enhanced care pathways, SOCRATES offers a mechanism to improve the quality and efficiency of care, with the ability to measure real-time changes in outcomes.

Metabolically programmed quality control system for dolichol-linked oligosaccharides

PubMed Central

Harada, Yoichiro; Nakajima, Kazuki; Masahara-Negishi, Yuki; Freeze, Hudson H.; Angata, Takashi; Taniguchi, Naoyuki; Suzuki, Tadashi

2013-01-01

The glycolipid Glc3Man9GlcNAc2-pyrophosphate-dolichol serves as the precursor for asparagine (N)-linked protein glycosylation in mammals. The biosynthesis of dolichol-linked oligosaccharides (DLOs) is arrested in low-glucose environments via unknown mechanisms, resulting in abnormal N-glycosylation. Here, we show that under glucose deprivation, DLOs are prematurely degraded during the early stages of DLO biosynthesis by pyrophosphatase, leading to the release of singly phosphorylated oligosaccharides into the cytosol. We identified that the level of GDP-mannose (Man), which serves as a donor substrate for DLO biosynthesis, is substantially reduced under glucose deprivation. We provide evidence that the selective shutdown of the GDP-Man biosynthetic pathway is sufficient to induce the release of phosphorylated oligosaccharides. These results indicate that glucose-regulated metabolic changes in the GDP-Man biosynthetic pathway cause the biosynthetic arrest of DLOs and facilitate their premature degradation by pyrophosphatase. We propose that this degradation system may avoid abnormal N-glycosylation with premature oligosaccharides under conditions that impair efficient DLO biosynthesis. PMID:24218558

CHIP is a novel tumor suppressor in pancreatic cancer and inhibits tumor growth through targeting EGFR

PubMed Central

Wang, Tianxiao; Yang, Jingxuan; Xu, Jianwei; Li, Jian; Cao, Zhe; Zhou, Li; You, Lei; Shu, Hong; Lu, Zhaohui; Li, Huihua; Li, Min; Zhang, Taiping; Zhao, Yupei

2014-01-01

Carboxyl terminus of heat shock protein 70-interacting protein (CHIP) is an E3 ubiquitin ligase that is involved in protein quality control and mediates several tumor-related proteins in many cancers, but the function of CHIP in pancreatic cancer is not known. Here we show that CHIP interacts and ubiquitinates epidermal growth factor receptor (EGFR) for proteasome-mediated degradation in pancreatic cancer cells, thereby inhibiting the activation of EGFR downstream pathways. CHIP suppressed cell proliferation, anchor-independent growth, invasion and migration, as well as enhanced apoptosis induced by erlotinib in vitro and in vivo. The expression of CHIP was decreased in pancreatic cancer tissues or sera. Low CHIP expression in tumor tissues was correlated with tumor differentiation and shorter overall survival. These observations indicate that CHIP serves as a novel tumor suppressor by down-regulating EGFR pathway in pancreatic cancer cells, decreased expression of CHIP was associated with poor prognosis in pancreatic cancer. PMID:24722501

The Roles of PINK1, Parkin and Mitochondrial Fidelity in Parkinson's Disease

PubMed Central

Pickrell, Alicia M.; Youle, Richard J.

2015-01-01

Understanding the function of genes mutated in hereditary forms of Parkinson's disease yields insight into disease etiology and reveals new pathways in cell biology. Although mutations or variants in many genes increase the susceptibility to Parkinson's disease, only a handful of monogenic causes of Parkinsonism have been identified. Biochemical and genetic studies reveal that the products of two genes that are mutated in autosomal recessive Parkinsonism, PINK1 and Parkin, normally work together in the same pathway to govern mitochondrial quality control, bolstering previous evidence that mitochondrial damage is involved in Parkinson's disease. PINK1 accumulates on the outer membrane of damaged mitochondria, activates Parkin's E3 ubiquitin ligase activity and recruits Parkin to the dysfunctional mitochondrion. Then, Parkin ubiquitinates outer mitochondrial membrane proteins to trigger selective autophagy. This review covers the normal functions that PINK1 and Parkin play within cells, their molecular mechanisms of action, and the pathophysiological consequences of their loss. PMID:25611507

Culture-general and -specific associations of attachment avoidance and anxiety with perceived parental warmth and psychological control among Turk and Belgian adolescents.

PubMed

Güngör, Derya; Bornstein, Marc H

2010-10-01

Both the adolescent peer attachment and perceived parenting style literatures emphasize the role of the quality of the parent-child relationship in children's healthy adjustment beyond the family, but few studies have investigated links between adolescents' peer attachment and perceptions of parenting. We investigate relations of adolescents' perceptions of warmth and psychological control from parents with avoidance and anxiety in attachment to close friends in two contrasting cultures. Altogether, 262 Turk and 263 Belgian youth between 14 and 18 years of age participated. Cross-culturally, attachment avoidance was negatively related to maternal warmth, and attachment anxiety positively related to maternal and paternal control and negatively to paternal warmth. Beyond these general relations, attachment avoidance was associated with paternal psychological control in Belgians but not in Turks. The study provides cross-cultural evidence for specific relations between peer attachment and perceived parenting and suggests a culture-specific pathway for the development of attachment avoidance.

Atomic-scale control of magnetic anisotropy via novel spin–orbit coupling effect in La 2/3Sr 1/3MnO 3/SrIrO 3 superlattices

DOE PAGES

Yi, Di; Liu, Jian; Hsu, Shang-Lin; ...

2016-05-19

Magnetic anisotropy (MA) is one of the most important material properties for modern spintronic devices. Conventional manipulation of the intrinsic MA, i.e., magnetocrystalline anisotropy (MCA), typically depends upon crystal symmetry. Extrinsic control over the MA is usually achieved by introducing shape anisotropy or exchange bias from another magnetically ordered material. Here we demonstrate a pathway to manipulate MA of 3d transition-metal oxides (TMOs) by digitally inserting nonmagnetic 5d TMOs with pronounced spin-orbit coupling (SOC). High-quality superlattices comprising ferromagnetic La 2/3Sr 1/3MnO 3 (LSMO) and paramagnetic SrIrO 3 (SIO) are synthesized with the precise control of thickness at the atomic scale.more » Magnetic easy-axis reorientation is observed by controlling the dimensionality of SIO, mediated through the emergence of a novel spin-orbit state within the nominally paramagnetic SIO.« less

Alternative Pathways in Family Child Care Quality Rating and Improvement Systems

ERIC Educational Resources Information Center

Kelton, Robyn E.; Talan, Teri N.; Bloom, Paula J.

2013-01-01

As research continues to underscore the positive impact high-quality early childhood programs have on young children, numerous states have implemented quality rating and improvement systems (QRIS) to measure and improve the services young children receive across a wide range of early learning settings. These state systems range from two to five…

In Pursuit of Teacher Quality: Three Models of Success.

ERIC Educational Resources Information Center

Dandy, Evelyn; O'Dell, Sandra; McKinney, Marilyn; Perkins, Peggy G.; Miller, Susan Peterson; Reiman, Alan; Peace, Sandra DeAngelis; Williams, Doris Terry; Duncan, JoAnn Hines

This document is comprised of three papers by various authors, summarizing three different models of programs that successfully promote teacher quality that were introduced at the National Conference on Teacher Quality in January 2000, hosted by the U.S. Department of Education. The first program described, the Pathways to Teaching Program of…

Overcoming Exclusion through Quality Schooling. Pathways to Access. Research Monograph No. 65

ERIC Educational Resources Information Center

Govinda, R.; Bandyopadhyay, Madhumita

2011-01-01

In the era of globalisation, provision of quality education is increasingly gaining importance across the world. Like elsewhere, it has already been realised in India that equal attention is needed simultaneously on access, equity and quality to achieve the goal of universalisation of elementary education. It has also been experienced that…

The governance of quality management in dutch health care: new developments and strategic challenges.

PubMed

Maarse, J A M; Ruwaard, D; Spreeuwenberg, C

2013-01-01

This article gives a brief sketch of quality management in Dutch health care. Our focus is upon the governance of guideline development and quality measurement. Governance is conceptualized as the structure and process of steering of quality management. The governance structure of guideline development in the Netherlands can be conceptualized as a network without central coordination. Much depends upon the self-initiative of stakeholders. A similar picture can be found in quality measurement. Special attention is given to the development of care standards for chronic disease. Care standards have a broader scope than guidelines and take an explicit patient perspective. They not only contain evidence-based and up-to-date guidelines for the care pathway but also contain standards for self-management. Furthermore, they comprise a set of indicators for measuring the quality of care of the entire pathway covered by the standard. The final part of the article discusses the mission, tasks and strategic challenges of the newly established National Health Care Institute (Zorginstituut Nederland), which is scheduled to be operative in 2013.

[Review of the initiation and development of the conception of clinical pathway].

PubMed

Wang, Zhen-E; Shangguan, Qing-Miao; Wu, Ping

2010-11-01

Dupont, an American company, used the concept of "pathway" in industry to improve the quality of their products in 1957. In the 1970s, under the pressure of a rise in medical costs, some people realized the concept of the "key pathway" could be used in medicine too. In 1985, the Boston New England Medical Center Hospital (NEMC) succeeded in using the concept of the clinical pathway in medical practice, and afterwards the concept gradually found worldwide application. In 1996, the Fourth Military Medical University in China reported the application of clinical pathway in America. The West China Hospital began to try out the clinical pathway in 1998 and the concept gradually found application in China.

Unannounced versus announced hospital surveys: a nationwide cluster-randomized controlled trial.

PubMed

Ehlers, Lars Holger; Simonsen, Katherina Beltoft; Jensen, Morten Berg; Rasmussen, Gitte Sand; Olesen, Anne Vingaard

2017-06-01

To evaluate the effectiveness of unannounced versus announced surveys in detecting non-compliance with accreditation standards in public hospitals. A nationwide cluster-randomized controlled trial. All public hospitals in Denmark were invited. Twenty-three hospitals (77%) (3 university hospitals, 5 psychiatric hospitals and 15 general hospitals) agreed to participate. Twelve hospitals were randomized to receive unannounced surveys (intervention group) and eleven hospitals to receive announced surveys (control group). We hypothesized that the hospitals receiving the unannounced surveys would reveal a higher degree of non-compliance with accreditation standards than the hospitals receiving announced surveys. Nine surveyors trained and employed by the Danish Institute for Quality and Accreditation in Healthcare (IKAS) were randomized into teams and conducted all surveys. The outcome was the surveyors' assessment of the hospitals' level of compliance with 113 performance indicators-an abbreviated set of the Danish Healthcare Quality Programme (DDKM) version 2, covering organizational standards, patient pathway standards and patient safety standards. Compliance with performance indicators was analyzed using binomial regression analysis with bootstrapped robust standard errors. In all, 16 202 measurements were acceptable for data analysis. The risk of observing non-compliance with performance indicators for the intervention group compared with the control group was statistically insignificant (risk difference (RD) = -0.6 percentage points [-2.51-1.31], P = 0.54). A converged analysis of the six patient safety critical standards, requiring 100% compliance to gain accreditation status revealed no statistically significant difference (RD = -0.78 percentage points [-4.01-2.44], P = 0.99). Unannounced hospital surveys were not more effective than announced surveys in detecting quality problems in Danish hospitals. ClinicalTrials.gov NCT02348567, https://clinicaltrials.gov/ct2/show/NCT02348567?term=NCT02348567. © The Author 2017. Published by Oxford University Press in association with the International Society for Quality in Health Care.

Effects of canonical NF-κB signaling pathway on the proliferation and odonto/osteogenic differentiation of human stem cells from apical papilla.

PubMed

Li, Junjun; Yan, Ming; Wang, Zilu; Jing, Shuanglin; Li, Yao; Liu, Genxia; Yu, Jinhua; Fan, Zhipeng

2014-01-01

NF-κB signaling pathway plays a complicated role in the biological functions of mesenchymal stem cells. However, the effects of NF-κB pathway on the odonto/osteogenic differentiation of stem cells from apical papilla (SCAPs) remain unclear. The present study was designed to evaluate the effects of canonical NF-κB pathway on the osteo/odontogenic capacity of SCAPs in vitro. Western blot results demonstrated that NF-κB pathway in SCAPs was successfully activated by TNF-α or blocked by BMS-345541. NF-κB pathway-activated SCAPs presented a higher proliferation activity compared with control groups, as indicated by dimethyl-thiazol-diphenyl tetrazolium bromide assay (MTT) and flow cytometry assay (FCM). Wound scratch assay revealed that NF-κB pathway-activated SCAPs presented an improved migration capacity, enhanced alkaline phosphatase (ALP) activity, and upregulated mineralization capacity of SCAPs, as compared with control groups. Meanwhile, the odonto/osteogenic markers (ALP/ALP, RUNX2/RUNX2, OSX/OSX, OCN/OCN, OPN/OPN, BSP/BSP, DSPP/DSP, and DMP-1/DMP-1) in NF-κB pathway-activated SCAPs were also significantly upregulated as compared with control groups at both protein and mRNA levels. However, NF-κB pathway-inhibited SCAPs exhibited a lower proliferation/migration capacity, and decreased odonto/osteogenic ability in comparison with control groups. Our findings suggest that classical NF-κB pathway plays a paramount role in the proliferation and committed differentiation of SCAPs.

Holistic needs assessment and care plans for women with gynaecological cancer: do they improve cancer-specific health-related quality of life? A randomised controlled trial using mixed methods.

PubMed

Sandsund, Catherine; Towers, Richard; Thomas, Karen; Tigue, Ruth; Lalji, Amyn; Fernandes, Andreia; Doyle, Natalie; Jordan, Jake; Gage, Heather; Shaw, Clare

2017-08-28

Holistic needs assessment (HNA) and care planning are proposed to address unmet needs of people treated for cancer. We tested whether HNA and care planning by an allied health professional improved cancer-specific quality of life for women following curative treatment for stage I-III gynaecological cancer. Consecutive women were invited to participate in a randomised controlled study (HNA and care planning vs usual care) at a UK cancer centre. Data were collected by questionnaire at baseline, 3 and 6 months. The outcomes were 6-month change in European Organisation for Research and Treatment of Cancer (EORTC) Quality of Life Questionnaire-C30 (version 3), global score (primary) and, in EORTC subscales, generic quality of life and self-efficacy (secondary). The study was blinded for data management and analysis. Differences in outcomes were compared between groups. Health service utilisation and quality-adjusted life years (QALY) (from Short Form-6) were gathered for a cost-effectiveness analysis. Thematic analysis was used to interpret data from an exit interview. 150 women consented (75 per group); 10 undertook interviews. For 124 participants (61 intervention, 63 controls) with complete data, no statistically significant differences were seen between groups in the primary endpoint. The majority of those interviewed reported important personal gains they attributed to the intervention, which reflected trends to improvement seen in EORTC functional and symptom scales. Economic analysis suggests a 62% probability of cost-effectiveness at a £30 000/QALY threshold. Care plan development with an allied health professional is cost-effective, acceptable and useful for some women treated for stage I-III gynaecological cancer. We recommend its introduction early in the pathway to support person-centred care. © Article author(s) (or their employer(s) unless otherwise stated in the text of the article) 2017. All rights reserved. No commercial use is permitted unless otherwise expressly granted.

Proteomic insights into the protective mechanisms of an in vitro oxidative stress model of early stage Parkinson's disease.

PubMed

Bauereis, Brian; Haskins, William E; Lebaron, Richard G; Renthal, Robert

2011-01-13

Previous studies in Parkinson's disease (PD) models suggest that early events along the path to neurodegeneration involve activation of the ubiquitin-proteasome system (UPS), endoplasmic reticulum-associated degradation (ERAD), and the unfolded protein response (UPR) pathways, in both the sporadic and familial forms of the disease, and thus ER stress may be a common feature. Furthermore, impairments in protein degradation have been linked to oxidative stress as well as pathways associated with ER stress. We hypothesize that oxidative stress is a primary initiator in a multi-factorial cascade driving dopaminergic (DA) neurons towards death in the early stages of the disease. We now report results from proteomic analysis of a rotenone-induced oxidative stress model of PD in the human neuroblastoma cell line, SH-SY5Y. Cells were exposed to sub-micromolar concentrations of rotenone for 48h prior to whole cell protein extraction and shotgun proteomic analysis. Evidence for activation of the UPR comes from our observation of up-regulated binding immunoglobulin protein (BiP), heat shock proteins, and foldases. We also observed up-regulation of proteins that contribute to the degradation of misfolded or unfolded proteins controlled by the UPS and ERAD pathways. Activation of the UPR may allow neurons to maintain protein homeostasis in the cytosol and ER despite an increase in reactive oxygen species due to oxidative stress, and activation of the UPS and ERAD may further augment clean-up and quality control in the cell. Copyright © 2010 Elsevier Ireland Ltd. All rights reserved.

R2R3 MYB transcription factors: key regulators of the flavonoid biosynthetic pathway in grapevine.

PubMed

Czemmel, Stefan; Heppel, Simon C; Bogs, Jochen

2012-06-01

Flavonoids compose one of the most abundant and important subgroups of secondary metabolites with more than 6,000 compounds detected so far in higher plants. They are found in various compositions and concentrations in nearly all plant tissues. Besides the attraction of pollinators and dispersers to fruits and flowers, flavonoids also protect against a plethora of stresses including pathogen attack, wounding and UV irradiation. Flavonoid content and composition of fruits such as grapes, bilberries, strawberries and apples as well as food extracts such as green tea, wine and chocolate have been associated with fruit quality including taste, colour and health-promoting effects. To unravel the beneficial potentials of flavonoids on fruit quality, research has been focused recently on the molecular basis of flavonoid biosynthesis and regulation in economically important fruit-producing plants such as grapevine (Vitis vinifera L.). Transcription factors and genes encoding biosynthetic enzymes have been characterized, studies that set a benchmark for future research on the regulatory networks controlling flavonoid biosynthesis and diversity. This review summarizes recent advances in the knowledge of regulatory cascades involved in flavonoid biosynthesis in grapevine. Transcriptional regulation of flavonoid biosynthesis during berry development is highlighted, with a particular focus on MYB transcription factors as molecular clocks, key regulators and powerful biotechnological tools to identify novel pathway enzymes to optimize flavonoid content and composition in grapes.

Estimating Environmental Co-benefits of U.S. GHG Reduction Pathways Using the GCAM-USA Integrated Assessment Model

EPA Science Inventory

Previous studies have shown that mitigating climate change through curbing greenhouse gas (GHG) emissions can bring about substantial environmental co-benefits, such as for air quality and reductions in energy-related water demand. A variety of pathways are available for reducing...

Regulators of homologous recombination repair as novel targets for cancer treatment

PubMed Central

Krajewska, Małgorzata; Fehrmann, Rudolf S. N.; de Vries, Elisabeth G. E.; van Vugt, Marcel A. T. M.

2015-01-01

To cope with DNA damage, cells possess a complex signaling network called the ‘DNA damage response’, which coordinates cell cycle control with DNA repair. The importance of this network is underscored by the cancer predisposition that frequently goes along with hereditary mutations in DNA repair genes. One especially important DNA repair pathway in this respect is homologous recombination (HR) repair. Defects in HR repair are observed in various cancers, including hereditary breast, and ovarian cancer. Intriguingly, tumor cells with defective HR repair show increased sensitivity to chemotherapeutic reagents, including platinum-containing agents. These observations suggest that HR-proficient tumor cells might be sensitized to chemotherapeutics if HR repair could be therapeutically inactivated. HR repair is an extensively regulated process, which depends strongly on the activity of various other pathways, including cell cycle pathways, protein-control pathways, and growth factor-activated receptor signaling pathways. In this review, we discuss how the mechanistic wiring of HR is controlled by cell-intrinsic or extracellular pathways. Furthermore, we have performed a meta-analysis on available genome-wide RNA interference studies to identify additional pathways that control HR repair. Finally, we discuss how these HR-regulatory pathways may provide therapeutic targets in the context of radio/chemosensitization. PMID:25852742

Introducing care pathway commissioning to primary dental care: measuring performance.

PubMed

Harris, R; Bridgman, C; Ahmad, M; Bowes, L; Haley, R; Saleem, S; Singh, R; Taylor, S

2011-12-09

Care pathways have been used in a variety of ways: firstly to support quality improvement through standardising clinical processes, but also for secondary purposes, by purchasers of healthcare, to monitor activity and health outcomes and to commission services. This paper focuses on reporting a secondary use of care pathways: to commission and monitor performance of primary dental care services. Findings of a project involving three dental practices implementing a system based on rating patients according to their risk of disease and need for care are outlined. Data from surgery-based clinical databases and interviews from commissioners and providers are reported. The use of both process and outcome key performance indicators in this context is discussed, as well as issues which arise such as attributability of outcome measures and strategic approaches to improving quality of care.

MO-F-211-01: Methods for Completing Practice Quality Improvement (PQI).

PubMed

Johnson, J; Brown, K; Ibbott, G; Pawlicki, T

2012-06-01

Practice Quality Improvement (PQI) is becoming an expected part of routine practice in healthcare as an approach to provide more efficient, effective and high quality care. Additionally, as part of the ABR's Maintenance of Certification (MOC) pathway, medical physicists are now expected to complete a PQI project. This session will describe the history behind and benefits of the ABR's MOC program, provide details of quality improvement methods and how to successfully complete a PQI project. PQI methods include various commonly used engineering and management tools. The Plan-Do-Study-Act (PDSA) cycle will be presented as one project planning and implementation tool. Other PQI analysis instruments such as flowcharts, Pareto charts, process control charts and fishbone diagrams will also be explained with examples. Cause analysis, solution development and implementation, and post-implementation measurement will be presented. Project identification and definition as well as appropriate measurement tool selection will be offered. Methods to choose key quality metrics (key quality indicators) will also be addressed. Several sample PQI projects and templates available through the AAPM and other organizations will be described. At least three examples of completed PQI projects will be shared. 1. Identify and define a PQI project 2. Identify and select measurement methods/techniques for use with the PQI project 3. Describe example(s) of completed projects. © 2012 American Association of Physicists in Medicine.

Drosophila insulin and target of rapamycin (TOR) pathways regulate GSK3 beta activity to control Myc stability and determine Myc expression in vivo.

PubMed

Parisi, Federica; Riccardo, Sara; Daniel, Margaret; Saqcena, Mahesh; Kundu, Nandini; Pession, Annalisa; Grifoni, Daniela; Stocker, Hugo; Tabak, Esteban; Bellosta, Paola

2011-09-27

Genetic studies in Drosophila melanogaster reveal an important role for Myc in controlling growth. Similar studies have also shown how components of the insulin and target of rapamycin (TOR) pathways are key regulators of growth. Despite a few suggestions that Myc transcriptional activity lies downstream of these pathways, a molecular mechanism linking these signaling pathways to Myc has not been clearly described. Using biochemical and genetic approaches we tried to identify novel mechanisms that control Myc activity upon activation of insulin and TOR signaling pathways. Our biochemical studies show that insulin induces Myc protein accumulation in Drosophila S2 cells, which correlates with a decrease in the activity of glycogen synthase kinase 3-beta (GSK3β ) a kinase that is responsible for Myc protein degradation. Induction of Myc by insulin is inhibited by the presence of the TOR inhibitor rapamycin, suggesting that insulin-induced Myc protein accumulation depends on the activation of TOR complex 1. Treatment with amino acids that directly activate the TOR pathway results in Myc protein accumulation, which also depends on the ability of S6K kinase to inhibit GSK3β activity. Myc upregulation by insulin and TOR pathways is a mechanism conserved in cells from the wing imaginal disc, where expression of Dp110 and Rheb also induces Myc protein accumulation, while inhibition of insulin and TOR pathways result in the opposite effect. Our functional analysis, aimed at quantifying the relative contribution of Myc to ommatidial growth downstream of insulin and TOR pathways, revealed that Myc activity is necessary to sustain the proliferation of cells from the ommatidia upon Dp110 expression, while its contribution downstream of TOR is significant to control the size of the ommatidia. Our study presents novel evidence that Myc activity acts downstream of insulin and TOR pathways to control growth in Drosophila. At the biochemical level we found that both these pathways converge at GSK3β to control Myc protein stability, while our genetic analysis shows that insulin and TOR pathways have different requirements for Myc activity during development of the eye, suggesting that Myc might be differentially induced by these pathways during growth or proliferation of cells that make up the ommatidia.

Fluorescence-based bioassays for the detection and evaluation of food materials.

PubMed

Nishi, Kentaro; Isobe, Shin-Ichiro; Zhu, Yun; Kiyama, Ryoiti

2015-10-13

We summarize here the recent progress in fluorescence-based bioassays for the detection and evaluation of food materials by focusing on fluorescent dyes used in bioassays and applications of these assays for food safety, quality and efficacy. Fluorescent dyes have been used in various bioassays, such as biosensing, cell assay, energy transfer-based assay, probing, protein/immunological assay and microarray/biochip assay. Among the arrays used in microarray/biochip assay, fluorescence-based microarrays/biochips, such as antibody/protein microarrays, bead/suspension arrays, capillary/sensor arrays, DNA microarrays/polymerase chain reaction (PCR)-based arrays, glycan/lectin arrays, immunoassay/enzyme-linked immunosorbent assay (ELISA)-based arrays, microfluidic chips and tissue arrays, have been developed and used for the assessment of allergy/poisoning/toxicity, contamination and efficacy/mechanism, and quality control/safety. DNA microarray assays have been used widely for food safety and quality as well as searches for active components. DNA microarray-based gene expression profiling may be useful for such purposes due to its advantages in the evaluation of pathway-based intracellular signaling in response to food materials.

