Identifying Stimuli that Alter Immediate and Subsequent Levels of Vocal Stereotypy: A Further Analysis of Functionally Matched Stimulation

ERIC Educational Resources Information Center

Lanovaz, Marc J.; Fletcher, Sarah E.; Rapp, John T.

2009-01-01

We used a three-component multiple-schedule with a brief reversal design to evaluate the effects of structurally unmatched and matched stimuli on immediate and subsequent vocal stereotypy that was displayed by three children with autism spectrum disorders. For 2 of the 3 participants, access to matched stimuli, unmatched stimuli, and music…

Trial-Based Functional Analysis Informs Treatment for Vocal Scripting.

PubMed

Rispoli, Mandy; Brodhead, Matthew; Wolfe, Katie; Gregori, Emily

2018-05-01

Research on trial-based functional analysis has primarily focused on socially maintained challenging behaviors. However, procedural modifications may be necessary to clarify ambiguous assessment results. The purposes of this study were to evaluate the utility of iterative modifications to trial-based functional analysis on the identification of putative reinforcement and subsequent treatment for vocal scripting. For all participants, modifications to the trial-based functional analysis identified a primary function of automatic reinforcement. The structure of the trial-based format led to identification of social attention as an abolishing operation for vocal scripting. A noncontingent attention treatment was evaluated using withdrawal designs for each participant. This noncontingent attention treatment resulted in near zero levels of vocal scripting for all participants. Implications for research and practice are presented.

A functional magnetic resonance imaging study mapping the episodic memory encoding network in temporal lobe epilepsy

PubMed Central

Sidhu, Meneka K.; Stretton, Jason; Winston, Gavin P.; Bonelli, Silvia; Centeno, Maria; Vollmar, Christian; Symms, Mark; Thompson, Pamela J.; Koepp, Matthias J.

2013-01-01

Functional magnetic resonance imaging has demonstrated reorganization of memory encoding networks within the temporal lobe in temporal lobe epilepsy, but little is known of the extra-temporal networks in these patients. We investigated the temporal and extra-temporal reorganization of memory encoding networks in refractory temporal lobe epilepsy and the neural correlates of successful subsequent memory formation. We studied 44 patients with unilateral temporal lobe epilepsy and hippocampal sclerosis (24 left) and 26 healthy control subjects. All participants performed a functional magnetic resonance imaging memory encoding paradigm of faces and words with subsequent out-of-scanner recognition assessments. A blocked analysis was used to investigate activations during encoding and neural correlates of subsequent memory were investigated using an event-related analysis. Event-related activations were then correlated with out-of-scanner verbal and visual memory scores. During word encoding, control subjects activated the left prefrontal cortex and left hippocampus whereas patients with left hippocampal sclerosis showed significant additional right temporal and extra-temporal activations. Control subjects displayed subsequent verbal memory effects within left parahippocampal gyrus, left orbitofrontal cortex and fusiform gyrus whereas patients with left hippocampal sclerosis activated only right posterior hippocampus, parahippocampus and fusiform gyrus. Correlational analysis showed that patients with left hippocampal sclerosis with better verbal memory additionally activated left orbitofrontal cortex, anterior cingulate cortex and left posterior hippocampus. During face encoding, control subjects showed right lateralized prefrontal cortex and bilateral hippocampal activations. Patients with right hippocampal sclerosis showed increased temporal activations within the superior temporal gyri bilaterally and no increased extra-temporal areas of activation compared with control subjects. Control subjects showed subsequent visual memory effects within right amygdala, hippocampus, fusiform gyrus and orbitofrontal cortex. Patients with right hippocampal sclerosis showed subsequent visual memory effects within right posterior hippocampus, parahippocampal and fusiform gyri, and predominantly left hemisphere extra-temporal activations within the insula and orbitofrontal cortex. Correlational analysis showed that patients with right hippocampal sclerosis with better visual memory activated the amygdala bilaterally, right anterior parahippocampal gyrus and left insula. Right sided extra-temporal areas of reorganization observed in patients with left hippocampal sclerosis during word encoding and bilateral lateral temporal reorganization in patients with right hippocampal sclerosis during face encoding were not associated with subsequent memory formation. Reorganization within the medial temporal lobe, however, is an efficient process. The orbitofrontal cortex is critical to subsequent memory formation in control subjects and patients. Activations within anterior cingulum and insula correlated with better verbal and visual subsequent memory in patients with left and right hippocampal sclerosis, respectively, representing effective extra-temporal recruitment. PMID:23674488

Functional analysis and treatment of the diurnal bruxism of a 16-year-old girl with autism.