Fluorescence-Based Bioassays for the Detection and Evaluation of Food Materials

PubMed Central

Nishi, Kentaro; Isobe, Shin-Ichiro; Zhu, Yun; Kiyama, Ryoiti

2015-01-01

We summarize here the recent progress in fluorescence-based bioassays for the detection and evaluation of food materials by focusing on fluorescent dyes used in bioassays and applications of these assays for food safety, quality and efficacy. Fluorescent dyes have been used in various bioassays, such as biosensing, cell assay, energy transfer-based assay, probing, protein/immunological assay and microarray/biochip assay. Among the arrays used in microarray/biochip assay, fluorescence-based microarrays/biochips, such as antibody/protein microarrays, bead/suspension arrays, capillary/sensor arrays, DNA microarrays/polymerase chain reaction (PCR)-based arrays, glycan/lectin arrays, immunoassay/enzyme-linked immunosorbent assay (ELISA)-based arrays, microfluidic chips and tissue arrays, have been developed and used for the assessment of allergy/poisoning/toxicity, contamination and efficacy/mechanism, and quality control/safety. DNA microarray assays have been used widely for food safety and quality as well as searches for active components. DNA microarray-based gene expression profiling may be useful for such purposes due to its advantages in the evaluation of pathway-based intracellular signaling in response to food materials. PMID:26473869

Resilience in high-risk adolescents of mothers with recurrent depressive disorder: The contribution of fathers.

PubMed

Mahedy, Liam; Harold, Gordon T; Maughan, Barbara; Gardner, Frances; Araya, Ricardo; Bevan Jones, Rhys; Hammerton, Gemma; Sellers, Ruth; Thapar, Anita; Collishaw, Stephan

2018-06-01

This study examines the role of paternal emotional support as a resilience promoter in offspring of mothers with depression by considering the role of fathers' mental health and the quality of the couple relationship. Two hundred and sixty-five mothers with recurrent unipolar depression, partners and adolescents from Wales were assessed. Paternal emotional support, couple relationship quality, and paternal depression were assessed at baseline; adolescent mental health symptoms were assessed using the Child and Adolescent Psychiatric Assessment at follow-up. Results showed evidence of an indirect pathway whereby couple relationship quality predicted paternal emotional support (β = -.21, 95% CI [-.34, -.08]; p = .002) which in turn predicted adolescent depression (β = -.18, 95% CI [-.33, -.04]; p = .02), but not disruptive behaviours (β = -.08, 95% CI [-.22, .07]; p = .30), after controlling for relevant confounders. The findings highlight that fathers and the broader family system play an important role in enhancing resilience to depression symptoms in at-risk adolescents. Copyright © 2018 The Authors. Published by Elsevier Ltd.. All rights reserved.

Transcriptome sequencing and annotation of the microalgae Dunaliella tertiolecta: Pathway description and gene discovery for production of next-generation biofuels

PubMed Central

2011-01-01

Background Biodiesel or ethanol derived from lipids or starch produced by microalgae may overcome many of the sustainability challenges previously ascribed to petroleum-based fuels and first generation plant-based biofuels. The paucity of microalgae genome sequences, however, limits gene-based biofuel feedstock optimization studies. Here we describe the sequencing and de novo transcriptome assembly for the non-model microalgae species, Dunaliella tertiolecta, and identify pathways and genes of importance related to biofuel production. Results Next generation DNA pyrosequencing technology applied to D. tertiolecta transcripts produced 1,363,336 high quality reads with an average length of 400 bases. Following quality and size trimming, ~ 45% of the high quality reads were assembled into 33,307 isotigs with a 31-fold coverage and 376,482 singletons. Assembled sequences and singletons were subjected to BLAST similarity searches and annotated with Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) orthology (KO) identifiers. These analyses identified the majority of lipid and starch biosynthesis and catabolism pathways in D. tertiolecta. Conclusions The construction of metabolic pathways involved in the biosynthesis and catabolism of fatty acids, triacylglycrols, and starch in D. tertiolecta as well as the assembled transcriptome provide a foundation for the molecular genetics and functional genomics required to direct metabolic engineering efforts that seek to enhance the quantity and character of microalgae-based biofuel feedstock. PMID:21401935

Identification of differential pathways in papillary thyroid carcinoma utilizing pathway co-expression analysis.

PubMed

Qiu, Wei-Hai; Chen, Gui-Yan; Cui, Lu; Zhang, Ting-Ming; Wei, Feng; Yang, Yong

2016-01-01

To identify differential pathways between papillary thyroid carcinoma (PTC) patients and normal controls utilizing a novel method which combined pathway with co-expression network. The proposed method included three steps. In the first step, we conducted pretreatments for background pathways and gained representative pathways in PTC. Subsequently, a co-expression network for representative pathways was constructed using empirical Bayes (EB) approach to assign a weight value for each pathway. Finally, random model was extracted to set the thresholds of identifying differential pathways. We obtained 1267 representative pathways and their weight values based on the co-expressed pathway network, and then by meeting the criterion (Weight > 0.0296), 87 differential pathways in total across PTC patients and normal controls were identified. The top three ranked differential pathways were CREB phosphorylation, attachment of GPI anchor to urokinase plasminogen activator receptor (uPAR) and loss of function of SMAD2/3 in cancer. In conclusion, we successfully identified differential pathways (such as CREB phosphorylation, attachment of GPI anchor to uPAR and post-translational modification: synthesis of GPI-anchored proteins) for PTC using the proposed pathway co-expression method, and these pathways might be potential biomarkers for target therapy and detection of PTC.

Advanced Sensors and Controls for Building Applications: Market Assessment and Potential R&D Pathways

DOE Office of Scientific and Technical Information (OSTI.GOV)

Brambley, M. R.; Haves, P.; McDonald, S. C.

2005-04-01

This document provides a market assessment of existing building sensors and controls and presents a range of technology pathways (R&D options) for pursuing advanced sensors and building control strategies.

PATHway I: design and rationale for the investigation of the feasibility, clinical effectiveness and cost-effectiveness of a technology-enabled cardiac rehabilitation platform.

PubMed

Claes, Jomme; Buys, Roselien; Woods, Catherine; Briggs, Andrew; Geue, Claudia; Aitken, Moira; Moyna, Niall; Moran, Kieran; McCaffrey, Noel; Chouvarda, Ioanna; Walsh, Deirdre; Budts, Werner; Filos, Dimitris; Triantafyllidis, Andreas; Maglaveras, Nicos; Cornelissen, Véronique A

2017-06-30

Exercise-based cardiac rehabilitation (CR) independently alters the clinical course of cardiovascular diseases resulting in a significant reduction in all-cause and cardiac mortality. However, only 15%-30% of all eligible patients participate in a phase 2 ambulatory programme. The uptake rate of community-based programmes following phase 2 CR and adherence to long-term exercise is extremely poor. Newer care models, involving telerehabilitation programmes that are delivered remotely, show considerable promise for increasing adherence. In this view, the PATHway (Physical Activity Towards Health) platform was developed and now needs to be evaluated in terms of its feasibility and clinical efficacy. In a multicentre randomised controlled pilot trial, 120 participants (m/f, age 40-80 years) completing a phase 2 ambulatory CR programme will be randomised on a 1:1 basis to PATHway or usual care. PATHway involves a comprehensive, internet-enabled, sensor-based home CR platform and provides individualised heart rate monitored exercise programmes (exerclasses and exergames) as the basis on which to provide a personalised lifestyle intervention programme. The control group will receive usual care. Study outcomes will be assessed at baseline, 3 months and 6 months after completion of phase 2 of the CR programme. The primary outcome is the change in active energy expenditure. Secondary outcomes include cardiopulmonary endurance capacity, muscle strength, body composition, cardiovascular risk factors, peripheral endothelial vascular function, patient satisfaction, health-related quality of life (HRQoL), well-being, mediators of behaviour change and safety. HRQoL and healthcare costs will be taken into account in cost-effectiveness evaluation. The study will be conducted in accordance with the Declaration of Helsinki. This protocol has been approved by the director and clinical director of the PATHway study and by the ethical committee of each participating site. Results will be disseminated via peer-reviewed scientific journals and presentations at congresses and events. NCT02717806. This trial is currently in the pre-results stage. © Article author(s) (or their employer(s) unless otherwise stated in the text of the article) 2017. All rights reserved. No commercial use is permitted unless otherwise expressly granted.

Inflammatory Pathway Genes Associated with Inter-Individual Variability in the Trajectories of Morning and Evening Fatigue in Patients Receiving Chemotherapy

PubMed Central

Wright, Fay; Hammer, Marilyn; Paul, Steven M.; Aouizerat, Bradley E.; Kober, Kord M.; Conley, Yvette P.; Cooper, Bruce A.; Dunn, Laura B.; Levine, Jon D.; Melkus, Gail DEramo; Miaskowski, Christine

2017-01-01

Fatigue, a highly prevalent and distressing symptom during chemotherapy (CTX), demonstrates diurnal and interindividual variability in severity. Little is known about the associations between variations in genes involved in inflammatory processes and morning and evening fatigue severity during CTX. The purposes of this study, in a sample of oncology patients (N=543) with breast, gastrointestinal (GI), gynecological (GYN), or lung cancer who received two cycles of CTX, were to determine whether variations in genes involved in inflammatory processes were associated with inter-individual variability in initial levels as well as in the trajectories of morning and evening fatigue. Patients completed the Lee Fatigue Scale to determine morning and evening fatigue severity a total of six times over two cycles of CTX. Using a whole exome array, 309 single nucleotide polymorphisms among the 64 candidate genes that passed all quality control filters were evaluated using hierarchical linear modeling (HLM). Based on the results of the HLM analyses, the final SNPs were evaluated for their potential impact on protein function using two bioinformational tools. The following inflammatory pathways were represented: chemokines (3 genes); cytokines (12 genes); inflammasome (11 genes); Janus kinase/signal transducers and activators of transcription (JAK/STAT, 10 genes); mitogen-activated protein kinase/jun amino-terminal kinases (MAPK/JNK, 3 genes); nuclear factor-kappa beta (NFkB, 18 genes); and NFkB and MAP/JNK (7 genes). After controlling for self-reported and genomic estimates of race and ethnicity, polymorphisms in six genes from the cytokine (2 genes); inflammasome (2 genes); and NFkB (2 genes) pathways were associated with both morning and evening fatigue. Polymorphisms in six genes from the inflammasome (1 gene); JAK/STAT (1 gene); and NFkB (4 genes) pathways were associated with only morning fatigue. Polymorphisms in three genes from the inflammasome (2 genes) and the NFkB (1 gene) pathways were associated with only evening fatigue. Taken together, these findings add to the growing body of evidence that suggests that morning and evening fatigue are distinct symptoms. PMID:28110208

Comparing the transcriptomes of embryos from domesticated and wild Atlantic salmon (Salmo salar L.) stocks and examining factors that influence heritability of gene expression.

PubMed

Bicskei, Beatrix; Taggart, John B; Glover, Kevin A; Bron, James E

2016-03-17

Due to selective breeding, domesticated and wild Atlantic salmon are genetically diverged, which raises concerns about farmed escapees having the potential to alter the genetic composition of wild populations and thereby disrupting local adaptation. Documenting transcriptional differences between wild and domesticated stocks under controlled conditions is one way to explore the consequences of domestication and selection. We compared the transcriptomes of wild and domesticated Atlantic salmon embryos, by using a custom 44k oligonucleotide microarray to identify perturbed gene pathways between the two stocks, and to document the inheritance patterns of differentially-expressed genes by examining gene expression in their reciprocal hybrids. Data from 24 array interrogations were analysed: four reciprocal cross types (W♀ × W♂, D♀ × W♂; W♀ × D♂, D♀ × D♂) × six biological replicates. A common set of 31,491 features on the microarrays passed quality control, of which about 62 % were assigned a KEGG Orthology number. A total of 6037 distinct genes were identified for gene-set enrichment/pathway analysis. The most highly enriched functional groups that were perturbed between the two stocks were cellular signalling and immune system, ribosome and RNA transport, and focal adhesion and gap junction pathways, relating to cell communication and cell adhesion molecules. Most transcripts that were differentially expressed between the stocks were governed by additive gene interaction (33 to 42 %). Maternal dominance and over-dominance were also prevalent modes of inheritance, with no convincing evidence for a stock effect. Our data indicate that even at this relatively early developmental stage, transcriptional differences exist between the two stocks and affect pathways that are relevant to wild versus domesticated environments. Many of the identified differentially perturbed pathways are involved in organogenesis, which is expected to be an active process at the eyed egg stage. The dominant effects are more largely due to the maternal line than to the origin of the stock. This finding is particularly relevant in the context of potential introgression between farmed and wild fish, since female escapees tend to have a higher spawning success rate compared to males.

Estradiol targets T cell signaling pathways in human systemic lupus.

PubMed

Walters, Emily; Rider, Virginia; Abdou, Nabih I; Greenwell, Cindy; Svojanovsky, Stan; Smith, Peter; Kimler, Bruce F

2009-12-01

The major risk factor for developing systemic lupus erythematosus (SLE) is being female. The present study utilized gene profiles of activated T cells from females with SLE and healthy controls to identify signaling pathways uniquely regulated by estradiol that could contribute to SLE pathogenesis. Selected downstream pathway genes (+/- estradiol) were measured by real time polymerase chain amplification. Estradiol uniquely upregulated six pathways in SLE T cells that control T cell function including interferon-alpha signaling. Measurement of interferon-alpha pathway target gene expression revealed significant differences (p= 0.043) in DRIP150 (+/- estradiol) in SLE T cell samples while IFIT1 expression was bimodal and correlated moderately (r= 0.55) with disease activity. The results indicate that estradiol alters signaling pathways in activated SLE T cells that control T cell function. Differential expression of transcriptional coactivators could influence estrogen-dependent gene regulation in T cell signaling and contribute to SLE onset and disease pathogenesis.

Disentangling nutrient concentrations trends in transfer pathways of agricultural watersheds

NASA Astrophysics Data System (ADS)

Mellander, P. E.; Jordan, P.

2017-12-01

Targeted schemes designed to attenuate agricultural pollution to water are needed to reach goals of sustainable food production. Such approaches require insight into temporal and spatial variability in the most representative flows and active pollution transfer pathways. Interpreting changes in total stream flow can be misleading since some changes may only be apparent in specific pathways. The aim of this study was to investigate changing land use pressures on water quality. The objectives were to assess intra-annual and inter-annual changes in phosphorus (P) and nitrogen (N) concentrations and loads in apportioned pathways. Pathways were separated using hydrograph and loadograph separation techniques on a seven-year dataset of sub-hourly river discharge and concentrations of NO3-N, reactive P and total P in two intensively managed agricultural watersheds of contrasting hydrology in Ireland. Active transfer pathways were dictated by soil drainage. There were intra-annual variability in both P and N concentrations in different pathways and loads, and these had the largest influence of all-year baseflow (BF) concentrations and summer quickflow (QF) concentrations. Nutrient loss responded to seasonality in the river discharge in all pathways in both watersheds and was mostly transport limited. In both watersheds there were inter-annual trends in P concentration in some pathways and seasons that did not correspond to the trend of total river P concentration. The response in stream water quality to management, mitigation measures and changes in weather may be hidden by counteracting responses in different pathways. The hydrology had a major impact on seasonal changes in N and P loss. By apportioning different transfer pathways more information on the temporal and site-specific nature of nutrient transfer was provided. BF and QF pathways largely contributed to the river P concentrations in summer while all pathways contributed to the P and N loads in wintertime. The data indicated that increasing trends in river P concentrations were mostly linked to trends in BF concentration in both catchment types. This may be explained by increased point source influence, increased vertical transfer through increased soil P loading, or decreased stream bed attenuation. Each will require different policy considerations.

Anemia, tumor hypoxemia, and the cancer patient

DOE Office of Scientific and Technical Information (OSTI.GOV)

Varlotto, John; Stevenson, Mary Ann; Department of Radiation Oncology, Beth Israel/Deaconess Medical Center, Harvard Medical School, Boston, MA

2005-09-01

Purpose: To review the impact of anemia/tumor hypoxemia on the quality of life and survival in cancer patients, and to assess the problems associated with the correction of this difficulty. Methods: MEDLINE searches were performed to find relevant literature regarding anemia and/or tumor hypoxia in cancer patients. Articles were evaluated in order to assess the epidemiology, adverse patient effects, anemia correction guidelines, and mechanisms of hypoxia-induced cancer cell growth and/or therapeutic resistance. Past and current clinical studies of radiosensitization via tumor oxygenation/hypoxic cell sensitization were reviewed. All clinical studies using multi-variate analysis were analyzed to show whether or not anemiamore » and/or tumor hypoxemia affected tumor control and patient survival. Articles dealing with the correction of anemia via transfusion and/or erythropoietin were reviewed in order to show the impact of the rectification on the quality of life and survival of cancer patients. Results: Approximately 40-64% of patients presenting for cancer therapy are anemic. The rate of anemia rises with the use of chemotherapy, radiotherapy, and hormonal therapy for prostate cancer. Anemia is associated with reductions both in quality of life and survival. Tumor hypoxemia has been hypothesized to lead to tumor growth and resistance to therapy because it leads to angiogenesis, genetic mutations, resistance to apoptosis, and a resistance to free radicals from chemotherapy and radiotherapy. Nineteen clinical studies of anemia and eight clinical studies of tumor hypoxemia were found that used multi-variate analysis to determine the effect of these conditions on the local control and/or survival of cancer patients. Despite differing definitions of anemia and hypoxemia, all studies have shown a correlation between low hemoglobin levels and/or higher amounts of tumor hypoxia with poorer prognosis. Radiosensitization through improvements in tumor oxygenation/hypoxic cell sensitization has met with limited success via the use of hyperbaric oxygen, electron-affinic radiosensitizers, and mitomycin. Improvements in tumor oxygenation via the use of carbogen and nicotinamide, RSR13, and tirapazamine have shown promising clinical results and are all currently being tested in Phase III trials. The National Comprehensive Cancer Network (NCCN) guidelines recommend transfusion or erythropoietin for symptomatic patients with a hemoglobin of 10-11 g/dl and state that erythropoietin should strongly be considered if hemoglobin falls to less than 10 g/dl. These recommendations were based on studies that revealed an improvement in the quality of life of cancer patients, but not patient survival with anemia correction. Phase III studies evaluating the correction of anemia via erythropoietin have shown mixed results with some studies reporting a decrease in patient survival despite an improvement in hemoglobin levels. Diverse functions of erythropoietin are reviewed, including its potential to inhibit apoptosis via the JAK2/STAT5/BCL-X pathway. Correction of anemia by the use of blood transfusions has also shown a decrement in patient survival, possibly through inflammatory and/or immunosuppressive pathways. Conclusions: Anemia is a prevalent condition associated with cancer and its therapies. Proper Phase III trials are necessary to find the best way to correct anemia for specific patients. Future studies of erythropoietin must evaluate the possible anti-apoptotic effects by directly assessing the tumor for erythropoietin receptors or the presence of the JAK2/STAT5/BCL-X pathway. Due to the ability of transfusions to cause immunosuppression, most probably through inflammatory pathways, it may be best to study the effects of transfusion with the prolonged use of anti-inflammatory medications.« less

Anorexia in cancer: role of feeding-regulatory peptides

PubMed Central

Perboni, Simona; Inui, Akio

2006-01-01

Anorexia is one of the most common symptoms in advanced cancer and is a frequent cause of discomfort for cancer patients and their families. The pathogenesis of cancer anorexia is multi-factorial and involves most of the hypothalamic neuronal signalling pathways modulating energy homeostasis. It is considered to be the result of a failure of usual appetite and satiety signals. Loss of appetite can arise from decreased taste and smell of food, as well as from dysfunctional hypothalamic signalling pathways and cytokine production. Cytokines in particular, appear to play a key role in energy balance through persistent activation of the melanocortin system and inhibition of the neuropeptide Y pathway. The imbalance between anorexigenic and orexigenic peptides leads to suppression of appetite, and increased satiety and satiation associated with marked weight loss and decline in physical performance. High levels of serotonin also appear to contribute to these effects and recent findings implicate corticotropin-releasing factor in the pathogenesis of cancer anorexia as well. Despite significant advances in our understanding of the regulation of food intake and energy expenditure, few effective therapies are available. A better appreciation of the molecular and neuronal mechanisms that control body weight homeostasis may lead to the development of new therapies for improving the survival and quality of life of these patients. PMID:16815804

Comprehensive coverage of cardiovascular disease data in the disease portals at the Rat Genome Database.

PubMed

Wang, Shur-Jen; Laulederkind, Stanley J F; Hayman, G Thomas; Petri, Victoria; Smith, Jennifer R; Tutaj, Marek; Nigam, Rajni; Dwinell, Melinda R; Shimoyama, Mary

2016-08-01

Cardiovascular diseases are complex diseases caused by a combination of genetic and environmental factors. To facilitate progress in complex disease research, the Rat Genome Database (RGD) provides the community with a disease portal where genome objects and biological data related to cardiovascular diseases are systematically organized. The purpose of this study is to present biocuration at RGD, including disease, genetic, and pathway data. The RGD curation team uses controlled vocabularies/ontologies to organize data curated from the published literature or imported from disease and pathway databases. These organized annotations are associated with genes, strains, and quantitative trait loci (QTLs), thus linking functional annotations to genome objects. Screen shots from the web pages are used to demonstrate the organization of annotations at RGD. The human cardiovascular disease genes identified by annotations were grouped according to data sources and their annotation profiles were compared by in-house tools and other enrichment tools available to the public. The analysis results show that the imported cardiovascular disease genes from ClinVar and OMIM are functionally different from the RGD manually curated genes in terms of pathway and Gene Ontology annotations. The inclusion of disease genes from other databases enriches the collection of disease genes not only in quantity but also in quality. Copyright © 2016 the American Physiological Society.

Negative regulators of the RIG-I-like receptor signaling pathway

PubMed Central

Quicke, Kendra M.; Diamond, Michael S.; Suthar, Mehul S.

2017-01-01

SUMMARY Upon recognition of specific molecular patterns on viruses, bacteria and fungi, host cells trigger an innate immune response, which culminates in the production of type I interferons (IFN), pro-inflammatory cytokines and chemokines, and restricts pathogen replication and spread within the host. At each stage of the immune response, there are stimulatory and inhibitory signals that regulate the magnitude, quality, and character of the response. Positive regulation promotes an antiviral state to control and eventually clear infection whereas negative regulation dampens inflammation and prevents immune-mediated tissue damage. An over-exuberant innate immune response can lead to the destruction of cells and tissues, and the development of spontaneous autoimmunity. The RIG-I-like receptors (RLRs) retinoic acid-inducible gene I (RIG-I) and melanoma differentiation-associated gene 5 (MDA5) belong to a family of cytosolic host RNA helicases that recognize distinct non-self RNA signatures and trigger innate immune responses against several RNA virus infections. The RLR signaling pathway is tightly regulated to achieve a well-orchestrated response aimed at maximizing antiviral immunity and minimizing immune-mediated pathology. This review highlights contemporary findings on negative regulators of the RLR signaling pathway, with specific focus on the proteins and biological processes that directly regulate RIG-I, MDA5 and MAVS function. PMID:28295214

PINK1/Parkin-Dependent Mitochondrial Surveillance: From Pleiotropy to Parkinson's Disease

PubMed Central

Mouton-Liger, Francois; Jacoupy, Maxime; Corvol, Jean-Christophe; Corti, Olga

2017-01-01

Parkinson's disease (PD) is one of the most frequent neurodegenerative disease caused by the preferential, progressive degeneration of the dopaminergic (DA) neurons of the substantia nigra (SN) pars compacta. PD is characterized by a multifaceted pathological process involving protein misfolding, mitochondrial dysfunction, neuroinflammation and metabolism deregulation. The molecular mechanisms governing the complex interplay between the different facets of this process are still unknown. PARK2/Parkin and PARK6/PINK1, two genes responsible for familial forms of PD, act as a ubiquitous core signaling pathway, coupling mitochondrial stress to mitochondrial surveillance, by regulating mitochondrial dynamics, the removal of damaged mitochondrial components by mitochondria-derived vesicles, mitophagy, and mitochondrial biogenesis. Over the last decade, PINK1/Parkin-dependent mitochondrial quality control emerged as a pleiotropic regulatory pathway. Loss of its function impinges on a number of physiological processes suspected to contribute to PD pathogenesis. Its role in the regulation of innate immunity and inflammatory processes stands out, providing compelling support to the contribution of non-cell-autonomous immune mechanisms in PD. In this review, we illustrate the central role of this multifunctional pathway at the crossroads between mitochondrial stress, neuroinflammation and metabolism. We discuss how its dysfunction may contribute to PD pathogenesis and pinpoint major unresolved questions in the field. PMID:28507507

Whole transcriptome profiling of taste bud cells.

PubMed

Sukumaran, Sunil K; Lewandowski, Brian C; Qin, Yumei; Kotha, Ramana; Bachmanov, Alexander A; Margolskee, Robert F

2017-08-08

Analysis of single-cell RNA-Seq data can provide insights into the specific functions of individual cell types that compose complex tissues. Here, we examined gene expression in two distinct subpopulations of mouse taste cells: Tas1r3-expressing type II cells and physiologically identified type III cells. Our RNA-Seq libraries met high quality control standards and accurately captured differential expression of marker genes for type II (e.g. the Tas1r genes, Plcb2, Trpm5) and type III (e.g. Pkd2l1, Ncam, Snap25) taste cells. Bioinformatics analysis showed that genes regulating responses to stimuli were up-regulated in type II cells, while pathways related to neuronal function were up-regulated in type III cells. We also identified highly expressed genes and pathways associated with chemotaxis and axon guidance, providing new insights into the mechanisms underlying integration of new taste cells into the taste bud. We validated our results by immunohistochemically confirming expression of selected genes encoding synaptic (Cplx2 and Pclo) and semaphorin signalling pathway (Crmp2, PlexinB1, Fes and Sema4a) components. The approach described here could provide a comprehensive map of gene expression for all taste cell subpopulations and will be particularly relevant for cell types in taste buds and other tissues that can be identified only by physiological methods.

Serum Metabolic Profiling Reveals Altered Metabolic Pathways in Patients with Post-traumatic Cognitive Impairments

PubMed Central

Yi, Lunzhao; Shi, Shuting; Wang, Yang; Huang, Wei; Xia, Zi-an; Xing, Zhihua; Peng, Weijun; Wang, Zhe

2016-01-01

Cognitive impairment, the leading cause of traumatic brain injury (TBI)-related disability, adversely affects the quality of life of TBI patients, and exacts a personal and economic cost that is difficult to quantify. The underlying pathophysiological mechanism is currently unknown, and an effective treatment of the disease has not yet been identified. This study aimed to advance our understanding of the mechanism of disease pathogenesis; thus, metabolomics based on gas chromatography/mass spectrometry (GC-MS), coupled with multivariate and univariate statistical methods were used to identify potential biomarkers and the associated metabolic pathways of post-TBI cognitive impairment. A biomarker panel consisting of nine serum metabolites (serine, pyroglutamic acid, phenylalanine, galactose, palmitic acid, arachidonic acid, linoleic acid, citric acid, and 2,3,4-trihydroxybutyrate) was identified to be able to discriminate between TBI patients with cognitive impairment, TBI patients without cognitive impairment and healthy controls. Furthermore, associations between these metabolite markers and the metabolism of amino acids, lipids and carbohydrates were identified. In conclusion, our study is the first to identify several serum metabolite markers and investigate the altered metabolic pathway that is associated with post-TBI cognitive impairment. These markers appear to be suitable for further investigation of the disease mechanisms of post-TBI cognitive impairment. PMID:26883691

The secretory pathway: exploring yeast diversity.

PubMed

Delic, Marizela; Valli, Minoska; Graf, Alexandra B; Pfeffer, Martin; Mattanovich, Diethard; Gasser, Brigitte

2013-11-01

Protein secretion is an essential process for living organisms. In eukaryotes, this encompasses numerous steps mediated by several hundred cellular proteins. The core functions of translocation through the endoplasmic reticulum membrane, primary glycosylation, folding and quality control, and vesicle-mediated secretion are similar from yeasts to higher eukaryotes. However, recent research has revealed significant functional differences between yeasts and mammalian cells, and even among diverse yeast species. This review provides a current overview of the canonical protein secretion pathway in the model yeast Saccharomyces cerevisiae, highlighting differences to mammalian cells as well as currently unresolved questions, and provides a genomic comparison of the S. cerevisiae pathway to seven other yeast species where secretion has been investigated due to their attraction as protein production platforms, or for their relevance as pathogens. The analysis of Candida albicans, Candida glabrata, Kluyveromyces lactis, Pichia pastoris, Hansenula polymorpha, Yarrowia lipolytica, and Schizosaccharomyces pombe reveals that many - but not all - secretion steps are more redundant in S. cerevisiae due to duplicated genes, while some processes are even absent in this model yeast. Recent research obviates that even where homologous genes are present, small differences in protein sequence and/or differences in the regulation of gene expression may lead to quite different protein secretion phenotypes. © 2013 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved.

Determination of asymmetric Nα-acetyldimethylarginine in humans: a phase II metabolite of asymmetric dimethylarginine.

PubMed

Martens-Lobenhoffer, Jens; Rodionov, Roman N; Bode-Böger, Stefanie M

2014-05-01

Asymmetric dimethylarginine (ADMA) is produced by protein methylation, a common mechanism of posttranslational protein modification. Elevated levels of ADMA lead to impaired endothelial nitric oxide production and subsequently to a range of cardiovascular and other diseases related to decreased nitric oxide production. Knowledge of the elimination pathways of ADMA and the possibility of influencing them is therefore of major clinical interest. One of these pathways is the N-acetylation and subsequent renal elimination of ADMA in the form of asymmetric Nα-acetyldimethylarginine (Ac-ADMA). In this work, we describe the first method to quantitatively determine Ac-ADMA in human plasma and urine. Ac-ADMA was separated by HPLC on a porous graphitic carbon column and selectively analyzed by tandem mass spectrometry. Ac-ADMA and the internal standard D7-Ac-ADMA were synthesized in-house. Precision and accuracy of the method were better than 5% in plasma and urine quality control samples. First results obtained with this method in samples of healthy volunteers showed plasma levels of 0.643±0.454 nmol/L and urine levels of 152.7±76.7 nmol/L or 13.0±8.9 nmol/mmol creatinine. The method is a suitable tool for investigating this currently mostly neglected ADMA elimination pathway. Copyright © 2014 Elsevier Inc. All rights reserved.

Whole genome scan reveals the genetic signature of African Ankole cattle breed and potential for higher quality beef.

PubMed

Taye, Mengistie; Kim, Jaemin; Yoon, Sook Hee; Lee, Wonseok; Hanotte, Olivier; Dessie, Tadelle; Kemp, Stephen; Mwai, Okeyo Ally; Caetano-Anolles, Kelsey; Cho, Seoae; Oh, Sung Jong; Lee, Hak-Kyo; Kim, Heebal

2017-02-09

Africa is home to numerous cattle breeds whose diversity has been shaped by subtle combinations of human and natural selection. African Sanga cattle are an intermediate type of cattle resulting from interbreeding between Bos taurus and Bos indicus subspecies. Recently, research has asserted the potential of Sanga breeds for commercial beef production with better meat quality as compared to Bos indicus breeds. Here, we identified meat quality related gene regions that are positively selected in Ankole (Sanga) cattle breeds as compared to indicus (Boran, Ogaden, and Kenana) breeds using cross-population (XP-EHH and XP-CLR) statistical methods. We identified 238 (XP-EHH) and 213 (XP-CLR) positively selected genes, of which 97 were detected from both statistics. Among the genes obtained, we primarily reported those involved in different biological process and pathways associated with meat quality traits. Genes (CAPZB, COL9A2, PDGFRA, MAP3K5, ZNF410, and PKM2) involved in muscle structure and metabolism affect meat tenderness. Genes (PLA2G2A, PARK2, ZNF410, MAP2K3, PLCD3, PLCD1, and ROCK1) related to intramuscular fat (IMF) are involved in adipose metabolism and adipogenesis. MB and SLC48A1 affect meat color. In addition, we identified genes (TIMP2, PKM2, PRKG1, MAP3K5, and ATP8A1) related to feeding efficiency. Among the enriched Gene Ontology Biological Process (GO BP) terms, actin cytoskeleton organization, actin filament-based process, and protein ubiquitination are associated with meat tenderness whereas cellular component organization, negative regulation of actin filament depolymerization and negative regulation of protein complex disassembly are involved in adipocyte regulation. The MAPK pathway is responsible for cell proliferation and plays an important role in hyperplastic growth, which has a positive effect on meat tenderness. Results revealed several candidate genes positively selected in Ankole cattle in relation to meat quality characteristics. The genes identified are involved in muscle structure and metabolism, and adipose metabolism and adipogenesis. These genes help in the understanding of the biological mechanisms controlling beef quality characteristics in African Ankole cattle. These results provide a basis for further research on the genomic characteristics of Ankole and other Sanga cattle breeds for quality beef.

Roles of intramolecular and intermolecular interactions in functional regulation of the Hsp70 J-protein co-chaperone sis1

DOE PAGES

Yu, Hyun Young; Ziegelhoffer, Thomas; Osipiuk, Jerzy; ...

2015-02-13

Unlike other Hsp70 molecular chaperones, those of the eukaryotic cytosol have four residues, EEVD, at their C-termini. EEVD(Hsp70) binds adaptor proteins of the Hsp90 chaperone system and mitochondrial membrane preprotein receptors, thereby facilitating processing of Hsp70-bound clients through protein folding and translocation pathways. Among J-protein co-chaperones functioning in these pathways Sis1 is unique, as it also binds the EEVD(Hsp70) motif. However, little is known about the role of the Sis1:EEVD(Hsp70) interaction. We found that deletion of EEVD(Hsp70) abolished the ability of Sis1, but not the ubiquitous J-protein Ydj1, to partner with Hsp70 in in vitro protein refolding. Sis1 co-chaperone activitymore » with Hsp70ΔEEVD was restored upon substitution of a glutamic acid of the J-domain. Structural analysis revealed that this key glutamic acid, which is not present in Ydj1, forms a salt bridge with an arginine of the immediately adjacent glycine-rich region. Thus, restoration of Sis1 in vitro activity suggests that intramolecular interaction(s) between the J-domain and glycine-rich region controls co-chaperone activity, which is optimal only when Sis1 interacts with the EEVD(Hsp70) motif. Yet, we found that disruption of the Sis1:EEVD(Hsp70) interaction enhances the ability of Sis1 to substitute for Ydj1 in vivo. Our results are consistent with the idea that interaction of Sis1 with EEVD(Hsp70) minimizes transfer of Sis1-bound clients to Hsp70s that are primed for client transfer to folding and translocation pathways by their preassociation with EEVD-binding adaptor proteins. Finally, these interactions may be one means by which cells triage Ydj1- and Sis1-bound clients to productive and quality control pathways, respectively.« less

Roles of Intramolecular and Intermolecular Interactions in Functional Regulation of the Hsp70 J-protein Co-Chaperone Sis1

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yu, Hyun Young; Ziegelhoffer, Thomas; Osipiuk, Jerzy

2015-04-01

Unlike other Hsp70 molecular chaperones, those of the eukaryotic cytosol have four residues, EEVD, at heir C-termini. EEVD(Hsp70) binds adaptor proteins of the Hsp90 chaperone system and mitochondrial membrane preprotein receptors, thereby facilitating processing of Hsp70-bound clients through protein folding and translocation pathways. Among J-protein co-chaperones functioning in these pathways, Sis1 is unique, as it also binds the EEVD(Hsp70) motif. However, little is known about the role of the Sis1:EEVD(Hsp70) interaction. We found that deletion of EEVD(Hsp70) abolished the ability of Sis1, but not the ubiquitous J-protein Ydj1, to partner with Hsp70 in in vitro protein refolding. Sis1 co-chaperone activitymore » with Hsp70ΔEEVD was restored upon substitution of a glutamic acid of the J-domain. Structural analysis revealed that this key glutamic acid, which is not present in Ydj1, forms a salt bridge with an arginine of the immediately adjacent glycine-rich region. Thus, restoration of Sis1 in vitro activity suggests that intramolecular interactions between the J-domain and glycine-rich region control co-chaperone activity, which is optimal only when Sis1 interacts with the EEVD(Hsp70) motif. However, we found that disruption of the Sis1:EEVD(Hsp70) interaction enhances the ability of Sis1 to substitute for Ydj1 in vivo. Our results are consistent with the idea that interaction of Sis1 with EEVD(Hsp70) minimizes transfer of Sis1-bound clients to Hsp70s that are primed for client transfer to folding and translocation pathways by their preassociation with EEVD binding adaptor proteins. These interactions may be one means by which cells triage Ydj1- and Sis1-bound clients to productive and quality control pathways, respectively.« less

Causal mechanisms of soil organic matter decomposition: Deconstructing salinity and flooding impacts in coastal wetlands

USGS Publications Warehouse

Stagg, Camille L.; Schoolmaster, Donald; Krauss, Ken W.; Cormier, Nicole; Conner, William H.

2017-01-01

Coastal wetlands significantly contribute to global carbon storage potential. Sea-level rise and other climate change-induced disturbances threaten coastal wetland sustainability and carbon storage capacity. It is critical that we understand the mechanisms controlling wetland carbon loss so that we can predict and manage these resources in anticipation of climate change. However, our current understanding of the mechanisms that control soil organic matter decomposition, in particular the impacts of elevated salinity, are limited, and literature reports are contradictory. In an attempt to improve our understanding of these complex processes, we measured root and rhizome decomposition and developed a causal model to identify and quantify the mechanisms that influence soil organic matter decomposition in coastal wetlands that are impacted by sea-level rise. We identified three causal pathways: 1) a direct pathway representing the effects of flooding on soil moisture, 2) a direct pathway representing the effects of salinity on decomposer microbial communities and soil biogeochemistry, and 3) an indirect pathway representing the effects of salinity on litter quality through changes in plant community composition over time. We used this model to test the effects of alternate scenarios on the response of tidal freshwater forested wetlands and oligohaline marshes to short- and long-term climate-induced disturbances of flooding and salinity. In tidal freshwater forested wetlands, the model predicted less decomposition in response to drought, hurricane salinity pulsing, and long-term sea-level rise. In contrast, in the oligohaline marsh, the model predicted no change in response to sea-level rise, and increased decomposition following a drought or a hurricane salinity pulse. Our results show that it is critical to consider the temporal scale of disturbance and the magnitude of exposure when assessing the effects of salinity intrusion on carbon mineralization in coastal wetlands. Here we identify three causal mechanisms that can reconcile disparities between long-term and short-term salinity impacts on organic matter decomposition.

Roles of intramolecular and intermolecular interactions in functional regulation of the Hsp70 J-protein co-chaperone Sis1.

PubMed

Yu, Hyun Young; Ziegelhoffer, Thomas; Osipiuk, Jerzy; Ciesielski, Szymon J; Baranowski, Maciej; Zhou, Min; Joachimiak, Andrzej; Craig, Elizabeth A

2015-04-10

Unlike other Hsp70 molecular chaperones, those of the eukaryotic cytosol have four residues, EEVD, at their C-termini. EEVD(Hsp70) binds adaptor proteins of the Hsp90 chaperone system and mitochondrial membrane preprotein receptors, thereby facilitating processing of Hsp70-bound clients through protein folding and translocation pathways. Among J-protein co-chaperones functioning in these pathways, Sis1 is unique, as it also binds the EEVD(Hsp70) motif. However, little is known about the role of the Sis1:EEVD(Hsp70) interaction. We found that deletion of EEVD(Hsp70) abolished the ability of Sis1, but not the ubiquitous J-protein Ydj1, to partner with Hsp70 in in vitro protein refolding. Sis1 co-chaperone activity with Hsp70∆EEVD was restored upon substitution of a glutamic acid of the J-domain. Structural analysis revealed that this key glutamic acid, which is not present in Ydj1, forms a salt bridge with an arginine of the immediately adjacent glycine-rich region. Thus, restoration of Sis1 in vitro activity suggests that intramolecular interactions between the J-domain and glycine-rich region control co-chaperone activity, which is optimal only when Sis1 interacts with the EEVD(Hsp70) motif. However, we found that disruption of the Sis1:EEVD(Hsp70) interaction enhances the ability of Sis1 to substitute for Ydj1 in vivo. Our results are consistent with the idea that interaction of Sis1 with EEVD(Hsp70) minimizes transfer of Sis1-bound clients to Hsp70s that are primed for client transfer to folding and translocation pathways by their preassociation with EEVD binding adaptor proteins. These interactions may be one means by which cells triage Ydj1- and Sis1-bound clients to productive and quality control pathways, respectively. Copyright © 2015 Elsevier Ltd. All rights reserved.

Roles of Intramolecular and Intermolecular Interactions in Functional Regulation of the Hsp70 J-protein Co-chaperone Sis1

PubMed Central

Yu, Hyun Young; Ziegelhoffer, Thomas; Osipiuk, Jerzy; Ciesielski, Szymon J.; Baranowski, Maciej; Zhou, Min; Joachimiak, Andrzej; Craig, Elizabeth A.

2015-01-01

Unlike other Hsp70 molecular chaperones, those of the eukaryotic cytosol have four residues, EEVD, at their C-termini. EEVD(Hsp70) binds adaptor proteins of the Hsp90 chaperone system and mitochondrial membrane preprotein receptors, thereby facilitating processing of Hsp70-bound clients through protein folding and translocation pathways. Among J-protein co-chaperones functioning in these pathways Sis1 is unique, as it also binds the EEVD(Hsp70) motif. However, little is known about the role of the Sis1:EEVD(Hsp70) interaction. We found that deletion of EEVD(Hsp70) abolished the ability of Sis1, but not the ubiquitous J-protein Ydj1, to partner with Hsp70 in in vitro protein refolding. Sis1 co-chaperone activity with Hsp70ΔEEVD was restored upon substitution of a glutamic acid of the J-domain. Structural analysis revealed that this key glutamic acid, which is not present in Ydj1, forms a salt bridge with an arginine of the immediately adjacent glycine-rich region. Thus, restoration of Sis1 in vitro activity suggests that intramolecular interaction(s) between the J-domain and glycine-rich region controls co-chaperone activity, which is optimal only when Sis1 interacts with the EEVD(Hsp70) motif. Yet, we found that disruption of the Sis1:EEVD(Hsp70) interaction enhances the ability of Sis1 to substitute for Ydj1 in vivo. Our results are consistent with the idea that interaction of Sis1 with EEVD(Hsp70) minimizes transfer of Sis1-bound clients to Hsp70s that are primed for client transfer to folding and translocation pathways by their preassociation with EEVD-binding adaptor proteins. These interactions may be one means by which cells triage Ydj1- and Sis1-bound clients to productive and quality control pathways, respectively. PMID:25687964

Causal mechanisms of soil organic matter decomposition: deconstructing salinity and flooding impacts in coastal wetlands.

PubMed

Stagg, Camille L; Schoolmaster, Donald R; Krauss, Ken W; Cormier, Nicole; Conner, William H

2017-08-01

Coastal wetlands significantly contribute to global carbon storage potential. Sea-level rise and other climate-change-induced disturbances threaten coastal wetland sustainability and carbon storage capacity. It is critical that we understand the mechanisms controlling wetland carbon loss so that we can predict and manage these resources in anticipation of climate change. However, our current understanding of the mechanisms that control soil organic matter decomposition, in particular the impacts of elevated salinity, are limited, and literature reports are contradictory. In an attempt to improve our understanding of these complex processes, we measured root and rhizome decomposition and developed a causal model to identify and quantify the mechanisms that influence soil organic matter decomposition in coastal wetlands that are impacted by sea-level rise. We identified three causal pathways: (1) a direct pathway representing the effects of flooding on soil moisture, (2) a direct pathway representing the effects of salinity on decomposer microbial communities and soil biogeochemistry, and (3) an indirect pathway representing the effects of salinity on litter quality through changes in plant community composition over time. We used this model to test the effects of alternate scenarios on the response of tidal freshwater forested wetlands and oligohaline marshes to short- and long-term climate-induced disturbances of flooding and salinity. In tidal freshwater forested wetlands, the model predicted less decomposition in response to drought, hurricane salinity pulsing, and long-term sea-level rise. In contrast, in the oligohaline marsh, the model predicted no change in response to drought and sea-level rise, and increased decomposition following a hurricane salinity pulse. Our results show that it is critical to consider the temporal scale of disturbance and the magnitude of exposure when assessing the effects of salinity intrusion on carbon mineralization in coastal wetlands. Here, we identify three causal mechanisms that can reconcile disparities between long-term and short-term salinity impacts on organic matter decomposition. © 2017 by the Ecological Society of America.

Effects of Canonical NF-κB Signaling Pathway on the Proliferation and Odonto/Osteogenic Differentiation of Human Stem Cells from Apical Papilla

PubMed Central

Li, Junjun; Yan, Ming; Wang, Zilu; Jing, Shuanglin; Li, Yao; Liu, Genxia; Yu, Jinhua; Fan, Zhipeng

2014-01-01

Background Information. NF-κB signaling pathway plays a complicated role in the biological functions of mesenchymal stem cells. However, the effects of NF-κB pathway on the odonto/osteogenic differentiation of stem cells from apical papilla (SCAPs) remain unclear. The present study was designed to evaluate the effects of canonical NF-κB pathway on the osteo/odontogenic capacity of SCAPs in vitro. Results. Western blot results demonstrated that NF-κB pathway in SCAPs was successfully activated by TNF-α or blocked by BMS-345541. NF-κB pathway-activated SCAPs presented a higher proliferation activity compared with control groups, as indicated by dimethyl-thiazol-diphenyl tetrazolium bromide assay (MTT) and flow cytometry assay (FCM). Wound scratch assay revealed that NF-κB pathway-activated SCAPs presented an improved migration capacity, enhanced alkaline phosphatase (ALP) activity, and upregulated mineralization capacity of SCAPs, as compared with control groups. Meanwhile, the odonto/osteogenic markers (ALP/ALP, RUNX2/RUNX2, OSX/OSX, OCN/OCN, OPN/OPN, BSP/BSP, DSPP/DSP, and DMP-1/DMP-1) in NF-κB pathway-activated SCAPs were also significantly upregulated as compared with control groups at both protein and mRNA levels. However, NF-κB pathway-inhibited SCAPs exhibited a lower proliferation/migration capacity, and decreased odonto/osteogenic ability in comparison with control groups. Conclusion. Our findings suggest that classical NF-κB pathway plays a paramount role in the proliferation and committed differentiation of SCAPs. PMID:24864235

Fungal-to-bacterial dominance of soil detrital food-webs: Consequences for biogeochemistry

NASA Astrophysics Data System (ADS)

Rousk, Johannes; Frey, Serita

2015-04-01

Resolving fungal and bacterial groups within the microbial decomposer community is thought to capture disparate microbial life strategies, associating bacteria with an r-selected strategy for carbon (C) and nutrient use, and fungi with a K-selected strategy. Additionally, food-web models have established a widely held belief that the bacterial decomposer pathway in soil supports high turnover rates of easily available substrates, while the slower fungal pathway supports the decomposition of more complex organic material, thus characterising the biogeochemistry of the ecosystem. Three field-experiments to generate gradients of SOC-quality were assessed. (1) the Detritus Input, Removal, and Trenching - DIRT - experiment in a temperate forest in mixed hardwood stands at Harvard Forest LTER, US. There, experimentally adjusted litter input and root input had affected the SOC quality during 23 years. (2) field-application of 14-C labelled glucose to grassland soils, sampled over the course of 13 months to generate an age-gradient of SOM (1 day - 13 months). (3) The Park Grass Experiment at Rothamsted, UK, where 150-years continuous N-fertilisation (0, 50, 100, 150 kg N ha-1 y-1) has affected the quality of SOM in grassland soils. A combination of carbon stable and radio isotope studies, fungal and bacterial growth and biomass measurements, and C and N mineralisation (15N pool dilution) assays were used to investigate how SOC-quality influenced fungal and bacterial food-web pathways and the implications this had for C and nutrient turnover. There was no support that decomposer food-webs dominated by bacteria support high turnover rates of easily available substrates, while slower fungal-dominated decomposition pathways support the decomposition of more complex organic material. Rather, an association between high quality SOC and fungi emerges from the results. This suggests that we need to revise our basic understanding for soil microbial communities and the processes they regulate in soil.

Impact of organizational infrastructure on beta-blocker and aspirin therapy for acute myocardial infarction.

PubMed

Ellerbeck, Edward F; Bhimaraj, Arvind; Hall, Sandra

2006-09-01

Although organizational change has been advocated as a critical component of quality improvement, there is little data available on the variation and effectiveness of organizational elements in the care of acute myocardial infarction (AMI). This study was designed to examine the impact of organizational infrastructure on the use of aspirin and beta-blockers during and after AMI. We assessed organizational infrastructure for AMI care in 44 hospitals in Kansas and linked these data to patient-specific process of care data collected in Kansas as part of the Cooperative Cardiovascular Project. While controlling for clustering within hospitals, we examined the relationships between hospital infrastructure and use of aspirin and beta-blocker both at admission and discharge. Hospitals varied widely in their inclusion of aspirin and beta-blockers in AMI pathways, protocols, and standardized order sets. Hospitals also varied in the involvement of their physicians in AMI quality improvement and in their ability to identify a physician champion for AMI care. Patients were more likely to receive aspirin on admission in hospitals that included aspirin in their emergency department order sets (odds ratio [OR] 1.57, 95% confidence interval [CI] 1.01-2.48) and were more likely to receive beta-blockers on admission and at discharge if beta-blockers were included in an emergency department protocol or pathway (OR 2.14, 95% CI 1.25-3.77 and OR 3.5, 95% CI 1.14-14.38, respectively). Use of beta-blockers at discharge was also associated with commitment of administration to AMI care and the presence of a physician champion. Quality improvement efforts should include a close examination of the organization of AMI care to assure that critical elements in the care of AMI patients are not inadvertently omitted.