PubMed

Armstrong, Amy; Knapp, Vicki Madaus; McAdam, David B

2014-01-01

Bruxism is defined as the clenching and grinding of teeth. This study used a functional analysis to examine whether the bruxism of a 16-year-old girl with autism was maintained by automatic reinforcement or social consequences. A subsequent component analysis of the intervention package described by Barnoy, Najdowski, Tarbox, Wilke, and Nollet (2009) showed that a vocal reprimand (e.g., "stop grinding") effectively reduced the participant's bruxism. Results were maintained across time, and effects extended to novel staff members. © Society for the Experimental Analysis of Behavior.

Application of Independent Component Analysis for the Data Mining of Simultaneous EEG-fMRI: Preliminary Experience on Sleep Onset

PubMed Central

Lee, Jong-Hwan; Oh, Sungsuk; Jolesz, Ferenc A.; Park, Hyunwook; Yoo, Seung-Schik

2010-01-01

The simultaneous acquisition of electroencephalogram (EEG) and functional MRI (fMRI) signals is potentially advantageous because of the superior resolution that is achieved in both the temporal and spatial domains, respectively. However, ballistocardiographic artifacts along with the ocular artifacts are a major obstacle for the detection of the EEG signatures of interest. Since the sources corresponding to these artifacts are independent from those producing the EEG signatures, we applied the Infomax-based independent component analysis (ICA) technique to separate the EEG signatures from the artifacts. The isolated EEG signatures were further utilized to model the canonical hemodynamic response functions (HRFs). Subsequently, the brain areas from which these EEG signatures originated were identified as locales of activation patterns from the analysis of fMRI data. Upon the identification and subsequent evaluation of brain areas generating interictal epileptic discharge (IED) spikes from an epileptic subject, the presented method was successfully applied to detect the theta- and alpha-rhythms that are sleep onset related EEG signatures along with the subsequent neural circuitries from a sleep deprived volunteer. These results suggest that the ICA technique may be useful for the preprocessing of simultaneous EEG-fMRI acquisitions, especially when a reference paradigm is unavailable. PMID:19922343

Application of independent component analysis for the data mining of simultaneous Eeg-fMRI: preliminary experience on sleep onset.

PubMed

Lee, Jong-Hwan; Oh, Sungsuk; Jolesz, Ferenc A; Park, Hyunwook; Yoo, Seung-Schik

2009-01-01

The simultaneous acquisition of electroencephalogram (EEG) and functional MRI (fMRI) signals is potentially advantageous because of the superior resolution that is achieved in both the temporal and spatial domains, respectively. However, ballistocardiographic artifacts along with ocular artifacts are a major obstacle for the detection of the EEG signatures of interest. Since the sources corresponding to these artifacts are independent from those producing the EEG signatures, we applied the Infomax-based independent component analysis (ICA) technique to separate the EEG signatures from the artifacts. The isolated EEG signatures were further utilized to model the canonical hemodynamic response functions (HRFs). Subsequently, the brain areas from which these EEG signatures originated were identified as locales of activation patterns from the analysis of fMRI data. Upon the identification and subsequent evaluation of brain areas generating interictal epileptic discharge (IED) spikes from an epileptic subject, the presented method was successfully applied to detect the theta and alpha rhythms that are sleep onset-related EEG signatures along with the subsequent neural circuitries from a sleep-deprived volunteer. These results suggest that the ICA technique may be useful for the preprocessing of simultaneous EEG-fMRI acquisitions, especially when a reference paradigm is unavailable.

Emergence and subsequent functional specialization of kindlins during evolution of cell adhesiveness

PubMed Central

Meller, Julia; Rogozin, Igor B.; Poliakov, Eugenia; Meller, Nahum; Bedanov-Pack, Mark; Plow, Edward F.; Qin, Jun; Podrez, Eugene A.; Byzova, Tatiana V.

2015-01-01

Kindlins are integrin-interacting proteins essential for integrin-mediated cell adhesiveness. In this study, we focused on the evolutionary origin and functional specialization of kindlins as a part of the evolutionary adaptation of cell adhesive machinery. Database searches revealed that many members of the integrin machinery (including talin and integrins) existed before kindlin emergence in evolution. Among the analyzed species, all metazoan lineages—but none of the premetazoans—had at least one kindlin-encoding gene, whereas talin was present in several premetazoan lineages. Kindlin appears to originate from a duplication of the sequence encoding the N-terminal fragment of talin (the talin head domain) with a subsequent insertion of the PH domain of separate origin. Sequence analysis identified a member of the actin filament–associated protein 1 (AFAP1) superfamily as the most likely origin of the kindlin PH domain. The functional divergence between kindlin paralogues was assessed using the sequence swap (chimera) approach. Comparison of kindlin 2 (K2)/kindlin 3 (K3) chimeras revealed that the F2 subdomain, in particular its C-terminal part, is crucial for the differential functional properties of K2 and K3. The presence of this segment enables K2 but not K3 to localize to focal adhesions. Sequence analysis of the C-terminal part of the F2 subdomain of K3 suggests that insertion of a variable glycine-rich sequence in vertebrates contributed to the loss of constitutive K3 targeting to focal adhesions. Thus emergence and subsequent functional specialization of kindlins allowed multicellular organisms to develop additional tissue-specific adaptations of cell adhesiveness. PMID:25540429

BATMAN-TCM: a Bioinformatics Analysis Tool for Molecular mechANism of Traditional Chinese Medicine.

PubMed

Liu, Zhongyang; Guo, Feifei; Wang, Yong; Li, Chun; Zhang, Xinlei; Li, Honglei; Diao, Lihong; Gu, Jiangyong; Wang, Wei; Li, Dong; He, Fuchu

2016-02-16

Traditional Chinese Medicine (TCM), with a history of thousands of years of clinical practice, is gaining more and more attention and application worldwide. And TCM-based new drug development, especially for the treatment of complex diseases is promising. However, owing to the TCM's diverse ingredients and their complex interaction with human body, it is still quite difficult to uncover its molecular mechanism, which greatly hinders the TCM modernization and internationalization. Here we developed the first online Bioinformatics Analysis Tool for Molecular mechANism of TCM (BATMAN-TCM). Its main functions include 1) TCM ingredients' target prediction; 2) functional analyses of targets including biological pathway, Gene Ontology functional term and disease enrichment analyses; 3) the visualization of ingredient-target-pathway/disease association network and KEGG biological pathway with highlighted targets; 4) comparison analysis of multiple TCMs. Finally, we applied BATMAN-TCM to Qishen Yiqi dripping Pill (QSYQ) and combined with subsequent experimental validation to reveal the functions of renin-angiotensin system responsible for QSYQ's cardioprotective effects for the first time. BATMAN-TCM will contribute to the understanding of the "multi-component, multi-target and multi-pathway" combinational therapeutic mechanism of TCM, and provide valuable clues for subsequent experimental validation, accelerating the elucidation of TCM's molecular mechanism. BATMAN-TCM is available at http://bionet.ncpsb.org/batman-tcm.

Human factors evaluation of teletherapy: Function and task analysis. Volume 2

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

Kaye, R.D.; Henriksen, K.; Jones, R.

1995-07-01

As a treatment methodology, teletherapy selectively destroys cancerous and other tissue by exposure to an external beam of ionizing radiation. Sources of radiation are either a radioactive isotope, typically Cobalt-60 (Co-60), or a linear accelerator. Records maintained by the NRC have identified instances of teletherapy misadministration where the delivered radiation dose has differed from the radiation prescription (e.g., instances where fractions were delivered to the wrong patient, to the wrong body part, or were too great or too little with respect to the defined treatment volume). Both human error and machine malfunction have led to misadministrations. Effective and safe treatmentmore » requires a concern for precision and consistency of human-human and human-machine interactions throughout the course of therapy. The present study is the first part of a series of human factors evaluations for identifying the root causes that lead to human error in the teletherapy environment. The human factors evaluations included: (1) a function and task analysis of teletherapy activities, (2) an evaluation of the human-system interfaces, (3) an evaluation of procedures used by teletherapy staff, (4) an evaluation of the training and qualifications of treatment staff (excluding the oncologists), (5) an evaluation of organizational practices and policies, and (6) an identification of problems and alternative approaches for NRC and industry attention. The present report addresses the function and task analysis of teletherapy activities and provides the foundation for the conduct of the subsequent evaluations. The report includes sections on background, methodology, a description of the function and task analysis, and use of the task analysis findings for the subsequent tasks. The function and task analysis data base also is included.« less