RNA-seq transcriptome analysis of formalin fixed, paraffin-embedded canine meningioma

PubMed Central

Grenier, Jennifer K.; Foureman, Polly A.; Sloma, Erica A.

2017-01-01

Meningiomas are the most commonly reported primary intracranial tumor in dogs and humans and between the two species there are similarities in histology and biologic behavior. Due to these similarities, dogs have been proposed as models for meningioma pathobiology. However, little is known about specific pathways and individual genes that are involved in the development and progression of canine meningioma. In addition, studies are lacking that utilize RNAseq to characterize gene expression in clinical cases of canine meningioma. The primary objective of this study was to develop a technique for which high quality RNA can be extracted from formalin-fixed, paraffin embedded tissue and then used for transcriptome analysis to determine patterns of gene expression. RNA was extracted from thirteen canine meningiomas–eleven from formalin fixed and two flash-frozen. These represented six grade I and seven grade II meningiomas based on the World Health Organization classification system for human meningioma. RNA was also extracted from fresh frozen leptomeninges from three control dogs for comparison. RNAseq libraries made from formalin fixed tissue were of sufficient quality to successfully identify 125 significantly differentially expressed genes, the majority of which were related to oncogenic processes. Twelve genes (AQP1, BMPER, FBLN2, FRZB, MEDAG, MYC, PAMR1, PDGFRL, PDPN, PECAM1, PERP, ZC2HC1C) were validated using qPCR. Among the differentially expressed genes were oncogenes, tumor suppressors, transcription factors, VEGF-related genes, and members of the WNT pathway. Our work demonstrates that RNA of sufficient quality can be extracted from FFPE canine meningioma samples to provide biologically relevant transcriptome analyses using a next-generation sequencing technique, such as RNA-seq. PMID:29073243

Radiological Medical Device Innovation: Approvals via the Premarket Approval Pathway From 2000 to 2015.

PubMed

Ghobadi, Comeron W; Hayman, Emily L; Finkle, Joshua H; Walter, Jessica R; Xu, Shuai

2017-01-01

The aim of this study was to critically assess the clinical evidence leading to radiologic medical device approvals via the premarket approval pathway from 2000 to 2015. This study used the publically available FDA premarket database for radiologic device approvals over the past 15 years (September 1, 2000, to August 31, 2015). Approval characteristics were collected for each device, and statistical analysis was performed on the data for each pivotal trial. Additionally, methodological quality of the pivotal trial was determined using the Quality Assessment of Diagnostic Accuracy Studies tool. Twenty-three class III radiologic device approvals were identified, with breast imaging accounting for 16 (70%) and computer-aided detection software accounting for 9 (39%) approvals. The median premarket approval time was 475 days (range, 180-1,116). Twenty-one devices were approved on the basis of multireader, multicenter studies, one on the basis of a randomized controlled trial, and one on the basis of a preclinical technical equivalence trial. The median number of patients per pivotal trial was 201 (range, 25-3,946). Twenty-six of the 34 pivotal trials (76%) had at least one methodologic bias. Breast imaging devices had a greater number of patients per pivotal trial (P = .009) and more prospective studies. With regard to all modalities, increased time to device approval correlated with weaker trial quality (r = 0.600, P < .001). Radiologic devices are largely approved by multireader, multicenter studies, the recommended standard for assessing diagnostic technologies. Given that radiologic devices play a key role in modern medicine, further efforts should be made to increase transparency of clinical data leading to approval. Copyright © 2016 American College of Radiology. Published by Elsevier Inc. All rights reserved.

xMSanalyzer: automated pipeline for improved feature detection and downstream analysis of large-scale, non-targeted metabolomics data.

PubMed

Uppal, Karan; Soltow, Quinlyn A; Strobel, Frederick H; Pittard, W Stephen; Gernert, Kim M; Yu, Tianwei; Jones, Dean P

2013-01-16

Detection of low abundance metabolites is important for de novo mapping of metabolic pathways related to diet, microbiome or environmental exposures. Multiple algorithms are available to extract m/z features from liquid chromatography-mass spectral data in a conservative manner, which tends to preclude detection of low abundance chemicals and chemicals found in small subsets of samples. The present study provides software to enhance such algorithms for feature detection, quality assessment, and annotation. xMSanalyzer is a set of utilities for automated processing of metabolomics data. The utilites can be classified into four main modules to: 1) improve feature detection for replicate analyses by systematic re-extraction with multiple parameter settings and data merger to optimize the balance between sensitivity and reliability, 2) evaluate sample quality and feature consistency, 3) detect feature overlap between datasets, and 4) characterize high-resolution m/z matches to small molecule metabolites and biological pathways using multiple chemical databases. The package was tested with plasma samples and shown to more than double the number of features extracted while improving quantitative reliability of detection. MS/MS analysis of a random subset of peaks that were exclusively detected using xMSanalyzer confirmed that the optimization scheme improves detection of real metabolites. xMSanalyzer is a package of utilities for data extraction, quality control assessment, detection of overlapping and unique metabolites in multiple datasets, and batch annotation of metabolites. The program was designed to integrate with existing packages such as apLCMS and XCMS, but the framework can also be used to enhance data extraction for other LC/MS data software.

Investigating multiple dysregulated pathways in rheumatoid arthritis based on pathway interaction network.

PubMed

Song, Xian-Dong; Song, Xian-Xu; Liu, Gui-Bo; Ren, Chun-Hui; Sun, Yuan-Bo; Liu, Ke-Xin; Liu, Bo; Liang, Shuang; Zhu, Zhu

2018-03-01

The traditional methods of identifying biomarkers in rheumatoid arthritis (RA) have focussed on the differentially expressed pathways or individual pathways, which however, neglect the interactions between pathways. To better understand the pathogenesis of RA, we aimed to identify dysregulated pathway sets using a pathway interaction network (PIN), which considered interactions among pathways. Firstly, RA-related gene expression profile data, protein-protein interactions (PPI) data and pathway data were taken up from the corresponding databases. Secondly, principal component analysis method was used to calculate the pathway activity of each of the pathway, and then a seed pathway was identified using data gleaned from the pathway activity. A PIN was then constructed based on the gene expression profile, pathway data, and PPI information. Finally, the dysregulated pathways were extracted from the PIN based on the seed pathway using the method of support vector machines and an area under the curve (AUC) index. The PIN comprised of a total of 854 pathways and 1064 pathway interactions. The greatest change in the activity score between RA and control samples was observed in the pathway of epigenetic regulation of gene expression, which was extracted and regarded as the seed pathway. Starting with this seed pathway, one maximum pathway set containing 10 dysregulated pathways was extracted from the PIN, having an AUC of 0.8249, and the result indicated that this pathway set could distinguish RA from the controls. These 10 dysregulated pathways might be potential biomarkers for RA diagnosis and treatment in the future.

Pathways to Employment and Quality of Life for Apprenticeship and Traineeship Graduates with Disabilities

ERIC Educational Resources Information Center

Cocks, Errol; Thoresen, Stian H.; Lee, Elinda Ai Lim

2015-01-01

People with disabilities have low participation rates in employment and vocational education and training. Thirty adults with disabilities were sampled from an Australian longitudinal study of economic and social outcomes achieved by graduate apprentices and trainees. Participants were surveyed and interviewed to identify pathways from high school…

Rubric for Linked Learning Pathway Certification

ERIC Educational Resources Information Center

LaPlante, Arlene; Stearns, Roman

2010-01-01

This rubric was created to help pathway teams as they work together to develop and improve a comprehensive program of study. Specifically, the rubric can serve as a tool for: (1) Visioning; (2) Self-assessment; (3) Planning; and (4) Quality review. ConnectEd designed this rubric to be used in coordination with the Certification Criteria for Linked…

Creating Multiple Pathways in the Arts: A New York City Case Study

ERIC Educational Resources Information Center

Maguire, Cindy; Mishook, Jacob; Garcia, Ivonne; de Gaillande, Genevieve

2013-01-01

Increasingly, education policy makers understand the importance of students and families having access to a range of high quality educational opportunities inside and outside of school, 365 days a year. This paper explores the concept of multiple pathways in arts education to further conceptualize and build upon such opportunities, inside and…

Developing Teacher Leadership in Singapore: Multiple Pathways for Differentiated Journeys

ERIC Educational Resources Information Center

Goodwin, A. Lin; Low, Ee Ling; Ng, Pak Tee

2015-01-01

In this article, we examine quality teachers through teacher leadership development. Using Singapore as an illustrative case, we describe the redefinition of the teaching profession to include deliberate structures and multiple pathways designed to nurture teacher leaders, and the role of teacher leaders in supporting education reform. We go on to…

Developing confidence in adverse outcome pathway-based toxicity predictions effects of the fungicide imazalil on fathead minnow reproduction

EPA Science Inventory

An adverse outcome pathway (AOP) description linking inhibition of aromatase (cytochrome P450 [cyp] 19) to reproductive dysfunction was reviewed for scientific and technical quality and endorsed by the OECD (https://aopwiki.org/wiki/index.php/Aop:25). An intended application of t...

Developing confidence in adverse outcome pathway-based toxicity predictions effects of the fungicide imazalil on fathead minnow reproduction (Poster)

EPA Science Inventory

An adverse outcome pathway (AOP) description linking inhibition of aromatase (cytochrome P450 [cyp] 19) to reproductive dysfunction was reviewed for scientific and technical quality and endorsed by the OECD. An intended application of the AOP framework is to support the use of me...

The ETS-5 transcription factor regulates activity states in Caenorhabditis elegans by controlling satiety

PubMed Central

Juozaityte, Vaida; Pladevall-Morera, David; Podolska, Agnieszka; Nørgaard, Steffen; Pocock, Roger

2017-01-01

Animal behavior is shaped through interplay among genes, the environment, and previous experience. As in mammals, satiety signals induce quiescence in Caenorhabditis elegans. Here we report that the C. elegans transcription factor ETS-5, an ortholog of mammalian FEV/Pet1, controls satiety-induced quiescence. Nutritional status has a major influence on C. elegans behavior. When foraging, food availability controls behavioral state switching between active (roaming) and sedentary (dwelling) states; however, when provided with high-quality food, C. elegans become sated and enter quiescence. We show that ETS-5 acts to promote roaming and inhibit quiescence by setting the internal “satiety quotient” through fat regulation. Acting from the ASG and BAG sensory neurons, we show that ETS-5 functions in a complex network with serotonergic and neuropeptide signaling pathways to control food-regulated behavioral state switching. Taken together, our results identify a neuronal mechanism for controlling intestinal fat stores and organismal behavioral states in C. elegans, and establish a paradigm for the elucidation of obesity-relevant mechanisms. PMID:28193866

Implications of alternative assumptions regarding future air pollution control in scenarios similar to the Representative Concentration Pathways

NASA Astrophysics Data System (ADS)

Chuwah, Clifford; van Noije, Twan; van Vuuren, Detlef P.; Hazeleger, Wilco; Strunk, Achim; Deetman, Sebastiaan; Beltran, Angelica Mendoza; van Vliet, Jasper

2013-11-01

The uncertain, future development of emissions of short-lived trace gases and aerosols forms a key factor for future air quality and climate forcing. The Representative Concentration Pathways (RCPs) only explore part of this range as they all assume that worldwide ambitious air pollution control policies will be implemented. In this study, we explore how different assumptions on future air pollution policy and climate policy lead to different concentrations of air pollutants for a set of RCP-like scenarios developed using the IMAGE model. These scenarios combine low and high air pollution variants of the scenarios with radiative forcing targets in 2100 of 2.6 W m-2 and 6.0 W m-2. Simulations using the global atmospheric chemistry and transport model TM5 for the present-day climate show that both climate mitigation and air pollution control policies have large-scale effects on pollutant concentrations, often of similar magnitude. If no further air pollution policies would be implemented, pollution levels could be considerably higher than in the RCPs, especially in Asia. Air pollution control measures could significantly reduce the warming by tropospheric ozone and black carbon and the cooling by sulphate by 2020, and in the longer term contribute to enhanced warming by methane. These effects tend to cancel each other on a global scale. According to our estimates the effect of the worldwide implementation of air pollution control measures on the total global mean direct radiative forcing in 2050 is +0.09 W m-2 in the 6.0 W m-2 scenario and -0.16 W m-2 in the 2.6 W m-2 scenario.

Effects of oncological care pathways in primary and secondary care on patient, professional, and health systems outcomes: protocol for a systematic review and meta-analysis.

PubMed

van Hoeve, Jolanda C; Vernooij, Robin W M; Lawal, Adegboyega K; Fiander, Michelle; Nieboer, Peter; Siesling, Sabine; Rotter, Thomas

2018-03-27

The high impact of a cancer diagnosis on patients and their families and the increasing costs of cancer treatment call for optimal and efficient oncological care. To improve the quality of care and to minimize healthcare costs and its economic burden, many healthcare organizations introduce care pathways to improve efficiency across the continuum of cancer care. However, there is limited research on the effects of cancer care pathways in different settings. The aim of this systematic review and meta-analysis described in this protocol is to synthesize existing literature on the effects of oncological care pathways. We will conduct a systematic search strategy to identify all relevant literature in several biomedical databases, including Cochrane library, MEDLINE, Embase, and CINAHL. We will follow the methodology of Cochrane Effective Practice and Organisation of Care (EPOC), and we will include randomized trials, non-randomized trials, controlled before-after studies, and interrupted time series studies. In addition, we will include full economic evaluations (cost-effectiveness analyses, cost-utility analyses, and cost-benefit analyses), cost analyses, and comparative resource utilization studies, if available. Two reviewers will independently screen all studies and evaluate those included for risk of bias. From these studies, we will extract data regarding patient, professional, and health systems outcomes. Our systematic review will follow the PRISMA set of items for reporting in systematic reviews and meta-analyses. Following the protocol outlined in this article, we aim to identify, assess, and synthesize all available evidence in order to provide an evidence base on the effects of oncological care pathways as reported in the literature. PROSPERO CRD42017057592 .

Deepening our understanding of quality improvement in Europe (DUQuE): overview of a study of hospital quality management in seven countries

PubMed Central

Secanell, Mariona; Groene, Oliver; Arah, Onyebuchi A.; Lopez, Maria Andrée; Kutryba, Basia; Pfaff, Holger; Klazinga, Niek; Wagner, Cordula; Kristensen, Solvejg; Bartels, Paul Daniel; Garel, Pascal; Bruneau, Charles; Escoval, Ana; França, Margarida; Mora, Nuria; Suñol, Rosa; Klazinga, N; Kringos, DS; Lopez, MA; Secanell, M; Sunol, R; Vallejo, P; Bartels, P; Kristensen, S; Michel, P; Saillour-Glenisson, F; Vlcek, F; Car, M; Jones, S; Klaus, E; Bottaro, S; Garel, P; Saluvan, M; Bruneau, C; Depaigne-Loth, A; Shaw, C; Hammer, A; Ommen, O; Pfaff, H; Groene, O; Botje, D; Wagner, C; Kutaj-Wasikowska, H; Kutryba, B; Escoval, A; Lívio, A; Eiras, M; Franca, M; Leite, I; Almeman, F; Kus, H; Ozturk, K; Mannion, R; Arah, OA; Chow, A; DerSarkissian, M; Thompson, CA; Wang, A; Thompson, A

2014-01-01

Introduction and Objective This paper provides an overview of the DUQuE (Deepening our Understanding of Quality Improvement in Europe) project, the first study across multiple countries of the European Union (EU) to assess relationships between quality management and patient outcomes at EU level. The paper describes the conceptual framework and methods applied, highlighting the novel features of this study. Design DUQuE was designed as a multi-level cross-sectional study with data collection at hospital, pathway, professional and patient level in eight countries. Setting and Participants We aimed to collect data for the assessment of hospital-wide constructs from up to 30 randomly selected hospitals in each country, and additional data at pathway and patient level in 12 of these 30. Main outcome measures A comprehensive conceptual framework was developed to account for the multiple levels that influence hospital performance and patient outcomes. We assessed hospital-specific constructs (organizational culture and professional involvement), clinical pathway constructs (the organization of care processes for acute myocardial infarction, stroke, hip fracture and deliveries), patient-specific processes and outcomes (clinical effectiveness, patient safety and patient experience) and external constructs that could modify hospital quality (external assessment and perceived external pressure). Results Data was gathered from 188 hospitals in 7 participating countries. The overall participation and response rate were between 75% and 100% for the assessed measures. Conclusions This is the first study assessing relation between quality management and patient outcomes at EU level. The study involved a large number of respondents and achieved high response rates. This work will serve to develop guidance in how to assess quality management and makes recommendations on the best ways to improve quality in healthcare for hospital stakeholders, payers, researchers, and policy makers throughout the EU. PMID:24671120

Proteostasis: bad news and good news from the endoplasmic reticulum.

PubMed

Noack, Julia; Brambilla Pisoni, Giorgia; Molinari, Maurizio

2014-01-01

The endoplasmic reticulum (ER) is an intracellular compartment dedicated to the synthesis and maturation of secretory and membrane proteins, totalling about 30% of the total eukaryotic cells proteome. The capacity to produce correctly folded polypeptides and to transport them to their correct intra- or extracellular destinations relies on proteostasis networks that regulate and balance the activity of protein folding, quality control, transport and degradation machineries. Nutrient and environmental changes, pathogen infection aging and, more relevant for the topics discussed in this review, mutations that impair attainment of the correct 3D structure of nascent polypeptide chains may compromise the activity of the proteostasis networks with devastating consequences on cells, organs and organisms' homeostasis. Here we present a review of mechanisms regulating folding and quality control of proteins expressed in the ER, and we describe the protein degradation and the ER stress pathways activated by the expression of misfolded proteins in the ER lumen. Finally, we highlight select examples of proteopathies (also known as conformational disorders or protein misfolding diseases) caused by protein misfolding in the ER and/or affecting cellular proteostasis and therapeutic interventions that might alleviate or cure the disease symptoms.

Mitochondrial enzymes are protected from stress-induced aggregation by mitochondrial chaperones and the Pim1/LON protease

PubMed Central

Bender, Tom; Lewrenz, Ilka; Franken, Sebastian; Baitzel, Catherina; Voos, Wolfgang

2011-01-01

Proteins in a natural environment are constantly challenged by stress conditions, causing their destabilization, unfolding, and, ultimately, aggregation. Protein aggregation has been associated with a wide variety of pathological conditions, especially neurodegenerative disorders, stressing the importance of adequate cellular protein quality control measures to counteract aggregate formation. To secure protein homeostasis, mitochondria contain an elaborate protein quality control system, consisting of chaperones and ATP-dependent proteases. To determine the effects of protein aggregation on the functional integrity of mitochondria, we set out to identify aggregation-prone endogenous mitochondrial proteins. We could show that major metabolic pathways in mitochondria were affected by the aggregation of key enzyme components, which were largely inactivated after heat stress. Furthermore, treatment with elevated levels of reactive oxygen species strongly influenced the aggregation behavior, in particular in combination with elevated temperatures. Using specific chaperone mutant strains, we showed a protective effect of the mitochondrial Hsp70 and Hsp60 chaperone systems. Moreover, accumulation of aggregated polypeptides was strongly decreased by the AAA-protease Pim1/LON. We therefore propose that the proteolytic breakdown of aggregation-prone polypeptides represents a major protective strategy to prevent the in vivo formation of aggregates in mitochondria. PMID:21209324

TAPBPR bridges UDP-glucose:glycoprotein glucosyltransferase 1 onto MHC class I to provide quality control in the antigen presentation pathway

PubMed Central

Neerincx, Andreas; Hermann, Clemens; Antrobus, Robin; van Hateren, Andy; Cao, Huan; Trautwein, Nico; Stevanović, Stefan; Elliott, Tim; Deane, Janet E; Boyle, Louise H

2017-01-01

Recently, we revealed that TAPBPR is a peptide exchange catalyst that is important for optimal peptide selection by MHC class I molecules. Here, we asked whether any other co-factors associate with TAPBPR, which would explain its effect on peptide selection. We identify an interaction between TAPBPR and UDP-glucose:glycoprotein glucosyltransferase 1 (UGT1), a folding sensor in the calnexin/calreticulin quality control cycle that is known to regenerate the Glc1Man9GlcNAc2 moiety on glycoproteins. Our results suggest the formation of a multimeric complex, dependent on a conserved cysteine at position 94 in TAPBPR, in which TAPBPR promotes the association of UGT1 with peptide-receptive MHC class I molecules. We reveal that the interaction between TAPBPR and UGT1 facilities the reglucosylation of the glycan on MHC class I molecules, promoting their recognition by calreticulin. Our results suggest that in addition to being a peptide editor, TAPBPR improves peptide optimisation by promoting peptide-receptive MHC class I molecules to associate with the peptide-loading complex. DOI: http://dx.doi.org/10.7554/eLife.23049.001 PMID:28425917

Characteristics and origin of the relatively high-quality tight reservoir in the Silurian Xiaoheba Formation in the southeastern Sichuan Basin

PubMed Central

Gong, Xiaoxing; Shi, Zejin; Wang, Yong; Tian, Yaming; Li, Wenjie; Liu, Lei

2017-01-01

A mature understanding of the sandstone gas reservoir in the Xiaoheba Formation in the southeastern Sichuan Basin remains lacking. To assess the reservoir characteristics and the origin of the high-quality reservoir in the Xiaoheba Formation, this paper uses systematic field investigations, physical property analysis, thin section identification, scanning electron microscopy and electron microprobe methods. The results indicate that the Xiaoheba sandstone is an ultra-tight and ultra-low permeability reservoir, with an average porosity of 2.97% and an average permeability of 0.56×10−3 μm2. This promising reservoir is mainly distributed in the Lengshuixi and Shuangliuba regions and the latter has a relatively high-quality reservoir with an average porosity of 5.28% and average permeability of 0.53×10−3 μm2. The reservoir space comprises secondary intergranular dissolved pores, moldic pores and fractures. Microfacies, feldspar dissolution and fracture connectivity control the quality of this reservoir. The relatively weak compaction and cementation in the interbedded delta front distal bar and interdistributary bay microfacies indirectly protected the primary intergranular pores and enhanced late-stage dissolution. Late-stage potassium feldspar dissolution was controlled by the early-stage organic acid dissolution intensity and the distance from the hydrocarbon generation center. Early-stage fractures acted as pathways for organic acid migration and were therefore important factors in the formation of the reservoir. Based on these observations, the area to the west of the Shuangliuba and Lengshuixi regions has potential for gas exploration. PMID:28686735

The neurologic control of arousal and orgasm with specific attention to spinal cord lesions: Integrating preclinical and clinical sciences.

PubMed

Alexander, Marcalee Sipski; Marson, Lesley

2018-01-01

Preclinical research in animal models is important for understanding the neural pathways and pathophysiology underlying changes in sexual function after SCI. In vivo animal models, primarily rodents, have provided valuable information on the central pathways regulating sexual arousal and orgasm; however, further research is required in females and preclinical modeling of SCI that can be better translated to men and women. Translation of the autonomic and somatic regulation of sexual responses from preclinical models through clinical research correlates well with respect to the peripheral-spinal systems involved. However, due to the nature of sexual responses, parallel studies are necessary in animals and humans. Human studies of individuals with SCIs have provided information about the neurologic control of arousal and orgasm. Psychogenic arousal is related to the preservation of sensation at T11-L2 whereas orgasm requires the presence of an intact sacral reflex arc. Studies point to evidence of a spinal pattern generator at L3-5. Because of the exact nature of SCIs, further research using neuroimaging will be beneficial, not only to elucidate the neurological control of sexual responses after SCI, but also in able-bodied individuals. Understanding and ameliorating the effects of SCI on sexual function is important to the well-being and quality of life of individuals with SCIs and their partners, thus future research should focus more on this important topic. Published by Elsevier B.V.

Comprehensive nitrogen budgets for controlled tile drainage fields in eastern ontario, Canada.

PubMed

Sunohara, M D; Craiovan, E; Topp, E; Gottschall, N; Drury, C F; Lapen, D R

2014-03-01

Excessive N loading from subsurface tile drainage has been linked to water quality degradation. Controlled tile drainage (CTD) has the potential to reduce N losses via tile drainage and boost crop yields. While CTD can reduce N loss from tile drainage, it may increase losses through other pathways. A multiple-year field-scale accounting of major N inputs and outputs during the cropping season was conducted on freely drained and controlled tile drained agricultural fields under corn ( L.)-soybean [ (L.) Merr.] production systems in eastern Ontario, Canada. Greater predicted gaseous N emissions for corn and soybean and greater observed lateral seepage N losses were observed for corn and soybean fields under CTD relative to free-draining fields. However, observed N losses from tile were significantly lower for CTD fields, in relation to freely drained fields. Changes in residual soil N were essentially equivalent between drainage treatments, while mass balance residual terms were systematically negative (slightly more so for CTD). Increases in plant N uptake associated with CTD were observed, probably resulting in higher grain yields for corn and soybean. This study illustrates the benefits of CTD in decreasing subsurface tile drainage N losses and boosting crop yields, while demonstrating the potential for CTD to increase N losses via other pathways related to gaseous emissions and groundwater seepage. Copyright © by the American Society of Agronomy, Crop Science Society of America, and Soil Science Society of America, Inc.