Single-hole spectral function and spin-charge separation in the t-J model

NASA Astrophysics Data System (ADS)

Mishchenko, A. S.; Prokof'ev, N. V.; Svistunov, B. V.

2001-07-01

Worm algorithm Monte Carlo simulations of the hole Green function with subsequent spectral analysis were performed for 0.1<=J/t<=0.4 on lattices with up to L×L=32×32 sites at a temperature as low as T=J/40, and present, apparently, the hole spectral function in the thermodynamic limit. Spectral analysis reveals a δ-function-sharp quasiparticle peak at the lower edge of the spectrum that is incompatible with the power-law singularity and thus rules out the possibility of spin-charge separation in this parameter range. Spectral continuum features two peaks separated by a gap ~4÷5 t.

Mathematical modelling and linear stability analysis of laser fusion cutting

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

Hermanns, Torsten; Schulz, Wolfgang; Vossen, Georg

A model for laser fusion cutting is presented and investigated by linear stability analysis in order to study the tendency for dynamic behavior and subsequent ripple formation. The result is a so called stability function that describes the correlation of the setting values of the process and the process’ amount of dynamic behavior.

Distress modeling for DARWin-ME : final report.

DOT National Transportation Integrated Search

2013-12-01

Distress prediction models, or transfer functions, are key components of the Pavement M-E Design and relevant analysis. The accuracy of such models depends on a successful process of calibration and subsequent validation of model coefficients in the ...

From Genome to Function: Systematic Analysis of the Soil Bacterium Bacillus Subtilis

PubMed Central

Crawshaw, Samuel G.; Wipat, Anil

2001-01-01

Bacillus subtilis is a sporulating Gram-positive bacterium that lives primarily in the soil and associated water sources. Whilst this bacterium has been studied extensively in the laboratory, relatively few studies have been undertaken to study its activity in natural environments. The publication of the B. subtilis genome sequence and subsequent systematic functional analysis programme have provided an opportunity to develop tools for analysing the role and expression of Bacillus genes in situ. In this paper we discuss analytical approaches that are being developed to relate genes to function in environments such as the rhizosphere. PMID:18628943

Bion's discovery of alpha function: thinking under fire on the battlefield and in the consulting room.

PubMed

Brown, Lawrence J

2012-10-01

This paper has traced Bion's discovery of alpha function and its subsequent elaboration. His traumatic experiences as a young tank commander in World War I (overlaid on, and intertwined with, childhood conflicts) gave him firsthand exposure to very painful emotions that tested his capacity to manage. Later, in the 1950s, after his analysis with Melanie Klein and marriage to Francesca Bion, he undertook the analysis of psychotic patients and learned how they disassembled their ability to know reality as a defense against unbearable emotional truths in their lives. This led Bion to identify an aspect of dreaming that was necessary in order for reality experience to be given personal meaning so that one may learn from experience. Simultaneous with working out this new theory of dreaming, Bion also revisited his World War I experiences that had remained undigested and all these elements coalesced into a selected fact - his discovery of alpha function. In subsequent writings, Bion explored the constituent factors of alpha function, including the container/contained relationship, the PS↔D balance, reverie, tolerated doubt and other factors which I have termed the 'Constellation for Thinking'. Copyright © 2012 Institute of Psychoanalysis.

Impact of worsening renal function during the treatment of decompensated heart failure on changes in renal function during subsequent hospitalization.