Transcriptional profiling identifies differentially expressed genes in developing turkey skeletal muscle

PubMed Central

2011-01-01

Background Skeletal muscle growth and development from embryo to adult consists of a series of carefully regulated changes in gene expression. Understanding these developmental changes in agriculturally important species is essential to the production of high quality meat products. For example, consumer demand for lean, inexpensive meat products has driven the turkey industry to unprecedented production through intensive genetic selection. However, achievements of increased body weight and muscle mass have been countered by an increased incidence of myopathies and meat quality defects. In a previous study, we developed and validated a turkey skeletal muscle-specific microarray as a tool for functional genomics studies. The goals of the current study were to utilize this microarray to elucidate functional pathways of genes responsible for key events in turkey skeletal muscle development and to compare differences in gene expression between two genetic lines of turkeys. To achieve these goals, skeletal muscle samples were collected at three critical stages in muscle development: 18d embryo (hyperplasia), 1d post-hatch (shift from myoblast-mediated growth to satellite cell-modulated growth by hypertrophy), and 16wk (market age) from two genetic lines: a randombred control line (RBC2) maintained without selection pressure, and a line (F) selected from the RBC2 line for increased 16wk body weight. Array hybridizations were performed in two experiments: Experiment 1 directly compared the developmental stages within genetic line, while Experiment 2 directly compared the two lines within each developmental stage. Results A total of 3474 genes were differentially expressed (false discovery rate; FDR < 0.001) by overall effect of development, while 16 genes were differentially expressed (FDR < 0.10) by overall effect of genetic line. Ingenuity Pathways Analysis was used to group annotated genes into networks, functions, and canonical pathways. The expression of 28 genes involved in extracellular matrix regulation, cell death/apoptosis, and calcium signaling/muscle function, as well as genes with miscellaneous function was confirmed by qPCR. Conclusions The current study identified gene pathways and uncovered novel genes important in turkey muscle growth and development. Future experiments will focus further on several of these candidate genes and the expression and mechanism of action of their protein products. PMID:21385442

The Treatment Train approach to reducing non-point source pollution from agriculture

NASA Astrophysics Data System (ADS)

Barber, N.; Reaney, S. M.; Barker, P. A.; Benskin, C.; Burke, S.; Cleasby, W.; Haygarth, P.; Jonczyk, J. C.; Owen, G. J.; Snell, M. A.; Surridge, B.; Quinn, P. F.

2016-12-01

An experimental approach has been applied to an agricultural catchment in NW England, where non-point pollution adversely affects freshwater ecology. The aim of the work (as part of the River Eden Demonstration Test Catchment project) is to develop techniques to manage agricultural runoff whilst maintaining food production. The approach used is the Treatment Train (TT), which applies multiple connected mitigation options that control nutrient and fine sediment pollution at source, and address polluted runoff pathways at increasing spatial scale. The principal agricultural practices in the study sub-catchment (1.5 km2) are dairy and stock production. Farm yards can act as significant pollution sources by housing large numbers of animals; these areas are addressed initially with infrastructure improvements e.g. clean/dirty water separation and upgraded waste storage. In-stream high resolution monitoring of hydrology and water quality parameters showed high-discharge events to account for the majority of pollutant exports ( 80% total phosphorus; 95% fine sediment), and primary transfer routes to be surface and shallow sub-surface flow pathways, including drains. To manage these pathways and reduce hydrological connectivity, a series of mitigation features were constructed to intercept and temporarily store runoff. Farm tracks, field drains, first order ditches and overland flow pathways were all targeted. The efficacy of the mitigation features has been monitored at event and annual scale, using inflow-outflow sampling and sediment/nutrient accumulation measurements, respectively. Data presented here show varied but positive results in terms of reducing acute and chronic sediment and nutrient losses. An aerial fly-through of the catchment is used to demonstrate how the TT has been applied to a fully-functioning agricultural landscape. The elevated perspective provides a better understanding of the spatial arrangement of mitigation features, and how they can be implemented without impacting on the farm's primary function. The TT has the potential to yield benefits beyond those associated with water quality. Increasing catchment resilience through the use of landscape interventions can provide multiple benefits by mitigating for floods and droughts and creating ecological habitat.

Rule Mining Techniques to Predict Prokaryotic Metabolic Pathways.

PubMed

Saidi, Rabie; Boudellioua, Imane; Martin, Maria J; Solovyev, Victor

2017-01-01

It is becoming more evident that computational methods are needed for the identification and the mapping of pathways in new genomes. We introduce an automatic annotation system (ARBA4Path Association Rule-Based Annotator for Pathways) that utilizes rule mining techniques to predict metabolic pathways across wide range of prokaryotes. It was demonstrated that specific combinations of protein domains (recorded in our rules) strongly determine pathways in which proteins are involved and thus provide information that let us very accurately assign pathway membership (with precision of 0.999 and recall of 0.966) to proteins of a given prokaryotic taxon. Our system can be used to enhance the quality of automatically generated annotations as well as annotating proteins with unknown function. The prediction models are represented in the form of human-readable rules, and they can be used effectively to add absent pathway information to many proteins in UniProtKB/TrEMBL database.

What is a clinical pathway? Refinement of an operational definition to identify clinical pathway studies for a Cochrane systematic review.

PubMed

Lawal, Adegboyega K; Rotter, Thomas; Kinsman, Leigh; Machotta, Andreas; Ronellenfitsch, Ulrich; Scott, Shannon D; Goodridge, Donna; Plishka, Christopher; Groot, Gary

2016-02-23

Clinical pathways (CPWs) are a common component in the quest to improve the quality of health. CPWs are used to reduce variation, improve quality of care, and maximize the outcomes for specific groups of patients. An ongoing challenge is the operationalization of a definition of CPW in healthcare. This may be attributable to both the differences in definition and a lack of conceptualization in the field of clinical pathways. This correspondence article describes a process of refinement of an operational definition for CPW research and proposes an operational definition for the future syntheses of CPWs literature. Following the approach proposed by Kinsman et al. (BMC Medicine 8(1):31, 2010) and Wieland et al. (Alternative Therapies in Health and Medicine 17(2):50, 2011), we used a four-stage process to generate a five criteria checklist for the definition of CPWs. We refined the operational definition, through consensus, merging two of the checklist's criteria, leading to a more inclusive criterion for accommodating CPW studies conducted in various healthcare settings. The following four criteria for CPW operational definition, derived from the refinement process described above, are (1) the intervention was a structured multidisciplinary plan of care; (2) the intervention was used to translate guidelines or evidence into local structures; (3) the intervention detailed the steps in a course of treatment or care in a plan, pathway, algorithm, guideline, protocol or other 'inventory of actions' (i.e. the intervention had time-frames or criteria-based progression); and (4) the intervention aimed to standardize care for a specific population. An intervention meeting all four criteria was considered to be a CPW. The development of operational definitions for complex interventions is a useful approach to appraise and synthesize evidence for policy development and quality improvement.

Parenting in infancy and self-regulation in preschool: an investigation of the role of attachment history.

PubMed

Birmingham, R S; Bub, K L; Vaughn, B E

2017-04-01

Parenting and attachment are critical in the emergence of self-regulation (SR) in preschool. However, most studies use general indexes of parenting quality, failing to explore the unique contributions of sensitivity and home quality to SR. Further, the nature of the interplay between parenting and attachment history is not well understood. Using a sample of 938 children from The National Institute of Child Health and Human Development Study of Early Child Care and Youth Development, a series of structural equation models were fit to determine whether sensitivity and home quality concurrently predicted SR at 54 months, and whether attachment mediated or moderated these pathways. Results suggest that both sensitivity and home quality uniquely predict SR. Further, these early parenting variables were each indirectly associated with SR through children's attachment history. That is, higher levels of sensitivity and home quality predicted secure attachment history, which, along with parenting, predicted more advanced SR skills at 54 months. No moderated pathways emerged, suggesting that attachment history may be best conceptualized as a mediating mechanism.

The Strengthening Families Initiative and Child Care Quality Improvement: How Strengthening Families Influenced Change in Child Care Programs in One State

ERIC Educational Resources Information Center

Douglass, Anne; Klerman, Lorraine

2012-01-01

Research Findings: This study investigated how the Strengthening Families through Early Care and Education initiative in Illinois (SFI) influenced change in 4 child care programs. Findings indicate that SFI influenced quality improvements through 4 primary pathways: (a) Learning Networks, (b) the quality of training, (c) the engagement of program…

Economics of Quality Education and Paths Leading into and out of Quality Education: Evidence from Debre Markos University, Ethiopia

ERIC Educational Resources Information Center

Molla, Tsegaye

2017-01-01

The difference in economic development among nations entirely emanates from difference in human capital development as it is the priority pathway out of poverty, diverse socio-economic and environmental crises. Although, huge investment in human capital development has long been made, mere investment will never lead to quality labor force unless…

The quality of the evidence base for clinical pathway effectiveness: room for improvement in the design of evaluation trials.

PubMed

Rotter, Thomas; Kinsman, Leigh; James, Erica; Machotta, Andreas; Steyerberg, Ewout W

2012-06-18

The purpose of this article is to report on the quality of the existing evidence base regarding the effectiveness of clinical pathway (CPW) research in the hospital setting. The analysis is based on a recently published Cochrane review of the effectiveness of CPWs. An integral component of the review process was a rigorous appraisal of the methodological quality of published CPW evaluations. This allowed the identification of strengths and limitations of the evidence base for CPW effectiveness. We followed the validated Cochrane Effective Practice and Organisation of Care Group (EPOC) criteria for randomized and non-randomized clinical pathway evaluations. In addition, we tested the hypotheses that simple pre-post studies tend to overestimate CPW effects reported. Out of the 260 primary studies meeting CPW content criteria, only 27 studies met the EPOC study design criteria, with the majority of CPW studies (more than 70 %) excluded from the review on the basis that they were simple pre-post evaluations, mostly comparing two or more annual patient cohorts. Methodologically poor study designs are often used to evaluate CPWs and this compromises the quality of the existing evidence base. Cochrane EPOC methodological criteria, including the selection of rigorous study designs along with detailed descriptions of CPW development and implementation processes, are recommended for quantitative evaluations to improve the evidence base for the use of CPWs in hospitals.

Systematic evaluation of RNA quality, microarray data reliability and pathway analysis in fresh, fresh frozen and formalin-fixed paraffin-embedded tissue samples.

PubMed

Wimmer, Isabella; Tröscher, Anna R; Brunner, Florian; Rubino, Stephen J; Bien, Christian G; Weiner, Howard L; Lassmann, Hans; Bauer, Jan

2018-04-20

Formalin-fixed paraffin-embedded (FFPE) tissues are valuable resources commonly used in pathology. However, formalin fixation modifies nucleic acids challenging the isolation of high-quality RNA for genetic profiling. Here, we assessed feasibility and reliability of microarray studies analysing transcriptome data from fresh, fresh-frozen (FF) and FFPE tissues. We show that reproducible microarray data can be generated from only 2 ng FFPE-derived RNA. For RNA quality assessment, fragment size distribution (DV200) and qPCR proved most suitable. During RNA isolation, extending tissue lysis time to 10 hours reduced high-molecular-weight species, while additional incubation at 70 °C markedly increased RNA yields. Since FF- and FFPE-derived microarrays constitute different data entities, we used indirect measures to investigate gene signal variation and relative gene expression. Whole-genome analyses revealed high concordance rates, while reviewing on single-genes basis showed higher data variation in FFPE than FF arrays. Using an experimental model, gene set enrichment analysis (GSEA) of FFPE-derived microarrays and fresh tissue-derived RNA-Seq datasets yielded similarly affected pathways confirming the applicability of FFPE tissue in global gene expression analysis. Our study provides a workflow comprising RNA isolation, quality assessment and microarray profiling using minimal RNA input, thus enabling hypothesis-generating pathway analyses from limited amounts of precious, pathologically significant FFPE tissues.

The olfactory pathway mediates sheltering behavior of Caribbean spiny lobsters, Panulirus argus, to conspecific urine signals.

PubMed

Horner, Amy J; Weissburg, Marc J; Derby, Charles D

2008-03-01

The "noses" of diverse taxa are organized into different subsystems whose functions are often not well understood. The "nose" of decapod crustaceans is organized into two parallel pathways that originate in different populations of antennular sensilla and project to specific neuropils in the brain-the aesthetasc/olfactory lobe pathway and the non-aesthetasc/lateral antennular neuropil pathway. In this study, we investigated the role of these pathways in mediating shelter selection of Caribbean spiny lobsters, Panulirus argus, in response to conspecific urine signals. We compared the behavior of ablated animals and intact controls. Our results show that control and non-aesthetasc ablated lobsters have a significant overall preference for shelters emanating urine over control shelters. Thus the non-aesthetasc pathway does not play a critical role in shelter selection. In contrast, spiny lobsters with aesthetascs ablated did not show a preference for either shelter, suggesting that the aesthetasc/olfactory pathway is important for processing social odors. Our results show a difference in the function of these dual chemosensory pathways in responding to social cues, with the aesthetasc/olfactory lobe pathway playing a major role. We discuss our results in the context of why the noses of many animals contain multiple parallel chemosensory systems.

Headache service quality: evaluation of quality indicators in 14 specialist-care centres.

PubMed

Schramm, Sara; Uluduz, Derya; Gouveia, Raquel Gil; Jensen, Rigmor; Siva, Aksel; Uygunoglu, Ugur; Gvantsa, Giorgadze; Mania, Maka; Braschinsky, Mark; Filatova, Elena; Latysheva, Nina; Osipova, Vera; Skorobogatykh, Kirill; Azimova, Julia; Straube, Andreas; Eren, Ozan Emre; Martelletti, Paolo; De Angelis, Valerio; Negro, Andrea; Linde, Mattias; Hagen, Knut; Radojicic, Aleksandra; Zidverc-Trajkovic, Jasna; Podgorac, Ana; Paemeleire, Koen; De Pue, Annelien; Lampl, Christian; Steiner, Timothy J; Katsarava, Zaza

2016-12-01

The study was a collaboration between Lifting The Burden (LTB) and the European Headache Federation (EHF). Its aim was to evaluate the implementation of quality indicators for headache care Europe-wide in specialist headache centres (level-3 according to the EHF/LTB standard). Employing previously-developed instruments in 14 such centres, we made enquiries, in each, of health-care providers (doctors, nurses, psychologists, physiotherapists) and 50 patients, and analysed the medical records of 50 other patients. Enquiries were in 9 domains: diagnostic accuracy, individualized management, referral pathways, patient's education and reassurance, convenience and comfort, patient's satisfaction, equity and efficiency of the headache care, outcome assessment and safety. Our study showed that highly experienced headache centres treated their patients in general very well. The centres were content with their work and their patients were content with their treatment. Including disability and quality-of-life evaluations in clinical assessments, and protocols regarding safety, proved problematic: better standards for these are needed. Some centres had problems with follow-up: many specialised centres operated in one-touch systems, without possibility of controlling long-term management or the success of treatments dependent on this. This first Europe-wide quality study showed that the quality indicators were workable in specialist care. They demonstrated common trends, producing evidence of what is majority practice. They also uncovered deficits that might be remedied in order to improve quality. They offer the means of setting benchmarks against which service quality may be judged. The next step is to take the evaluation process into non-specialist care (EHF/LTB levels 1 and 2).

The cell cycle and acute kidney injury

PubMed Central

Price, Peter M.; Safirstein, Robert L.; Megyesi, Judit

2009-01-01

Acute kidney injury (AKI) activates pathways of cell death and cell proliferation. Although seemingly discrete and unrelated mechanisms, these pathways can now be shown to be connected and even to be controlled by similar pathways. The dependence of the severity of renal-cell injury on cell cycle pathways can be used to control and perhaps to prevent acute kidney injury. This review is written to address the correlation between cellular life and death in kidney tubules, especially in acute kidney injury. PMID:19536080

Bufalin attenuates the stage and metastatic potential of hepatocellular carcinoma in nude mice

PubMed Central

2014-01-01

Background Advanced hepatocellular carcinoma (HCC) patients undergo significant tumor growth and metastasis. Here, we investigated bufalin for treating HCC, which exhibits anti-tumor activities in many tumor cell lines. Method In our experiment, HCCLM3-R cells were injected into nude mice to form subcutaneous human HCC tumors that were implanted into the liver to establish orthotopic transplantation tumor models. Bufalin was injected intraperitoneally at 1 or 1.5 mg/kg. LY294002 (100 mg/kg), a potent inhibitor of Akt which reduced the levels of pAkt in HCCLM3 cell lines, was injected intraperitoneally into one group thrice weekly. The control was injected with an equal volume of saline. Morphological alterations were evaluated in the liver and lung by stereomicroscopy, the apoptotic rate was measured by TUNEL staining, and expression of AKT/GSK3β/β-catenin/E-cadherin signaling pathway-related proteins was detected by immunohistochemistry (IHC) and western blot analysis. Results These results suggested that the sizes and qualities of orthotopic transplanted tumors as well as pulmonary metastasis decreased markedly at the highest bufalin dose compared with that in the control. Orthotopic transplanted tumor tissues were necrotic in bufalin-treated groups and the apoptotic cell number was markedly higher at the highest bufalin dose compared with that in the control. Certain changes of expression of AKT/GSK3β/β-catenin/E-cadherin signaling pathway-related proteins were in tumor tissues, which were related to the bufalin dose. Similar results were observed in the LY294002-treated group. Conclusion Based on the above, one can draw conclusions that bufalin has significant anti-tumor activities and reduces the metastatic potential in an orthotopic transplantation tumor model of human HCC. Inhibition of AKT/GSK3β/β-catenin/E-cadherin signaling pathways by bufalin may show therapeutic effects in advanced HCC patients. PMID:24581171

Diet and adipose tissue distributions: The Multi-Ethnic Study of Atherosclerosis

USDA-ARS?s Scientific Manuscript database

Dietary quality affects cardiometabolic risk, yet its pathways of influence on regional adipose tissue depots involved in metabolic and diabetes risk are not well established. We aimed to investigate the relationship between dietary quality and regional adiposity. We investigated 5079 individuals in...

Consequences of divergent selection for residual feed intake in pigs on muscle energy metabolism and meat quality.

PubMed

Faure, J; Lefaucheur, L; Bonhomme, N; Ecolan, P; Meteau, K; Coustard, S Metayer; Kouba, M; Gilbert, H; Lebret, B

2013-01-01

Selection to decrease Residual Feed Intake (RFI) is a relevant way to improve feed efficiency in growing pigs. However, RFI criterion is correlated with body composition and muscle characteristics. Present study evaluated adaptive responses to divergent selection on RFI on muscle metabolism and homeostasis through AMP-activated protein kinase pathway. Consequences on technological and sensory meat quality were also analyzed in two lines of Large White pigs after six generations of divergent selection on RFI. RFI(-) pigs (n=60) exhibited similar growth rate but lower feed intake and conversion ratio, and were leaner than RFI(+) pigs (n=57). Despite higher glycogen content, metabolic enzyme capacities involved in glycolytic, fatty acid oxidation pathway and energy balance were reduced in the Longissimus muscle of the RFI(-) pigs. Reduced muscle homeostasis in the RFI(-) line influenced post-mortem metabolism and impaired technological quality traits of loin and ham but had only slight effects on meat eating quality. Copyright © 2012 Elsevier Ltd. All rights reserved.

Roles of the Raf/MEK/ERK and PI3K/PTEN/Akt/mTOR pathways in controlling growth and sensitivity to therapy-implications for cancer and aging

PubMed Central

Steelman, Linda S.; Chappell, William H.; Abrams, Stephen L.; Kempf, C. Ruth; Long, Jacquelyn; Laidler, Piotr; Mijatovic, Sanja; Maksimovic-Ivanic, Danijela; Stivala, Franca; Mazzarino, Maria C.; Donia, Marco; Fagone, Paolo; Malaponte, Graziella; Nicoletti, Ferdinando; Libra, Massimo; Milella, Michele; Tafuri, Agostino; Bonati, Antonio; Bäsecke, Jörg; Cocco, Lucio; Evangelisti, Camilla; Martelli, Alberto M.; Montalto, Giuseppe; Cervello, Melchiorre; McCubrey, James A.

2011-01-01

Dysregulated signaling through the Ras/Raf/MEK/ERK and PI3K/PTEN/Akt/mTOR pathways is often the result of genetic alterations in critical components in these pathways or upstream activators. Unrestricted cellular proliferation and decreased sensitivity to apoptotic-inducing agents are typically associated with activation of these pro-survival pathways. This review discusses the functions these pathways have in normal and neoplastic tissue growth and how they contribute to resistance to apoptotic stimuli. Crosstalk and commonly identified mutations that occur within these pathways that contribute to abnormal activation and cancer growth will also be addressed. Finally the recently described roles of these pathways in cancer stem cells, cellular senescence and aging will be evaluated. Controlling the expression of these pathways could ameliorate human health. PMID:21422497

Defining the Protein–Protein Interaction Network of the Human Hippo Pathway*

PubMed Central

Wang, Wenqi; Li, Xu; Huang, Jun; Feng, Lin; Dolinta, Keithlee G.; Chen, Junjie

2014-01-01

The Hippo pathway, which is conserved from Drosophila to mammals, has been recognized as a tumor suppressor signaling pathway governing cell proliferation and apoptosis, two key events involved in organ size control and tumorigenesis. Although several upstream regulators, the conserved kinase cascade and key downstream effectors including nuclear transcriptional factors have been defined, the global organization of this signaling pathway is not been fully understood. Thus, we conducted a proteomic analysis of human Hippo pathway, which revealed the involvement of an extensive protein–protein interaction network in this pathway. The mass spectrometry data were deposited to ProteomeXchange with identifier PXD000415. Our data suggest that 550 interactions within 343 unique protein components constitute the central protein–protein interaction landscape of human Hippo pathway. Our study provides a glimpse into the global organization of Hippo pathway, reveals previously unknown interactions within this pathway, and uncovers new potential components involved in the regulation of this pathway. Understanding these interactions will help us further dissect the Hippo signaling-pathway and extend our knowledge of organ size control. PMID:24126142

Water deficit alters differentially metabolic pathways affecting important flavor and quality traits in grape berries of Cabernet Sauvignon and Chardonnay

PubMed Central

Deluc, Laurent G; Quilici, David R; Decendit, Alain; Grimplet, Jérôme; Wheatley, Matthew D; Schlauch, Karen A; Mérillon, Jean-Michel; Cushman, John C; Cramer, Grant R

2009-01-01

Background Water deficit has significant effects on grape berry composition resulting in improved wine quality by the enhancement of color, flavors, or aromas. While some pathways or enzymes affected by water deficit have been identified, little is known about the global effects of water deficit on grape berry metabolism. Results The effects of long-term, seasonal water deficit on berries of Cabernet Sauvignon, a red-wine grape, and Chardonnay, a white-wine grape were analyzed by integrated transcript and metabolite profiling. Over the course of berry development, the steady-state transcript abundance of approximately 6,000 Unigenes differed significantly between the cultivars and the irrigation treatments. Water deficit most affected the phenylpropanoid, ABA, isoprenoid, carotenoid, amino acid and fatty acid metabolic pathways. Targeted metabolites were profiled to confirm putative changes in specific metabolic pathways. Water deficit activated the expression of numerous transcripts associated with glutamate and proline biosynthesis and some committed steps of the phenylpropanoid pathway that increased anthocyanin concentrations in Cabernet Sauvignon. In Chardonnay, water deficit activated parts of the phenylpropanoid, energy, carotenoid and isoprenoid metabolic pathways that contribute to increased concentrations of antheraxanthin, flavonols and aroma volatiles. Water deficit affected the ABA metabolic pathway in both cultivars. Berry ABA concentrations were highly correlated with 9-cis-epoxycarotenoid dioxygenase (NCED1) transcript abundance, whereas the mRNA expression of other NCED genes and ABA catabolic and glycosylation processes were largely unaffected. Water deficit nearly doubled ABA concentrations within berries of Cabernet Sauvignon, whereas it decreased ABA in Chardonnay at véraison and shortly thereafter. Conclusion The metabolic responses of grapes to water deficit varied with the cultivar and fruit pigmentation. Chardonnay berries, which lack any significant anthocyanin content, exhibited increased photoprotection mechanisms under water deficit conditions. Water deficit increased ABA, proline, sugar and anthocyanin concentrations in Cabernet Sauvignon, but not Chardonnay berries, consistent with the hypothesis that ABA enhanced accumulation of these compounds. Water deficit increased the transcript abundance of lipoxygenase and hydroperoxide lyase in fatty metabolism, a pathway known to affect berry and wine aromas. These changes in metabolism have important impacts on berry flavor and quality characteristics. Several of these metabolites are known to contribute to increased human-health benefits. PMID:19426499

Process mining routinely collected electronic health records to define real-life clinical pathways during chemotherapy.