PubMed

Testani, Jeffrey M; Cappola, Thomas P; McCauley, Brian D; Chen, Jennifer; Shen, James; Shannon, Richard P; Kimmel, Stephen E

2011-05-01

Worsening renal function (WRF) commonly complicates the treatment of acute decompensated heart failure. Despite considerable investigation in this area, it remains unclear to what degree WRF is a reflection of treatment- versus patient-related factors. We hypothesized that if WRF is significantly influenced by factors intrinsic to the patient, then WRF during an index hospitalization should predict WRF during subsequent hospitalization. Consecutive admissions to the Hospital of the University of Pennsylvania with a discharge diagnosis of congestive heart failure were reviewed. Patients with >1 hospitalization were retained for analysis. In total, 181 hospitalization pairs met the inclusion criteria. Baseline patient characteristics demonstrated significant correlation between hospitalizations (P ≤ .002 for all) but minimal association with WRF. In contrast, variables related to the aggressiveness of diuresis were weakly correlated between hospitalizations but significantly associated with WRF (P ≤ .024 for all). Consistent with the primary hypothesis, WRF during the index hospitalization was strongly associated with WRF during subsequent hospitalization (odds ratio [OR] 2.7, P = .003). This association was minimally altered after controlling for traditional baseline characteristics (OR 2.5, P = .006) and in-hospital treatment-related parameters (OR 2.8, P = .005). A prior history of WRF is strongly associated with subsequent episodes of WRF, independent of in-hospital treatment received. These results suggest that baseline factors intrinsic to the patient's cardiorenal pathophysiology have substantial influence on the subsequent development of WRF. Copyright © 2011 Mosby, Inc. All rights reserved.

Impact of Worsening Renal Function during the Treatment of Decompensated Heart Failure on Changes in Renal Function during Subsequent Hospitalization

PubMed Central

Testani, Jeffrey M.; Cappola, Thomas P.; McCauley, Brian D.; Chen, Jennifer; Shen, James; Shannon, Richard P.; Kimmel, Stephen E.

2011-01-01

Background Worsening renal function (WRF) commonly complicates the treatment of acute decompensated heart failure. Despite considerable investigation in this area, it remains unclear to what degree WRF is a reflection of treatment versus patient related factors. We hypothesized that if WRF is significantly influenced by factors intrinsic to the patient than WRF during an index hospitalization should predict WRF during subsequent hospitalization. Methods Consecutive admissions to the Hospital of the University of Pennsylvania with a discharge diagnosis of congestive heart failure were reviewed. Patients with >1 hospitalization were retained for analysis. Results In total 181 hospitalization pairs met the inclusion criteria. Baseline patient characteristics demonstrated significant correlation between hospitalizations (p≤0.002 for all) but minimal association with WRF. In contrast, variables related to the aggressiveness of diuresis were weakly correlated between hospitalizations but significantly associated with WRF (p≤0.024 for all). Consistent with the primary hypothesis, WRF during the index hospitalization was strongly associated with WRF during subsequent hospitalization (OR=2.7, p=0.003). This association was minimally altered after controlling for traditional baseline characteristics (OR=2.5, p=0.006) and in-hospital treatment related parameters (OR=2.8, p=0.005). Conclusions A prior history of WRF is strongly associated with subsequent episodes of WRF, independent of in-hospital treatment received. These results suggest that baseline factors intrinsic to the patient’s cardiorenal pathophysiology have substantial influence on the subsequent development of WRF. PMID:21570527

Effect of relevance on amygdala activation and association with the ventral striatum.

PubMed

Ousdal, Olga Therese; Reckless, Greg E; Server, Andres; Andreassen, Ole A; Jensen, Jimmy

2012-08-01

While the amygdala historically has been implicated in emotional stimuli processing, recent data suggest a general role in parceling out the relevance of stimuli, regardless of their emotional properties. Using functional magnetic resonance imaging, we tested the relevance hypothesis by investigating human amygdala responses to emotionally neutral stimuli while manipulating their relevance. The task was operationalized as highly relevant if a subsequent opportunity to respond for a reward depended on response accuracy of the task, and less relevant if the reward opportunity was independent of task performance. A region of interest analysis revealed bilateral amygdala activations in response to the high relevance condition compared to the low relevance condition. An exploratory whole-brain analysis yielded robust similar results in bilateral ventral striatum. A subsequent functional connectivity analysis demonstrated increased connectivity between amygdala and ventral striatum for the highly relevant stimuli compared to the less relevant stimuli. These findings suggest that the amygdala's processing profile goes beyond detection of emotions per se, and directly support the proposed role in relevance detection. In addition, the findings suggest a close relationship between amygdala and ventral striatal activity when processing relevant stimuli. Thus, the results may indicate that human amygdala modulates ventral striatum activity and subsequent behaviors beyond that observed for emotional cues, to encompass a broader range of relevant stimuli. Copyright © 2012 Elsevier Inc. All rights reserved.