PubMed

Baker, Karl; Dunwoodie, Elaine; Jones, Richard G; Newsham, Alex; Johnson, Owen; Price, Christopher P; Wolstenholme, Jane; Leal, Jose; McGinley, Patrick; Twelves, Chris; Hall, Geoff

2017-07-01

There is growing interest in the use of routinely collected electronic health records to enhance service delivery and facilitate clinical research. It should be possible to detect and measure patterns of care and use the data to monitor improvements but there are methodological and data quality challenges. Driven by the desire to model the impact of a patient self-test blood count monitoring service in patients on chemotherapy, we aimed to (i) establish reproducible methods of process-mining electronic health records, (ii) use the outputs derived to define and quantify patient pathways during chemotherapy, and (iii) to gather robust data which is structured to be able to inform a cost-effectiveness decision model of home monitoring of neutropenic status during chemotherapy. Electronic Health Records at a UK oncology centre were included if they had (i) a diagnosis of metastatic breast cancer and received adjuvant epirubicin and cyclosphosphamide chemotherapy or (ii) colorectal cancer and received palliative oxaliplatin and infusional 5-fluorouracil chemotherapy, and (iii) were first diagnosed with cancer between January 2004 and February 2013. Software and a Markov model were developed, producing a schematic of patient pathways during chemotherapy. Significant variance from the assumed care pathway was evident from the data. Of the 535 patients with breast cancer and 420 with colorectal cancer there were 474 and 329 pathway variants respectively. Only 27 (5%) and 26 (6%) completed the planned six cycles of chemotherapy without having unplanned hospital contact. Over the six cycles, 169 (31.6%) patients with breast cancer and 190 (45.2%) patients with colorectal cancer were admitted to hospital. The pathways of patients on chemotherapy are complex. An iterative approach to addressing semantic and data quality issues enabled the effective use of routinely collected patient records to produce accurate models of the real-life experiences of chemotherapy patients and generate clinically useful information. Very few patients experience the idealised patient pathway that is used to plan their care. A better understanding of real-life clinical pathways through process mining can contribute to care and data quality assurance, identifying unmet needs, facilitating quantification of innovation impact, communicating with stakeholders, and ultimately improving patient care and outcomes. Copyright © 2017 Elsevier B.V. All rights reserved.

Pathways for Academic Career and Employment (PACE) Program: Fiscal Year 2015 Report

ERIC Educational Resources Information Center

Iowa Department of Education, 2016

2016-01-01

The pathways for academic career and employment program (PACE) is established to provide funding to community colleges for the development of projects that will lead to gainful, quality, in-state employment for members of target populations by providing them with both effective academic and employment training to ensure gain. This is the second…

Parent and Peer Pathways to Adolescent Delinquency: Variations by Ethnicity and Neighborhood Context

ERIC Educational Resources Information Center

Deutsch, Arielle R.; Crockett, Lisa J.; Wolff, Jennifer M.; Russell, Stephen T.

2012-01-01

Effects of ethnicity and neighborhood quality often are confounded in research on adolescent delinquent behavior. This study examined the pathways to delinquency among 2,277 African American and 5,973 European American youth residing in high-risk and low-risk neighborhoods. Using data from a national study of youth, a meditational model was tested…

Long-Term Management Strategy for Dredged Material Disposal for Naval Facilities at Pearl Harbor, Hawaii. Phase II - Evaulation of Alternatives

DTIC Science & Technology

2000-03-01

26 Leachate Pathway.................................... 31 Plant Uptake Pathway.................................. 35 Volatization and Odor...Bi13 Appendix C - Surface Runoff Testing............................Cl Appendix D - Leachate Evaluation..............................D1 Appendix E...Oxidized Dredged Material..........................29 Table 7. Mixing Zone Requirement for Runoff Discharges............ 30 Table 8. Leachate Quality

Mutations in Four Glycosyl Hydrolases Reveal a Highly Coordinated Pathway for Rhodopsin Biosynthesis and N-Glycan Trimming in Drosophila melanogaster

PubMed Central

Rosenbaum, Erica E.; Vasiljevic, Eva; Brehm, Kimberley S.; Colley, Nansi Jo

2014-01-01

As newly synthesized glycoproteins move through the secretory pathway, the asparagine-linked glycan (N-glycan) undergoes extensive modifications involving the sequential removal and addition of sugar residues. These modifications are critical for the proper assembly, quality control and transport of glycoproteins during biosynthesis. The importance of N-glycosylation is illustrated by a growing list of diseases that result from defects in the biosynthesis and processing of N-linked glycans. The major rhodopsin in Drosophila melanogaster photoreceptors, Rh1, is highly unique among glycoproteins, as the N-glycan appears to be completely removed during Rh1 biosynthesis and maturation. However, much of the deglycosylation pathway for Rh1 remains unknown. To elucidate the key steps in Rh1 deglycosylation in vivo, we characterized mutant alleles of four Drosophila glycosyl hydrolases, namely α-mannosidase-II (α-Man-II), α-mannosidase-IIb (α-Man-IIb), a β-N-acetylglucosaminidase called fused lobes (Fdl), and hexosaminidase 1 (Hexo1). We have demonstrated that these four enzymes play essential and unique roles in a highly coordinated pathway for oligosaccharide trimming during Rh1 biosynthesis. Our results reveal that α-Man-II and α-Man-IIb are not isozymes like their mammalian counterparts, but rather function at distinct stages in Rh1 maturation. Also of significance, our results indicate that Hexo1 has a biosynthetic role in N-glycan processing during Rh1 maturation. This is unexpected given that in humans, the hexosaminidases are typically lysosomal enzymes involved in N-glycan catabolism with no known roles in protein biosynthesis. Here, we present a genetic dissection of glycoprotein processing in Drosophila and unveil key steps in N-glycan trimming during Rh1 biosynthesis. Taken together, our results provide fundamental advances towards understanding the complex and highly regulated pathway of N-glycosylation in vivo and reveal novel insights into the functions of glycosyl hydrolases in the secretory pathway. PMID:24785692

Wnt and Notch signaling pathway involved in wound healing by targeting c-Myc and Hes1 separately.

PubMed

Shi, Yan; Shu, Bin; Yang, Ronghua; Xu, Yingbin; Xing, Bangrong; Liu, Jian; Chen, Lei; Qi, Shaohai; Liu, Xusheng; Wang, Peng; Tang, Jinming; Xie, Julin

2015-06-16

Wnt and Notch signaling pathways are critically involved in relative cell fate decisions within the development of cutaneous tissues. Moreover, several studies identified the above two pathways as having a significant role during wound healing. However, their biological effects during cutaneous tissues repair are unclear. We employed a self-controlled model (Sprague-Dawley rats with full-thickness skin wounds) to observe the action and effect of Wnt/β-catenin and Notch signalings in vivo. The quality of wound repair relevant to the gain/loss-of-function Wnt/β-catenin and Notch activation was estimated by hematoxylin-and-eosin and Masson staining. Immunofluorescence analysis and Western blot analysis were used to elucidate the underlying mechanism of the regulation of Wnt and Notch signaling pathways in wound healing. Meanwhile, epidermal stem cells (ESCs) were cultured in keratinocyte serum-free medium with Jaggedl or in DAPT (N-[(3,5-difluorophenyl)acetyl]-L-alanyl-2-phenyl]glycine-1,1-dimethylethyl) to investigate whether the interruption of Notch signaling contributes to the expression of Wnt/β-catenin signaling. The results showed that in vivo the gain-of-function Wnt/β-catenin and Notch activation extended the ability to promote wound closure. We further determined that activation or inhibition of Wnt signaling and Notch signaling can affect the proliferation of ESCs, the differentiation and migration of keratinocytes, and follicle regeneration by targeting c-Myc and Hes1, which ultimately lead to enhanced or delayed wound healing. Furthermore, Western blot analysis suggested that the two pathways might interact in vivo and in vitro. These results suggest that Wnt and Notch signalings play important roles in cutaneous repair by targeting c-Myc and Hes1 separately. What's more, interaction between the above two pathways might act as a vital role in regulation of wound healing.

Clinical audit system as a quality improvement tool in the management of breast cancer.

PubMed

Vijayakumar, Chellappa; Maroju, Nanda Kishore; Srinivasan, Krishnamachari; Reddy, K Satyanarayana

2016-11-01

Quality improvement is recognized as a major factor that can transform healthcare management. This study is a clinical audit that aims at analysing treatment time as a quality indicator and explores the role of setting a target treatment time on reducing treatment delays. All newly diagnosed patients with breast cancer between September 2011 and August 2013 were included in the study. Clinical care pathway for breast cancer patients was standardized and the timeliness of care at each step of the pathway was calculated. Data collection was spread over three phases, baseline, audit cycle I, and audit cycle II. Each cycle was preceded by a quality improvement intervention, and followed by analysis. A total of 334 patients with breast cancer were included in the audit. The overall time from first visit to initiation of treatment was 66.3 days during the baseline period. This improved to 40.4 and 28.5 days at the end of Audit cycle I and II, respectively. The idealized target time of 28 days for initiating treatment was achieved in 5, 23.5, and 65.2% of patients in the baseline period, Audit cycle I, and Audit Cycle II, respectively. There was improvement noted across all steps of the clinical care pathway. This study confirms that audit is a powerful tool in quality improvement programs and helps achieve timely care. Gains achieved through an audit process may not be sustainable unless underlying patient factors and resource deficits are addressed. Copyright © 2016 IJS Publishing Group Ltd. Published by Elsevier Ltd. All rights reserved.

The Longitudinal Association Between Poor Sleep Quality and Cyberbullying, Mediated by Anger.

PubMed

Erreygers, Sara; Vandebosch, Heidi; Vranjes, Ivana; Baillien, Elfi; De Witte, Hans

2018-01-09

Adolescents tend to go to bed later and sleep less as they grow older, although their need for sleep stays the same throughout adolescence. Poor sleep has negative consequences on personal and interpersonal functioning, including increased aggressive tendencies. With adolescents' social life increasingly including interactions via digital media, these interactions may also become more aggressive when adolescents' sleep problems increase. One of the ways in which online aggression may be enacted is through cyberbullying. Although previous research has examined the role of sleep disruptions in offline bullying, the role of sleep in cyberbullying has not yet been addressed. Therefore, this study examines the longitudinal effect of poor sleep quality on later cyberbullying behavior. Thirteen- to fourteen-year-old adolescents completed self-report measures on sleep quality, anger, cyberbullying perpetration, and frequency of digital media use. Because one of the pathways through which sleep is proposed to be linked to aggression is an affective pathway, namely via angry affect, a mediation model of poor sleep quality predicting cyberbullying via feelings of anger was tested. Results from structural equation modeling and a bootstrap test indicated that poor sleep quality was indeed indirectly associated with later cyberbullying behavior through heightened feelings of anger, even when taking the effects of the use of digital media and previous cyberbullying behavior into account. This finding provides support for the proposed affective pathway linking sleep problems to aggression. As sleep problems and anger seem to play a predicting role in cyberbullying behavior, suggestions for cyberbullying intervention and prevention strategies are formulated.

A rapid response air quality analysis system for use in projects having stringent quality assurance requirements

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bowman, A.W.

1990-04-01

This paper describes an approach to solve air quality problems which frequently occur during iterations of the baseline change process. From a schedule standpoint, it is desirable to perform this evaluation in as short a time as possible while budgetary pressures limit the size of the staff available to do the work. Without a method in place to deal with baseline change proposal requests the environment analysts may not be able to produce the analysis results in the time frame expected. Using a concept called the Rapid Response Air Quality Analysis System (RAAS), the problems of timing and cost becomemore » tractable. The system could be adapted to assess other atmospheric pathway impacts, e.g., acoustics or visibility. The air quality analysis system used to perform the EA analysis (EA) for the Salt Repository Project (part of the Civilian Radioactive Waste Management Program), and later to evaluate the consequences of proposed baseline changes, consists of three components: Emission source data files; Emission rates contained in spreadsheets; Impact assessment model codes. The spreadsheets contain user-written codes (macros) that calculate emission rates from (1) emission source data (e.g., numbers and locations of sources, detailed operating schedules, and source specifications including horsepower, load factor, and duty cycle); (2) emission factors such as those published by the U.S. Environmental Protection Agency, and (3) control efficiencies.« less

Strain-Engineered Oxygen Vacancies in CaMnO3 Thin Films.

PubMed

Chandrasena, Ravini U; Yang, Weibing; Lei, Qingyu; Delgado-Jaime, Mario U; Wijesekara, Kanishka D; Golalikhani, Maryam; Davidson, Bruce A; Arenholz, Elke; Kobayashi, Keisuke; Kobata, Masaaki; de Groot, Frank M F; Aschauer, Ulrich; Spaldin, Nicola A; Xi, Xiaoxing; Gray, Alexander X

2017-02-08

We demonstrate a novel pathway to control and stabilize oxygen vacancies in complex transition-metal oxide thin films. Using atomic layer-by-layer pulsed laser deposition (PLD) from two separate targets, we synthesize high-quality single-crystalline CaMnO 3 films with systematically varying oxygen vacancy defect formation energies as controlled by coherent tensile strain. The systematic increase of the oxygen vacancy content in CaMnO 3 as a function of applied in-plane strain is observed and confirmed experimentally using high-resolution soft X-ray absorption spectroscopy (XAS) in conjunction with bulk-sensitive hard X-ray photoemission spectroscopy (HAXPES). The relevant defect states in the densities of states are identified and the vacancy content in the films quantified using the combination of first-principles theory and core-hole multiplet calculations with holistic fitting. Our findings open up a promising avenue for designing and controlling new ionically active properties and functionalities of complex transition-metal oxides via strain-induced oxygen-vacancy formation and ordering.

Transcriptomic basis of functional difference and coordination between seeds and the silique wall of Brassica napus during the seed-filling stage.

PubMed

Liu, Han; Yang, Qingyong; Fan, Chuchuan; Zhao, Xiaoqin; Wang, Xuemin; Zhou, Yongming

2015-04-01

The silique of oilseed rape (Brassica napus) is a composite organ including seeds and the silique wall (SW) that possesses distinctly physiological, biochemical and functional differentiations. Yet, the molecular events controlling such differences between the SW and seeds, as well as their coordination during silique development at transcriptional level are largely unknown. Here, we identified large sets of differentially expressed genes in the SW and seeds of siliques at 21-22 days after flowering with a Brassica 95K EST microarray. At this particular stage, there were 3278 SW preferentially expressed genes and 2425 seed preferentially expressed genes. Using the MapMan visualization software, genes differentially regulated in various metabolic pathways and sub-pathways between the SW and seeds were revealed. Photosynthesis and transport-related genes were more actively transcripted in the SW, while those involved in lipid metabolism were more active in seeds during the seed filling stage. On the other hand, genes involved in secondary metabolisms were selectively regulated in the SW and seeds. Large numbers of transcription factors were identified to be differentially expressed between the SW and seeds, suggesting a complex pattern of transcriptional control in these two organs. Furthermore, most genes discussed in categories or pathways showed a similar expression pattern through 21 DAF to 42 DAF. Our results thus provide insights into the coordination of seeds and the SW in the developing silique at the transcriptional levels, which will facilitate the functional studies of important genes for improving B. napus seed productivity and quality. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

Activation of the MAPK/ERK Cell-Signaling Pathway in Uterine Smooth Muscle Cells of Women With Adenomyosis.

PubMed

Streuli, Isabelle; Santulli, Pietro; Chouzenoux, Sandrine; Chapron, Charles; Batteux, Frédéric

2015-12-01

We investigated whether the myometrium might be intrinsically different in women with adenomyosis. We studied whether the mitogen-activated protein kinases/extracellular signal-regulated kinases (MAPKs/ERKs) and phosphoinositide 3-kinase/mammalian target of rapamycin/AKT (PI3K/mTOR/AKT) cell-signaling pathways, implicated in the pathogenesis of endometriosis, might also be activated in uterine smooth muscle cells (uSMCs) of women with adenomyosis and measured the production of reactive oxygen species (ROS), proinflammatory mediators that modulate cell proliferation and have been shown to activate the MAPK/ERK pathway in endometriosis. The uSMC cultures were derived from myometrium biopsies obtained during hysterectomy or myomectomy in women with adenomyosis and controls with leiomyoma. Proliferation of uSMCs and in vitro activation of the MAPK/ERK cell-signaling pathway were increased in women with adenomyosis compared to controls. The activation of the PI3K/mTOR/AKT pathway was not significant. The ROS production and ROS detoxification pathways were not different between uSMCs of women with adenomyosis and controls suggesting an ROS-independent activation of the MAPK/ERK pathway. Our results also provide evidence that protein kinase inhibitors and the rapanalogue temsirolimus can control proliferation of uSMCs in vitro suggesting an implication of the MAPK/ERK and the PI3K/mTOR/AKT pathways in proliferation of uSMCs in women with adenomyosis and leiomyomas. © The Author(s) 2015.

Elucidating a molecular mechanism that the deterioration of porcine meat quality responds to increased cortisol based on transcriptome sequencing.

PubMed

Wan, Xuebin; Wang, Dan; Xiong, Qi; Xiang, Hong; Li, Huanan; Wang, Hongshuai; Liu, Zezhang; Niu, Hongdan; Peng, Jian; Jiang, Siwen; Chai, Jin

2016-11-11

Stress response is tightly linked to meat quality. The current understanding of the intrinsic mechanism of meat deterioration under stress is limited. Here, male piglets were randomly assigned to cortisol and control groups. Our results showed that when serum cortisol level was significantly increased, the meat color at 1 h postmortem, muscle bundle ratio, apoptosis rate, and gene expression levels of calcium channel and cell apoptosis including SERCA1, IP3R1, BAX, Bcl-2, and Caspase-3, were notably increased. However, the value of drip loss at 24 h postmortem and serum CK were significantly decreased. Additionally, a large number of differentially expressed genes (DEGs) in GC regulation mechanism were screened out using transcriptome sequencing technology. A total of 223 DEGs were found, including 80 up-regulated genes and 143 down-regulated genes. A total of 204 genes were enriched in GO terms, and 140 genes annotated into in KEGG database. Numerous genes were primarily involved in defense, inflammatory and wound responses. This study not only identifies important genes and signalling pathways that may affect the meat quality but also offers a reference for breeding and feeding management to provide consumers with better quality pork products.

The influence of psychological variables on health-related quality of life among HIV-positive individuals with a history of intravenous drug use.

PubMed

Psaros, Christina; O'Cleirigh, Conall; Bullis, Jacqueline R; Markowitz, Sarah M; Safren, Steven A

2013-01-01

Intravenous drug use (IDU) remains a prominent pathway of HIV transmission in the United States, though little is known about modifiable factors influencing quality of life among IDUs. The goal of this study was to evaluate the influence of psychological variables (e.g., depression and anxiety) on health-related quality of life among HIV-positive individuals with a history of IDU who were enrolled in outpatient treatment for opioid dependence. 108 HIV-positive individuals with a history of IDU and participating in current outpatient treatment for opiate dependence who were screened for participation in a depression and adherence study reported sociodemographic data, depressive and anxiety symptoms, and health-related quality of life (HRQoL; Multidimensional Health Assessment using the ACTG-SF 21). Multiple regression models controlling for disease stage and background characteristics identified significant negative relationships between General Health Perception and Functioning without Pain for anxiety and depression, and between Role Functioning and Physical Functioning for anxiety. CD4 cell count was significantly related to Physical Functioning only. Results indicate that distress (both depression and anxiety) contribute significantly to variation in HRQoL over and above the effects of disease variables. Effective depression and anxiety treatment may result in improved overall functioning.

Control analysis of lipid biosynthesis in tissue cultures from oil crops shows that flux control is shared between fatty acid synthesis and lipid assembly.

PubMed Central

Ramli, Umi S; Baker, Darren S; Quant, Patti A; Harwood, John L

2002-01-01

Top-Down (Metabolic) Control Analysis (TDCA) was used to examine, quantitatively, lipid biosynthesis in tissue cultures from two commercially important oil crops, olive (Olea europaea L.) and oil palm (Elaeis guineensis Jacq.). A conceptually simplified system was defined comprising two blocks of reactions: fatty acid synthesis (Block A) and lipid assembly (Block B), which produced and consumed, respectively, a common and unique system intermediate, cytosolic acyl-CoA. We manipulated the steady-state levels of the system intermediate by adding exogenous oleic acid and, using two independent assays, measured the effect of the addition on the system fluxes (J(A) and J(B)). These were the rate of incorporation of radioactivity: (i) through Block A from [1-(14)C]acetate into fatty acids and (ii) via Block B from [U-(14)C]glycerol into complex lipids respectively. The data showed that fatty acid formation (Block A) exerted higher control than lipid assembly (Block B) in both tissues with the following group flux control coefficients (C):(i) Oil palm: *C(J(TL))(BlkA)=0.64+/-0.05 and *C(J(TL))(BlkB)=0.36+/-0.05(ii) Olive: *C(J(TL))(BlkA)=0.57+/-0.10 and *C(J(TL))(BlkB)=0.43+/-0.10where *C indicates the group flux control coefficient over the lipid biosynthesis flux (J(TL)) and the subscripts BlkA and BlkB refer to defined blocks of the system, Block A and Block B. Nevertheless, because both parts of the lipid biosynthetic pathway exert significant flux control, we suggest strongly that manipulation of single enzyme steps will not affect product yield appreciably. The present study represents the first use of TDCA to examine the overall lipid biosynthetic pathway in any tissue, and its findings are of immediate academic and economic relevance to the yield and nutritional quality of oil crops. PMID:12023882

The sigmaR regulon of Streptomyces coelicolor A32 reveals a key role in protein quality control during disulphide stress.

PubMed

Kallifidas, Dimitris; Thomas, Derek; Doughty, Phillip; Paget, Mark S B

2010-06-01

Diamide is an artificial disulphide-generating electrophile that mimics an oxidative shift in the cellular thiol-disulphide redox state (disulphide stress). The Gram-positive bacterium Streptomyces coelicolor senses and responds to disulphide stress through the sigma(R)-RsrA system, which comprises an extracytoplasmic function (ECF) sigma factor and a redox-active anti-sigma factor. Known targets that aid in the protection and recovery from disulphide stress include the thioredoxin system and genes involved in producing the major thiol buffer mycothiol. Here we determine the global response to diamide in wild-type and sigR mutant backgrounds to understand the role of sigma(R) in this response and to reveal additional regulatory pathways that allow cells to cope with disulphide stress. In addition to thiol oxidation, diamide was found to cause protein misfolding and aggregation, which elicited the induction of the HspR heat-shock regulon. Although this response is sigma(R)-independent, sigma(R) does directly control Clp and Lon ATP-dependent AAA(+) proteases, which may partly explain the reduced ability of a sigR mutant to resolubilize protein aggregates. sigma(R) also controls msrA and msrB methionine sulphoxide reductase genes, implying that sigma(R)-RsrA is responsible for the maintenance of both cysteine and methionine residues during oxidative stress. This work shows that the sigma(R)-RsrA system plays a more significant role in protein quality control than previously realized, and emphasizes the importance of controlling the cellular thiol-disulphide redox balance.

Report on Wisconsin Quality of Workforce Initiatives.

ERIC Educational Resources Information Center

Technical Education: Pathway to the Future, 1991

1991-01-01

This newsletter updates the reader on the latest Wisconsin initiatives to build tomorrow's work force through education, training, and cooperative ventures with business and industry. "Executive Cabinet for a Quality Workforce Defines Pathways to the Future" (Dwight York) discusses major reports related to the work of the executive…

Trade-offs in plant responses to herbivory influence trophic routes of production in a freshwater wetland.

PubMed

Cherry, Julia A; Gough, Laura

2009-09-01

Responses of aquatic macrophytes to leaf herbivory may differ from those documented for terrestrial plants, in part, because the potential to maximize growth following herbivory may be limited by the stress of being rooted in flooded, anaerobic sediments. Herbivory on aquatic macrophytes may have ecosystem consequences by altering the allocation of nutrients and production of biomass within individual plants and changing the quality and quantity of aboveground biomass available to consumers or decomposers. To test the effects of leaf herbivory on plant growth and production, herbivory of a dominant macrophyte, Nymphaea odorata, by chrysomelid beetles and crambid moths was controlled during a 2-year field experiment. Plants exposed to herbivory maintained, or tended to increase, biomass and aboveground net primary production relative to controls, which resulted in 1.5 times more aboveground primary production entering the detrital pathway of the wetland. In a complementary greenhouse experiment, the effects of simulated leaf herbivory on total plant responses, including biomass and nutrient allocation, were investigated. Plants in the greenhouse responded to moderate herbivory by maintaining aboveground biomass relative to controls, but this response occurred at the expense of belowground growth. Results of these studies suggest that N. odorata may tolerate moderate levels of herbivory by reallocating biomass and resources aboveground, which in turn influences the quantity, quality and fate of organic matter available to herbivores and decomposers.

Advanced Sensors and Controls for Building Applications: Market Assessment and Potential R&D Pathways

DOE Office of Scientific and Technical Information (OSTI.GOV)

Brambley, Michael R.; Haves, Philip; McDonald, Sean C.

2005-04-13

Significant energy savings can be achieved in commercial building operation, along with increased comfort and control for occupants, through the implementation of advanced technologies. This document provides a market assessment of existing building sensors and controls and presents a range of technology pathways (R&D options) for pursuing advanced sensors and building control strategies. This paper is actually a synthesis of five other white papers: the first describes the market assessment including estimates of market potential and energy savings for sensors and control strategies currently on the market as well as a discussion of market barriers to these technologies. The othermore » four cover technology pathways: (1) current applications and strategies for new applications, (2) sensors and controls, (3) networking, security, and protocols and standards, and (4) automated diagnostics, performance monitoring, commissioning, optimal control and tools. Each technology pathway chapter gives an overview of the technology or application. This is followed by a discussion of needs and the current status of the technology. Finally, a series of research topics is proposed.« less

Hyper-excitability of brainstem pathways in cerebral palsy.

PubMed

Smith, Allison Teresa; Gorassini, Monica Ann

2018-06-27

Individuals with cerebral palsy (CP) experience impairments in the control of head and neck movements, suggesting dysfunction in brainstem circuitry. To examine if brainstem circuitry is altered in CP we compared reflexes evoked in the sternocleidomastoid (SCM) muscle by trigeminal nerve stimulation in adults with CP and age/sex-matched controls. Increasing the intensity of trigeminal nerve stimulation produced progressive increases in the long-latency suppression of ongoing SCM EMG in controls. In contrast, participants with CP showed progressively increased facilitation around the same reflex window, suggesting heightened excitability of brainstem pathways. We also examined if there was altered activation of cortico-brainstem pathways in response to pre-natal injury of the brain. Motor-evoked potentials (MEPs) in the SCM that were conditioned by a prior trigeminal afferent stimulation were more facilitated in CP compared to controls, especially in ipsilateral MEPs that are likely mediated by cortico-reticulospinal pathways. In some participants with CP, but not in controls, a combined trigeminal nerve and cortical stimulation near threshold intensities produced large, long-lasting responses in both the SCM and biceps brachii muscles. We propose that the enhanced excitatory responses evoked from trigeminal and cortical inputs in CP are produced by heightened excitability of brainstem circuits, resulting in the augmented activation of reticulospinal pathways. Enhanced activation of reticulospinal pathways in response to early injury of the corticospinal tract may provide a compensated activation of the spinal cord, or alternatively, contribute to impairments in the precise control of head and neck functions.

Leisure and Quality of Life in an International and Multicultural Context: What Are Major Pathways Linking Leisure to Quality of Life?

ERIC Educational Resources Information Center

Iwasaki, Yoshitaka

2007-01-01

This paper aims at advancing the conceptualization of leisure as a contributor to quality of life (QOL) in an international and multicultural context, based on an extensive and critical review of literature on leisure and QOL from a global, international perspective. Given the central role of culture in conceptualizing this notion, this paper…

New Pathways for Teachers, New Promises for Students: A Vision for Developing Excellent Teachers. Teacher Quality 2.0. Special Report 3

ERIC Educational Resources Information Center

Knowles, Timothy

2013-01-01

This paper outlines a set of ideas for improving teacher quality in America's schools. In it, the author proposes a combination of incremental steps and ambitious ones, designed to stimulate policymakers, practitioners, and the public to accelerate efforts to develop high-quality teachers. The paper has four main sections. First, the author…

Increasing the uptake of long-acting reversible contraception in general practice: the Australian Contraceptive ChOice pRoject (ACCORd) cluster randomised controlled trial protocol.

PubMed

Mazza, Danielle; Black, Kirsten; Taft, Angela; Lucke, Jayne; McGeechan, Kevin; Haas, Marion; McKay, Heather; Peipert, Jeffery F

2016-10-07

The increased use of long-acting reversible contraceptives (LARCs), such as intrauterine devices and hormonal implants, has the potential to reduce unintended pregnancy and abortion rates. However, use of LARCs in Australia is very low, despite clinical practice guidance and statements by national and international peak bodies advocating their increased use. This protocol paper describes the Australian Contraceptive ChOice pRojet (ACCORd), a cluster randomised control trial that aims to test whether an educational intervention targeting general practitioners (GPs) and establishing a rapid referral service are a cost-effective means of increasing LARC uptake. The ACCORd intervention is adapted from the successful US Contraceptive CHOICE study and involves training GPs to provide 'LARC First' structured contraceptive counselling to women seeking contraception, and implementing rapid referral pathways for LARC insertion. Letters of invitation will be sent to 600 GPs in South-Eastern Melbourne. Using randomisation stratified by whether the GP inserts LARCs or not, a total of 54 groups will be allocated to the intervention (online 'LARC First' training and rapid referral pathways) or control arm (usual care). We aim to recruit 729 women from each arm. The primary outcome will be the number of LARCs inserted; secondary outcomes include the women's choice of contraceptive method and quality of life (Short Form Health Survey, SF-36). The costs and outcomes of the intervention and control will be compared in a cost-effectiveness analysis. The ACCORd study has been approved by the Monash University Human Research Ethics Committee: CF14/3990-2014002066 and CF16/188-2016000080. Any protocol modifications will be communicated to Ethics Committee and Trial Registration registry. The authors plan to disseminate trial outcomes through formal academic pathways comprising journal articles, nation and international conferences and reports, as well as using more 'popular' strategies including seminars, workshops and media engagements. ACTRN12615001346561. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/.

Impact of landscape disturbance on the quality of terrestrial sediment carbon in temperate streams

NASA Astrophysics Data System (ADS)

Fox, James F.; Ford, William I.

2016-09-01

Recent studies have shown the super saturation of fluvial networks with respect to carbon dioxide, and the concept that the high carbon dioxide is at least partially the result of turnover of sediment organic carbon that ranges in age from years to millennia. Currently, there is a need for more highly resolved studies at stream and river scales that enable estimates of terrestrial carbon turnover within fluvial networks. Our objective was to develop a new isotope-based metric to estimate the quality of sediment organic carbon delivered to temperate streams and to use the new metric to estimate carbon quality across landscape disturbance gradients. Carbon quality is defined to be consistent with in-stream turnover and our metric is used to measure the labile or recalcitrant nature of the terrestrial-derived carbon within streams. Our hypothesis was that intensively-disturbed landscapes would tend to produce low quality carbon because deep, recalcitrant soil carbon would be eroded and transported to the fluvial system while moderately disturbed or undisturbed landscapes would tend to produce higher quality carbon from well-developed surface soils and litter. The hypothesis was tested by applying the new carbon quality metric to 15 temperate streams with a wide range of landscape disturbance levels. We find that our hypothesis premised on an indirect relationship between the extent of landscape disturbance and the quality of sediment carbon in streams holds true for moderate and high disturbances but not for un-disturbed forests. We explain the results based on the connectivity, or dis-connectivity, between terrestrial carbon sources and pathways for sediment transport. While pathways are typically un-limited for disturbed landscapes, the un-disturbed forests have dis-connectivity between labile carbon of the forest floor and the stream corridor. Only in the case when trees fell into the stream corridor due to severe ice storms did the quality of sediment carbon increase in the streams. We argue that as scientists continue to estimate the in-stream turnover of terrestrially-derived carbon in fluvial carbon budgets, the assumption of pathway connectivity between carbon sources to the stream should be justified.

Effect of Dysphagia Screening Strategies on Clinical Outcomes After Stroke: A Systematic Review for the 2018 Guidelines for the Early Management of Patients With Acute Ischemic Stroke.

PubMed

Smith, Eric E; Kent, David M; Bulsara, Ketan R; Leung, Lester Y; Lichtman, Judith H; Reeves, Mathew J; Towfighi, Amytis; Whiteley, William N; Zahuranec, Darin B

2018-03-01

Dysphagia screening protocols have been recommended to identify patients at risk for aspiration. The American Heart Association convened an evidence review committee to systematically review evidence for the effectiveness of dysphagia screening protocols to reduce the risk of pneumonia, death, or dependency after stroke. The Medline, Embase, and Cochrane databases were searched on November 1, 2016, to identify randomized controlled trials (RCTs) comparing dysphagia screening protocols or quality interventions with increased dysphagia screening rates and reporting outcomes of pneumonia, death, or dependency. Three RCTs were identified. One RCT found that a combined nursing quality improvement intervention targeting fever and glucose management and dysphagia screening reduced death and dependency but without reducing the pneumonia rate. Another RCT failed to find evidence that pneumonia rates were reduced by adding the cough reflex to routine dysphagia screening. A smaller RCT randomly assigned 2 hospital wards to a stroke care pathway including dysphagia screening or regular care and found that patients on the stroke care pathway were less likely to require intubation and mechanical ventilation; however, the study was small and at risk for bias. There were insufficient RCT data to determine the effect of dysphagia screening protocols on reducing the rates of pneumonia, death, or dependency after stroke. Additional trials are needed to compare the validity, feasibility, and clinical effectiveness of different screening methods for dysphagia. © 2018 American Heart Association, Inc.

Microarray analysis of differentially expressed genes engaged in fruit development between Prunus mume and Prunus armeniaca.

PubMed

Li, Xiaoying; Korir, Nicholas Kibet; Liu, Lili; Shangguan, Lingfei; Wang, Yuzhu; Han, Jian; Chen, Ming; Fang, Jinggui

2012-11-15

Microarray analysis is a technique that can be employed to provide expression profiles of single genes and new insights to elucidate the biological mechanisms responsible for fruit development. To evaluate expression of genes mostly engaged in fruit development between Prunus mume and Prunus armeniaca, we first identified differentially expressed transcripts along the entire fruit life cycle by using microarrays spotted with 10,641 ESTs collected from P. mume and other Prunus EST sequences. A total of 1418 ESTs were selected after quality control of microarray spots and analysis for differential gene expression patterns during fruit development of P. mume and P. Armeniaca. From these, 707 up-regulated and 711 down-regulated genes showing more than two-fold differences in expression level were annotated by GO based on biological processes, molecular functions and cellular components. These differentially expressed genes were found to be involved in several important pathways of carbohydrate, galactose, and starch and sucrose metabolism as well as in biosynthesis of other secondary metabolites via KEGG. This could provide detailed information on the fruit quality differences during development and ripening of these two species. With the results obtained, we provide a practical database for comprehensive understanding of molecular events during fruit development and also lay a theoretical foundation for the cloning of genes regulating in a series of important rate-limiting enzymes involved in vital metabolic pathways during fruit development. Copyright © 2012 Elsevier GmbH. All rights reserved.

Simultaneous Analysis of Iridoid Glycosides and Anthraquinones in Morinda officinalis Using UPLC-QqQ-MS/MS and UPLC-Q/TOF-MSE.

PubMed

Zhao, Xiangsheng; Wei, Jianhe; Yang, Meihua

2018-05-03

Morinda officinalis is an important herbal medicine and functional food, and its main constituents include anthraquinone and iridoid glycosides. Quantification of the main compounds is a necessary step to understand the quality and therapeutic properties of M. officinalis , but this has not yet been performed based on liquid chromatography/tandem mass spectrometry (LC-MS/MS). Analytes were extracted from M. officinalis by reflux method. Ultrahigh-performance liquid chromatography coupled with a triple quadrupole mass spectrometry (UPLC-QqQ-MS) using multiple reaction monitoring (MRM) mode was applied for quantification. Fragmentation pathways of deacetyl asperulosidic acid and rubiadin were investigated based on UPLC with quadrupole time-of-flight tandem mass spectrometry (Q/TOF-MS) in the MS E centroid mode. The method showed a good linearity over a wide concentration range (R² ≥ 0.9930). The limits of quantification of six compounds ranged from 2.6 to 27.57 ng/mL. The intra- and inter-day precisions of the investigated components exhibited an RSD within 4.5% with mean recovery rates of 95.32⁻99.86%. Contents of selected compounds in M. officinalis varied significantly depending on region. The fragmentation pathway of deacetyl asperulosidic and rubiadin was proposed. A selective and sensitive method was developed for determining six target compounds in M. officinalis by UPLC-MS/MS. Furthermore, the proposed method will be helpful for quality control and identification main compounds of M. officinalis .

Radionuclides in surface and groundwater

USGS Publications Warehouse

Campbell, Kate M.

2009-01-01

Unique among all the contaminants that adversely affect surface and water quality, radioactive compounds pose a double threat from both toxicity and damaging radiation. The extreme energy potential of many of these materials makes them both useful and toxic. The unique properties of radioactive materials make them invaluable for medical, weapons, and energy applications. However, mining, production, use, and disposal of these compounds provide potential pathways for their release into the environment, posing a risk to both humans and wildlife. This chapter discusses the sources, uses, and regulation of radioactive compounds in the United States, biogeochemical processes that control mobility in the environment, examples of radionuclide contamination, and current work related to contaminated site remediation.

Processes occurring in reservoirs receiving biogenic and polluting substances

DOE Office of Scientific and Technical Information (OSTI.GOV)

Vasil'ev, Yu.S.; Rolle, N.N.

1988-04-01

Various aspects of biogenic pollution on the water quality of reservoirs and its effect on ichthyofauna were analyzed. The effects of fertilizer runoffs and other pollutant pathways, such as the decay of flooded vegetation, into reservoirs were addressed. The dependence of fish survival times on nitrite concentrations was charted. On the basis of an optimization model for the economic development of drainage basins with ecological limitations, the Leningrad Polytechnic Institute developed instructions for calculating the removal of biogenic elements and selecting water protection measures which were tested on a number of streams of the Lake Ladoga Basin and other areasmore » and which provide engineering means for evaluating and controlling the eutrophication of reservoirs.« less

Protein Homeostasis in Amyotrophic Lateral Sclerosis: Therapeutic Opportunities?

PubMed Central

Webster, Christopher P.; Smith, Emma F.; Shaw, Pamela J.; De Vos, Kurt J.

2017-01-01

Protein homeostasis (proteostasis), the correct balance between production and degradation of proteins, is essential for the health and survival of cells. Proteostasis requires an intricate network of protein quality control pathways (the proteostasis network) that work to prevent protein aggregation and maintain proteome health throughout the lifespan of the cell. Collapse of proteostasis has been implicated in the etiology of a number of neurodegenerative diseases, including amyotrophic lateral sclerosis (ALS), the most common adult onset motor neuron disorder. Here, we review the evidence linking dysfunctional proteostasis to the etiology of ALS and discuss how ALS-associated insults affect the proteostasis network. Finally, we discuss the potential therapeutic benefit of proteostasis network modulation in ALS. PMID:28512398

Unkempt is negatively regulated by mTOR and uncouples neuronal differentiation from growth control.

PubMed

Avet-Rochex, Amélie; Carvajal, Nancy; Christoforou, Christina P; Yeung, Kelvin; Maierbrugger, Katja T; Hobbs, Carl; Lalli, Giovanna; Cagin, Umut; Plachot, Cedric; McNeill, Helen; Bateman, Joseph M

2014-09-01

Neuronal differentiation is exquisitely controlled both spatially and temporally during nervous system development. Defects in the spatiotemporal control of neurogenesis cause incorrect formation of neural networks and lead to neurological disorders such as epilepsy and autism. The mTOR kinase integrates signals from mitogens, nutrients and energy levels to regulate growth, autophagy and metabolism. We previously identified the insulin receptor (InR)/mTOR pathway as a critical regulator of the timing of neuronal differentiation in the Drosophila melanogaster eye. Subsequently, this pathway has been shown to play a conserved role in regulating neurogenesis in vertebrates. However, the factors that mediate the neurogenic role of this pathway are completely unknown. To identify downstream effectors of the InR/mTOR pathway we screened transcriptional targets of mTOR for neuronal differentiation phenotypes in photoreceptor neurons. We identified the conserved gene unkempt (unk), which encodes a zinc finger/RING domain containing protein, as a negative regulator of the timing of photoreceptor differentiation. Loss of unk phenocopies InR/mTOR pathway activation and unk acts downstream of this pathway to regulate neurogenesis. In contrast to InR/mTOR signalling, unk does not regulate growth. unk therefore uncouples the role of the InR/mTOR pathway in neurogenesis from its role in growth control. We also identified the gene headcase (hdc) as a second downstream regulator of the InR/mTOR pathway controlling the timing of neurogenesis. Unk forms a complex with Hdc, and Hdc expression is regulated by unk and InR/mTOR signalling. Co-overexpression of unk and hdc completely suppresses the precocious neuronal differentiation phenotype caused by loss of Tsc1. Thus, Unk and Hdc are the first neurogenic components of the InR/mTOR pathway to be identified. Finally, we show that Unkempt-like is expressed in the developing mouse retina and in neural stem/progenitor cells, suggesting that the role of Unk in neurogenesis may be conserved in mammals.

Mitigation strategies of acrylamide, furans, heterocyclic amines and browning during the Maillard reaction in foods.

PubMed

Rannou, Cécile; Laroque, Delphine; Renault, Emilie; Prost, Carole; Sérot, Thierry

2016-12-01

The Maillard reaction (MR) occurs widely during food manufacture and storage, through controlled or uncontrolled pathways. Its consequences are ambiguous depending on the nature and processing of the food products. The MR is often used by food manufacturer to develop appealing aromas, colour or texture in food products (cereal based food, coffee, meat…). However, despite some positive aspects, the MR could decrease the nutritional value of food, generate potentially harmful compounds (e.g. acrylamide, furans, heterocyclic amines) or modify aroma or colour although it is not desired (milk, fruit juice). This paper presents a review of the different solutions available to control or moderate the MR in various food products from preventive to removal methods. A brief reminder of the role and influence of the MR on food quality and safety is also provided. Copyright © 2016 Elsevier Ltd. All rights reserved.

Norrin/Frizzled4 signaling in retinal vascular development and blood brain barrier plasticity.

PubMed

Wang, Yanshu; Rattner, Amir; Zhou, Yulian; Williams, John; Smallwood, Philip M; Nathans, Jeremy

2012-12-07

Norrin/Frizzled4 (Fz4) signaling activates the canonical Wnt pathway to control retinal vascular development. Using genetically engineered mice, we show that precocious Norrin production leads to premature retinal vascular invasion and delayed Norrin production leads to characteristic defects in intraretinal vascular architecture. In genetic mosaics, wild-type endothelial cells (ECs) instruct neighboring Fz4(-/-) ECs to produce an architecturally normal mosaic vasculature, a cell nonautonomous effect. However, over the ensuing weeks, Fz4(-/-) ECs are selectively eliminated from the mosaic vasculature, implying the existence of a quality control program that targets defective ECs. In the adult retina and cerebellum, gain or loss of Norrin/Fz4 signaling results in a cell-autonomous gain or loss, respectively, of blood retina barrier and blood brain barrier function, indicating an ongoing requirement for Frizzled signaling in barrier maintenance and substantial plasticity in mature CNS vascular structure. Copyright © 2012 Elsevier Inc. All rights reserved.

PAR1 participates in the ability of multidrug resistance and tumorigenesis by controlling Hippo-YAP pathway.

PubMed

Fujimoto, Daisuke; Ueda, Yuki; Hirono, Yasuo; Goi, Takanori; Yamaguchi, Akio

2015-10-27

The Hippo pathway significantly correlates with organ size control and tumorigenesis. The activity of YAP/TAZ, a transducer of the Hippo pathway, is required to sustain self-renewal and tumor-initiation capacities in cancer stem cells (CSCs). But, upstream signals that control the mammalian Hippo pathway have not been well understood. Here, we reveal a connection between the Protease-activated receptor 1 (PAR1) signaling pathway and the Hippo-YAP pathway in gastric cancer stem-like cells. The selective PAR1 agonist TFLLR-NH2 induces an increase in the fraction of side population cells which is enriched in CSCs, and promotes tumorigenesis, multi cancer drug resistance, cell morphological change, and cell invasion which are characteristics of CSCs. In addition, PAR1 activation inhibits the Hippo-YAP pathway kinase Lats via Rho GTPase. Lats kinase inhibition in turn results in increased nuclear localization of dephosphorylated YAP. Furthermore, PAR1 activation confers CSCs related traits via the Hippo-YAP pathway, and the Hippo-YAP pathway correlates with epithelial mesenchymal transition which is induced by PAR1 activation. Our research suggests that the PAR1 signaling deeply participates in the ability of multi drug resistance and tumorigenesis through interactions with the Hippo-YAP pathway signaling in gastric cancer stem-like cells. We presume that inhibited YAP is a new therapeutic target in the treatment human gastric cancer invasion and metastasis by dysregulated PAR1 or its agonists.

Evolutionary trends and functional anatomy of the human expanded autophagy network

PubMed Central

Till, Andreas; Saito, Rintaro; Merkurjev, Daria; Liu, Jing-Jing; Syed, Gulam Hussain; Kolnik, Martin; Siddiqui, Aleem; Glas, Martin; Scheffler, Björn; Ideker, Trey; Subramani, Suresh

2015-01-01

All eukaryotic cells utilize autophagy for protein and organelle turnover, thus assuring subcellular quality control, homeostasis, and survival. In order to address recent advances in identification of human autophagy associated genes, and to describe autophagy on a system-wide level, we established an autophagy-centered gene interaction network by merging various primary data sets and by retrieving respective interaction data. The resulting network (‘AXAN’) was analyzed with respect to subnetworks, e.g. the prime gene subnetwork (including the core machinery, signaling pathways and autophagy receptors) and the transcription subnetwork. To describe aspects of evolution within this network, we assessed the presence of protein orthologs across 99 eukaryotic model organisms. We visualized evolutionary trends for prime gene categories and evolutionary tracks for selected AXAN genes. This analysis confirms the eukaryotic origin of autophagy core genes while it points to a diverse evolutionary history of autophagy receptors. Next, we used module identification to describe the functional anatomy of the network at the level of pathway modules. In addition to obvious pathways (e.g., lysosomal degradation, insulin signaling) our data unveil the existence of context-related modules such as Rho GTPase signaling. Last, we used a tripartite, image-based RNAi – screen to test candidate genes predicted to play a role in regulation of autophagy. We verified the Rho GTPase, CDC42, as a novel regulator of autophagy-related signaling. This study emphasizes the applicability of system-wide approaches to gain novel insights into a complex biological process and to describe the human autophagy pathway at a hitherto unprecedented level of detail. PMID:26103419

Characterization of Spleen Transcriptome of Schizothorax prenanti during Aeromonas hydrophila Infection.

PubMed

Ye, Hua; Xiao, Shijun; Wang, Xiaoqing; Wang, Zhiyong; Zhang, Zhengshi; Zhu, Chengke; Hu, Bingjie; Lv, Changhuan; Zheng, Shuming; Luo, Hui

2018-04-01

Schizothorax prenanti (S. prenanti) is an indigenous fish species and is popularly cultured in southwestern China. In recent years, intensive farming of S. prenanti and water quality deterioration has increased the susceptibility of this fish to various pathogens, including Aeromonas hydrophila (A. hydrophila), which has caused severe damage to S. prenanti production. However, the understanding of molecular immune response of S. prenanti to A. hydrophila infection is still lacking. In order to better comprehend the S. prenanti time series immune response process against A. hydrophila, we conducted the first transcriptomic comparison in S. prenanti spleen at 4, 24, and 48 h after the infection challenge of A. hydrophila against their control counterparts. In total, 628 million clean reads were obtained from 18 libraries and assembled into 262,745 transcripts. After eliminating sequence redundancy, 69,373 unigenes with an average length of 1476 bp were obtained. Comparative analysis revealed 1890 unigenes with significantly differential expression, including 172, 455, 589 upregulated and 27, 676, 551 unigenes downregulated genes for 4, 24, and 48 h post-infection, respectively. Differentially expressed genes (DEGs) were validated using qPCR for 15 randomly selected genes. Enrichment and pathway analysis of DEGs was carried out to understand the functions of the immune-related genes. Our results revealed that many important functional genes relating to complement and coagulation cascades, chemokine signaling pathway, toll-like receptor signaling pathway, NOD-like receptor signaling pathway and leukocyte transendothelial migration were regulated during the infection of A. hydrophila, and the expression of those genes reflected the transcriptome profiles during the challenging stages.

Back to basics: a revealing secondary reduction of the mitochondrial protein import pathway in diverse intracellular parasites.

PubMed

Heinz, Eva; Lithgow, Trevor

2013-02-01

Mitochondria are present in all eukaryotes, but remodeling of their metabolic contribution has in some cases left them almost unrecognizable and they are referred to as mitochondria-like organelles, hydrogenosomes or, in the case where evolution has led to a great deal of simplification, as mitosomes. Mitochondria rely on the import of proteins encoded in the nucleus and the protein import machinery has been investigated in detail in yeast: several sophisticated molecular machines act in concert to import substrate proteins across the outer mitochondrial membrane and deliver them to a precise sub-mitochondrial compartment. Because these machines are so sophisticated, it has been a major challenge to conceptualize the first phase of their evolution. Here we review recent studies on the protein import pathway in parasitic species that have mitosomes: in the course of their evolution for highly specialized niches these parasites, particularly Cryptosporidia and Microsporidia, have secondarily lost numerous protein functions, in accordance with the evolution of their genomes towards a minimal size. Microsporidia are related to fungi, Cryptosporidia are apicomplexans and kin to the malaria parasite Plasmodium; and this great phylogenetic distance makes it remarkable that Microsporidia and Cryptosporidia have independently evolved skeletal protein import pathways that are almost identical. We suggest that the skeletal pathway reflects the protein import machinery of the first eukaryotes, and defines the essential roles of the core elements of the mitochondrial protein import machinery. This article is part of a Special Issue entitled: Protein Import and Quality Control in Mitochondria and Plastids. Copyright © 2012 Elsevier B.V. All rights reserved.

Cross-Talk Between Mitochondrial Fusion and the Hippo Pathway in Controlling Cell Proliferation During Drosophila Development.

PubMed

Deng, Qiannan; Guo, Ting; Zhou, Xiu; Xi, Yongmei; Yang, Xiaohang; Ge, Wanzhong

2016-08-01

Cell proliferation and tissue growth depend on the coordinated regulation of multiple signaling molecules and pathways during animal development. Previous studies have linked mitochondrial function and the Hippo signaling pathway in growth control. However, the underlying molecular mechanisms are not fully understood. Here we identify a Drosophila mitochondrial inner membrane protein ChChd3 as a novel regulator for tissue growth. Loss of ChChd3 leads to tissue undergrowth and cell proliferation defects. ChChd3 is required for mitochondrial fusion and removal of ChChd3 increases mitochondrial fragmentation. ChChd3 is another mitochondrial target of the Hippo pathway, although it is only partially required for Hippo pathway-mediated overgrowth. Interestingly, lack of ChChd3 leads to inactivation of Hippo activity under normal development, which is also dependent on the transcriptional coactivator Yorkie (Yki). Furthermore, loss of ChChd3 induces oxidative stress and activates the JNK pathway. In addition, depletion of other mitochondrial fusion components, Opa1 or Marf, inactivates the Hippo pathway as well. Taken together, we propose that there is a cross-talk between mitochondrial fusion and the Hippo pathway, which is essential in controlling cell proliferation and tissue homeostasis in Drosophila. Copyright © 2016 by the Genetics Society of America.

Future air pollution in the Shared Socio-economic Pathways

DOE PAGES

Rao, Shilpa; Klimont, Zbigniew; Smith, Steven J.; ...

2016-07-15

Emissions of air pollutants such as sulfur and nitrogen oxides and particulates have significant health impacts as well as effects on natural and anthropogenic ecosystems. These same emissions also can change atmospheric chemistry and the planetary energy balance, thereby impacting global and regional climate. Long-term scenarios for air pollutant emissions are needed as inputs to global climate and chemistry models, and for analysis linking air pollutant impacts across sectors. In this paper we present methodology and results for air pollutant emissions in Shared Socioeconomic Pathways (SSP) scenarios. We first present a set of three air pollution narratives that describe high,more » central, and low pollution control ambitions over the 21 st century. These narratives are then translated into quantitative guidance for use in integrated assessment models. We provide an overview of pollutant emission trajectories under the SSP scenarios. Pollutant emissions in these scenarios cover a wider range than the scenarios used in previous international climate model comparisons. Furthermore, the SSP scenarios provide the opportunity to access a more comprehensive range of future global and regional air quality outcomes.« less

DNA Microarray-Based Screening and Characterization of Traditional Chinese Medicine

PubMed Central

Kiyama, Ryoiti

2017-01-01

The application of DNA microarray assay (DMA) has entered a new era owing to recent innovations in omics technologies. This review summarizes recent applications of DMA-based gene expression profiling by focusing on the screening and characterization of traditional Chinese medicine. First, herbs, mushrooms, and dietary plants analyzed by DMA along with their effective components and their biological/physiological effects are summarized and discussed by examining their comprehensive list and a list of representative effective chemicals. Second, the mechanisms of action of traditional Chinese medicine are summarized by examining the genes and pathways responsible for the action, the cell functions involved in the action, and the activities found by DMA (silent estrogens). Third, applications of DMA for traditional Chinese medicine are discussed by examining reported examples and new protocols for its use in quality control. Further innovations in the signaling pathway-based evaluation of beneficial effects and the assessment of potential risks of traditional Chinese medicine are expected, just as are observed in other closely related fields, such as the therapeutic, environmental, nutritional, and pharmacological fields. PMID:28146102

Progressive quality control of secretory proteins in the early secretory compartment by ERp44

PubMed Central

Sannino, Sara; Anelli, Tiziana; Cortini, Margherita; Masui, Shoji; Degano, Massimo; Fagioli, Claudio; Inaba, Kenji; Sitia, Roberto

2014-01-01

ERp44 is a pH-regulated chaperone of the secretory pathway. In the acidic milieu of the Golgi, its C-terminal tail changes conformation, simultaneously exposing the substrate-binding site for cargo capture and the RDEL motif for ER retrieval via interactions with cognate receptors. Protonation of cysteine 29 in the active site allows tail movements in vitro and in vivo. Here we show that also conserved histidines in the C-terminal tail regulate ERp44 in vivo. Mutants lacking these histidines are hyperactive in retaining substrates. Surprisingly, they are also O-glycosylated and partially secreted. Co-expression of client proteins prevents secretion of the histidine mutants, forcing tail opening and RDEL accessibility. Client-induced RDEL exposure allows retrieval of proteins from distinct stations along the secretory pathway, as indicated by the changes in O-glycosylation patterns upon over-expression of different partners. The ensuing gradients may help optimising folding and assembly of different cargoes. Endogenous ERp44 is O-glycosylated and secreted by human primary endometrial cells, suggesting possible pathophysiological roles of these processes. PMID:25097228

Future air pollution in the Shared Socio-economic Pathways

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rao, Shilpa; Klimont, Zbigniew; Smith, Steven J.

Emissions of air pollutants such as sulfur and nitrogen oxides and particulates have significant health impacts as well as effects on natural and anthropogenic ecosystems. These same emissions also can change atmospheric chemistry and the planetary energy balance, thereby impacting global and regional climate. Long-term scenarios for air pollutant emissions are needed as inputs to global climate and chemistry models, and for analysis linking air pollutant impacts across sectors. In this paper we present methodology and results for air pollutant emissions in Shared Socioeconomic Pathways (SSP) scenarios. We first present a set of three air pollution narratives that describe high,more » central, and low pollution control ambitions over the 21 st century. These narratives are then translated into quantitative guidance for use in integrated assessment models. We provide an overview of pollutant emission trajectories under the SSP scenarios. Pollutant emissions in these scenarios cover a wider range than the scenarios used in previous international climate model comparisons. Furthermore, the SSP scenarios provide the opportunity to access a more comprehensive range of future global and regional air quality outcomes.« less

Integrated carboxylic carbon nanotube pathways with membranes for voltage-activated humidity detection and microclimate regulation.

PubMed

Pingitore, V; Miriello, D; Drioli, E; Gugliuzza, A

2015-06-14

This work describes some single walled carboxylic carbon nanotubes with outstanding transport properties when assembled in a 3D microarray working like a humidity membrane-sensor and an adjustable moisture regulator. Combined nano-assembly approaches are used to build up a better quality pathway through which assisted-charge and mass transport synchronically takes place. The structure-electrical response relationship is found, while controllable and tunable donor-acceptor interactions established at material interfaces are regarded as key factors for the accomplishment of charge transportation, enhanced electrical responses and adjustable moisture exchange. Raman and infrared spectroscopy provides indications about the fine structural and chemical features of the hybrid-composite membranes, resulting in perfect agreement with related morphology and electrical properties. Enhanced and modular electrical response to changes in the surrounding atmosphere is concerned with doping events, while assisted moisture regulation is discussed in relation to swelling and hopping actions. The electro-activated hybrid-composite membrane proposed in this work can be regarded as an attractive 'sense-to-act' precursor for smart long-distance monitoring systems with capability to adapt itself and provide local comfortable microenvironments.

The Role of p58IPK in Protecting the Stressed Endoplasmic Reticulum

PubMed Central

Rutkowski, D. Thomas; Kang, Sang-Wook; Goodman, Alan G.; Garrison, Jennifer L.; Taunton, Jack; Katze, Michael G.

2007-01-01

The preemptive quality control (pQC) pathway protects cells from acute endoplasmic reticulum (ER) stress by attenuating translocation of nascent proteins despite their targeting to translocons at the ER membrane. Here, we investigate the hypothesis that the DnaJ protein p58IPK plays an essential role in this process via HSP70 recruitment to the cytosolic face of translocons for extraction of translocationally attenuated nascent chains. Our analyses revealed that the heightened stress sensitivity of p58−/− cells was not due to an impairment of the pQC pathway or elevated ER substrate burden during acute stress. Instead, the lesion was in the protein processing capacity of the ER lumen, where p58IPK was found to normally reside in association with BiP. ER lumenal p58IPK could be coimmunoprecipitated with a newly synthesized secretory protein in vitro and stimulated protein maturation upon overexpression in cells. These results identify a previously unanticipated location for p58IPK in the ER lumen where its putative function as a cochaperone explains the stress-sensitivity phenotype of knockout cells and mice. PMID:17567950

Identification and Quantification of Alkaloid in KHR98 and Fragmentation Pathways in HPLC-Q-TOF-MS.

PubMed

Long, Jiakun; Wang, Yang; Xu, Chen; Liu, Tingting; Duan, Gengli; Yu, Yingjia

2018-05-01

Uncaria rhynchophylla is woody climber plant distributed mainly in China and Japan, the stems and hooks of which can be collected as "Gou-Teng" for the treatment of hyperpyrexia, epilepsy and preeclampsia. Fudan University first manufactured KHR98, the extract of Uncaria rhynchophylla. In order to study the active components and structural information of KHR98, we established a HPLC coupled with quadrupole time-of-flight (Q-TOF)-MS method for rapid analysis of alkaloids. In qualitative analysis, a total of eight compounds, including four known alkaloids and four unknown components, were detected and identified. The fragmentation behaviors, such as the fragment ion information and the fragmentation pathways of the eight components were summarized simultaneously, and the concentration of the above components was determined by HPLC-MS method. The quantitative method was proved to be reproducible, precise and accurate. This study shed light on the standardization and quality control of the KHR98 and provided a foundation for the further research on pharmacology, follow-up clinical research and New Drug Applications.

The ever-evolving role of mTOR in translation.

PubMed

Fonseca, Bruno D; Smith, Ewan M; Yelle, Nicolas; Alain, Tommy; Bushell, Martin; Pause, Arnim

2014-12-01

Control of translation allows for the production of stoichiometric levels of each protein in the cell. Attaining such a level of fine-tuned regulation of protein production requires the coordinated temporal and spatial control of numerous cellular signalling cascades impinging on the various components of the translational machinery. Foremost among these is the mTOR signalling pathway. The mTOR pathway regulates both the initiation and elongation steps of protein synthesis through the phosphorylation of numerous translation factors, while simultaneously ensuring adequate folding of nascent polypeptides through co-translational degradation of misfolded proteins. Perhaps most remarkably, mTOR is also a key regulator of the synthesis of ribosomal proteins and translation factors themselves. Two seminal studies have recently shown in translatome analysis that the mTOR pathway preferentially regulates the translation of mRNAs encoding ribosomal proteins and translation factors. Therefore, the role of the mTOR pathway in the control of protein synthesis extends far beyond immediate translational control. By controlling ribosome production (and ultimately ribosome availability), mTOR is a master long-term controller of protein synthesis. Herein, we review the literature spanning the early discoveries of mTOR on translation to the latest advances in our understanding of how the mTOR pathway controls the synthesis of ribosomal proteins. Crown Copyright © 2014. Published by Elsevier Ltd. All rights reserved.

Reconceptualising Post-PhD Research Pathways: A Model to Create New Postdoctoral Positions and Improve the Quality of Postdoctoral Training in Australia

ERIC Educational Resources Information Center

Berman, J.; Juniper, S.; Pitman, T.; Thomson, C.

2008-01-01

Focusing on the developmental needs of early career postdoctoral fellows--the lifeblood of an internationally competitive research-intensive university--this paper suggests an inextricably linked, two pronged approach to improving research performance at Australian universities. The first is to reconceptualise post-PhD research pathways and in…

Potential Impacts of two SO2 oxidation pathways on regional sulfate concentrations: acqueous-hase oxidation by NO2 and gas-phase oxidation by Stabilized Criegee Intermediates

EPA Science Inventory

We examine the potential impacts of two additional sulfate production pathways using the Community Multiscale Air Quality modeling system. First we evaluate the impact of the aqueous-phase oxidation of S(IV) by nitrogen dioxide using two published rate constants, differing by 1-2...

The Process and Impact of the Infant/Toddler Credential as Professional Development: Reflections from Multiple Perspectives and Recommendations for Policy

ERIC Educational Resources Information Center

Chen, Jennifer J.; Martin, Arlene; Erdosi-Mehaffey, Valeria

2017-01-01

Early childhood educators worldwide all strive to improve the quality of care and education for young children through sustainable pathways. One such pathway is professional development (PD). In the United States, ongoing PD has been recognized as critical to enhancing practitioners' professional competence. Situated within the broader context of…

Quantum optimal control pathways of ozone isomerization dynamics subject to competing dissociation: A two-state one-dimensional model

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kurosaki, Yuzuru, E-mail: kurosaki.yuzuru@jaea.go.jp; Ho, Tak-San, E-mail: tsho@Princeton.EDU; Rabitz, Herschel, E-mail: hrabitz@Princeton.EDU

We construct a two-state one-dimensional reaction-path model for ozone open → cyclic isomerization dynamics. The model is based on the intrinsic reaction coordinate connecting the cyclic and open isomers with the O{sub 2} + O asymptote on the ground-state {sup 1}A{sup ′} potential energy surface obtained with the high-level ab initio method. Using this two-state model time-dependent wave packet optimal control simulations are carried out. Two possible pathways are identified along with their respective band-limited optimal control fields; for pathway 1 the wave packet initially associated with the open isomer is first pumped into a shallow well on the excitedmore » electronic state potential curve and then driven back to the ground electronic state to form the cyclic isomer, whereas for pathway 2 the corresponding wave packet is excited directly to the primary well of the excited state potential curve. The simulations reveal that the optimal field for pathway 1 produces a final yield of nearly 100% with substantially smaller intensity than that obtained in a previous study [Y. Kurosaki, M. Artamonov, T.-S. Ho, and H. Rabitz, J. Chem. Phys. 131, 044306 (2009)] using a single-state one-dimensional model. Pathway 2, due to its strong coupling to the dissociation channel, is less effective than pathway 1. The simulations also show that nonlinear field effects due to molecular polarizability and hyperpolarizability are small for pathway 1 but could become significant for pathway 2 because much higher field intensity is involved in the latter. The results suggest that a practical control may be feasible with the aid of a few lowly excited electronic states for ozone isomerization.« less

Care pathways across the primary-hospital care continuum: using the multi-level framework in explaining care coordination

PubMed Central

2013-01-01

Background Care pathways are widely used in hospitals for a structured and detailed planning of the care process. There is a growing interest in extending care pathways into primary care to improve quality of care by increasing care coordination. Evidence is sparse about the relationship between care pathways and care coordination. The multi-level framework explores care coordination across organizations and states that (inter)organizational mechanisms have an effect on the relationships between healthcare professionals, resulting in quality and efficiency of care. The aim of this study was to assess the extent to which care pathways support or create elements of the multi-level framework necessary to improve care coordination across the primary - hospital care continuum. Methods This study is an in-depth analysis of five existing local community projects located in four different regions in Flanders (Belgium) to determine whether the available empirical evidence supported or refuted the theoretical expectations from the multi-level framework. Data were gathered using mixed methods, including structured face-to-face interviews, participant observations, documentation and a focus group. Multiple cases were analyzed performing a cross case synthesis to strengthen the results. Results The development of a care pathway across the primary-hospital care continuum, supported by a step-by-step scenario, led to the use of existing and newly constructed structures, data monitoring and the development of information tools. The construction and use of these inter-organizational mechanisms had a positive effect on exchanging information, formulating and sharing goals, defining and knowing each other’s roles, expectations and competences and building qualitative relationships. Conclusion Care pathways across the primary-hospital care continuum enhance the components of care coordination. PMID:23919518

Care pathways across the primary-hospital care continuum: using the multi-level framework in explaining care coordination.

PubMed

Van Houdt, Sabine; Heyrman, Jan; Vanhaecht, Kris; Sermeus, Walter; De Lepeleire, Jan

2013-08-06

Care pathways are widely used in hospitals for a structured and detailed planning of the care process. There is a growing interest in extending care pathways into primary care to improve quality of care by increasing care coordination. Evidence is sparse about the relationship between care pathways and care coordination.The multi-level framework explores care coordination across organizations and states that (inter)organizational mechanisms have an effect on the relationships between healthcare professionals, resulting in quality and efficiency of care.The aim of this study was to assess the extent to which care pathways support or create elements of the multi-level framework necessary to improve care coordination across the primary-hospital care continuum. This study is an in-depth analysis of five existing local community projects located in four different regions in Flanders (Belgium) to determine whether the available empirical evidence supported or refuted the theoretical expectations from the multi-level framework. Data were gathered using mixed methods, including structured face-to-face interviews, participant observations, documentation and a focus group. Multiple cases were analyzed performing a cross case synthesis to strengthen the results. The development of a care pathway across the primary-hospital care continuum, supported by a step-by-step scenario, led to the use of existing and newly constructed structures, data monitoring and the development of information tools. The construction and use of these inter-organizational mechanisms had a positive effect on exchanging information, formulating and sharing goals, defining and knowing each other's roles, expectations and competences and building qualitative relationships. Care pathways across the primary-hospital care continuum enhance the components of care coordination.

SEMPATH Ontology: modeling multidisciplinary treatment schemes utilizing semantics.

PubMed

Alexandrou, Dimitrios Al; Pardalis, Konstantinos V; Bouras, Thanassis D; Karakitsos, Petros; Mentzas, Gregoris N

2012-03-01

A dramatic increase of demand for provided treatment quality has occurred during last decades. The main challenge to be confronted, so as to increase treatment quality, is the personalization of treatment, since each patient constitutes a unique case. Healthcare provision encloses a complex environment since healthcare provision organizations are highly multidisciplinary. In this paper, we present the conceptualization of the domain of clinical pathways (CP). The SEMPATH (SEMantic PATHways) Oontology comprises three main parts: 1) the CP part; 2) the business and finance part; and 3) the quality assurance part. Our implementation achieves the conceptualization of the multidisciplinary domain of healthcare provision, in order to be further utilized for the implementation of a Semantic Web Rules (SWRL rules) repository. Finally, SEMPATH Ontology is utilized for the definition of a set of SWRL rules for the human papillomavirus) disease and its treatment scheme. © 2012 IEEE

Further Validation of the Pathways Housing First Fidelity Scale.

PubMed

Goering, Paula; Veldhuizen, Scott; Nelson, Geoffrey B; Stefancic, Ana; Tsemberis, Sam; Adair, Carol E; Distasio, Jino; Aubry, Tim; Stergiopoulos, Vicky; Streiner, David L

2016-01-01

This study examined whether Housing First fidelity ratings correspond to program operation descriptions from administrative data and predict client outcomes. A multisite, randomized controlled trial (At Home/Chez Soi) in five Canadian cities included two assessments of 12 programs over two years. Outcomes for 1,158 clients were measured every six months. Associations between fidelity ratings and administrative data (Spearman correlations) and participant outcomes (mixed-effects modeling) were examined. Fidelity ratings were generally good (mean ± SD=136.6 ± 10.3 out of a possible range of 38-152; 87% of maximum value). Fidelity was significantly associated with three of four measures of program operation, with correlations between .55 and .60. Greater program fidelity was associated with improvement in housing stability, community functioning, and quality of life. Variation in program fidelity was associated with operations and outcomes, supporting scale validity and intervention effectiveness. These findings reinforced the value of using fidelity monitoring to conduct quality assurance and technical assistance activities.

Inactivation of YAP oncoprotein by the Hippo pathway is involved in cell contact inhibition and tissue growth control

PubMed Central

Zhao, Bin; Wei, Xiaomu; Li, Weiquan; Udan, Ryan S.; Yang, Qian; Kim, Joungmok; Xie, Joe; Ikenoue, Tsuneo; Yu, Jindan; Li, Li; Zheng, Pan; Ye, Keqiang; Chinnaiyan, Arul; Halder, Georg; Lai, Zhi-Chun; Guan, Kun-Liang

2007-01-01

The Hippo pathway plays a key role in organ size control by regulating cell proliferation and apoptosis in Drosophila. Although recent genetic studies have shown that the Hippo pathway is regulated by the NF2 and Fat tumor suppressors, the physiological regulations of this pathway are unknown. Here we show that in mammalian cells, the transcription coactivator YAP (Yes-associated protein), is inhibited by cell density via the Hippo pathway. Phosphorylation by the Lats tumor suppressor kinase leads to cytoplasmic translocation and inactivation of the YAP oncoprotein. Furthermore, attenuation of this phosphorylation of YAP or Yorkie (Yki), the Drosophila homolog of YAP, potentiates their growth-promoting function in vivo. Moreover, YAP overexpression regulates gene expression in a manner opposite to cell density, and is able to overcome cell contact inhibition. Inhibition of YAP function restores contact inhibition in a human cancer cell line bearing deletion of Salvador (Sav), a Hippo pathway component. Interestingly, we observed that YAP protein is elevated and nuclear localized in some human liver and prostate cancers. Our observations demonstrate that YAP plays a key role in the Hippo pathway to control cell proliferation in response to cell contact. PMID:17974916

A mass balance approach to investigating geochemical controls on secondary water quality impacts at a crude oil spill site near Bemidji, MN

USGS Publications Warehouse

Ng, Gene-Hua Crystal; Bekins, Barbara A.; Cozzarelli, Isabelle M.; Baedecker, Mary Jo; Bennett, Philip C.; Amos, Richard T.

2014-01-01

Secondary water quality impacts can result from a broad range of coupled reactions triggered by primary groundwater contaminants. Data from a crude-oil spill research site near Bemidji, MN provide an ideal test case for investigating the complex interactions controlling secondary impacts, including depleted dissolved oxygen and elevated organic carbon, inorganic carbon, CH4, Mn, Fe, and other dissolved ions. To better understand these secondary impacts, this study began with an extensive data compilation of various data types, comprising aqueous, sediment, gas, and oil phases, covering a 260 m cross-sectional domain over 30 years. Mass balance calculations are used to quantify pathways that control secondary components, by using the data to constrain the sources and sinks for the important redox processes. The results show that oil constituents other than BTEX (benzene, toluene, ethylbenzene, o-, m- and p-xylenes), including n-alkanes and other aromatic compounds, play significant roles in plume evolution and secondary water quality impacts. The analysis underscores previous results on the importance of non-aqueous phases. Over 99.9% of the Fe2+ plume is attenuated by immobilization on sediments as Fe(II) and 85–95% of the carbon biodegradation products are outgassed. Gaps identified in carbon and Fe mass balances and in pH buffering mechanisms are used to formulate a new conceptual model. This new model includes direct out-gassing of CH4 and CO2 from organic carbon biodegradation, dissolution of directly produced CO2, and sorption with H+ exchange to improve pH buffering. The identification of these mechanisms extends understanding of natural attenuation of potential secondary impacts at enhanced reductive dechlorination sites, particularly for reduced Fe plumes, produced CH4, and pH perturbations.

A mass balance approach to investigating geochemical controls on secondary water quality impacts at a crude oil spill site near Bemidji, MN

NASA Astrophysics Data System (ADS)

Ng, G.-H. Crystal; Bekins, Barbara A.; Cozzarelli, Isabelle M.; Baedecker, Mary Jo; Bennett, Philip C.; Amos, Richard T.

2014-08-01

Secondary water quality impacts can result from a broad range of coupled reactions triggered by primary groundwater contaminants. Data from a crude-oil spill research site near Bemidji, MN provide an ideal test case for investigating the complex interactions controlling secondary impacts, including depleted dissolved oxygen and elevated organic carbon, inorganic carbon, CH4, Mn, Fe, and other dissolved ions. To better understand these secondary impacts, this study began with an extensive data compilation of various data types, comprising aqueous, sediment, gas, and oil phases, covering a 260 m cross-sectional domain over 30 years. Mass balance calculations are used to quantify pathways that control secondary components, by using the data to constrain the sources and sinks for the important redox processes. The results show that oil constituents other than BTEX (benzene, toluene, ethylbenzene, o-, m- and p-xylenes), including n-alkanes and other aromatic compounds, play significant roles in plume evolution and secondary water quality impacts. The analysis underscores previous results on the importance of non-aqueous phases. Over 99.9% of the Fe2 + plume is attenuated by immobilization on sediments as Fe(II) and 85-95% of the carbon biodegradation products are outgassed. Gaps identified in carbon and Fe mass balances and in pH buffering mechanisms are used to formulate a new conceptual model. This new model includes direct out-gassing of CH4 and CO2 from organic carbon biodegradation, dissolution of directly produced CO2, and sorption with H+ exchange to improve pH buffering. The identification of these mechanisms extends understanding of natural attenuation of potential secondary impacts at enhanced reductive dechlorination sites, particularly for reduced Fe plumes, produced CH4, and pH perturbations.