BATMAN-TCM: a Bioinformatics Analysis Tool for Molecular mechANism of Traditional Chinese Medicine

NASA Astrophysics Data System (ADS)

Liu, Zhongyang; Guo, Feifei; Wang, Yong; Li, Chun; Zhang, Xinlei; Li, Honglei; Diao, Lihong; Gu, Jiangyong; Wang, Wei; Li, Dong; He, Fuchu

2016-02-01

Traditional Chinese Medicine (TCM), with a history of thousands of years of clinical practice, is gaining more and more attention and application worldwide. And TCM-based new drug development, especially for the treatment of complex diseases is promising. However, owing to the TCM’s diverse ingredients and their complex interaction with human body, it is still quite difficult to uncover its molecular mechanism, which greatly hinders the TCM modernization and internationalization. Here we developed the first online Bioinformatics Analysis Tool for Molecular mechANism of TCM (BATMAN-TCM). Its main functions include 1) TCM ingredients’ target prediction; 2) functional analyses of targets including biological pathway, Gene Ontology functional term and disease enrichment analyses; 3) the visualization of ingredient-target-pathway/disease association network and KEGG biological pathway with highlighted targets; 4) comparison analysis of multiple TCMs. Finally, we applied BATMAN-TCM to Qishen Yiqi dripping Pill (QSYQ) and combined with subsequent experimental validation to reveal the functions of renin-angiotensin system responsible for QSYQ’s cardioprotective effects for the first time. BATMAN-TCM will contribute to the understanding of the “multi-component, multi-target and multi-pathway” combinational therapeutic mechanism of TCM, and provide valuable clues for subsequent experimental validation, accelerating the elucidation of TCM’s molecular mechanism. BATMAN-TCM is available at http://bionet.ncpsb.org/batman-tcm.

BATMAN-TCM: a Bioinformatics Analysis Tool for Molecular mechANism of Traditional Chinese Medicine

PubMed Central

Liu, Zhongyang; Guo, Feifei; Wang, Yong; Li, Chun; Zhang, Xinlei; Li, Honglei; Diao, Lihong; Gu, Jiangyong; Wang, Wei; Li, Dong; He, Fuchu

2016-01-01

Traditional Chinese Medicine (TCM), with a history of thousands of years of clinical practice, is gaining more and more attention and application worldwide. And TCM-based new drug development, especially for the treatment of complex diseases is promising. However, owing to the TCM’s diverse ingredients and their complex interaction with human body, it is still quite difficult to uncover its molecular mechanism, which greatly hinders the TCM modernization and internationalization. Here we developed the first online Bioinformatics Analysis Tool for Molecular mechANism of TCM (BATMAN-TCM). Its main functions include 1) TCM ingredients’ target prediction; 2) functional analyses of targets including biological pathway, Gene Ontology functional term and disease enrichment analyses; 3) the visualization of ingredient-target-pathway/disease association network and KEGG biological pathway with highlighted targets; 4) comparison analysis of multiple TCMs. Finally, we applied BATMAN-TCM to Qishen Yiqi dripping Pill (QSYQ) and combined with subsequent experimental validation to reveal the functions of renin-angiotensin system responsible for QSYQ’s cardioprotective effects for the first time. BATMAN-TCM will contribute to the understanding of the “multi-component, multi-target and multi-pathway” combinational therapeutic mechanism of TCM, and provide valuable clues for subsequent experimental validation, accelerating the elucidation of TCM’s molecular mechanism. BATMAN-TCM is available at http://bionet.ncpsb.org/batman-tcm. PMID:26879404

[Preoperative analysis in rhinoplasty].

PubMed

Nguyen, P S; Bardot, J; Duron, J B; Levet, Y; Aiach, G

2014-12-01

Preoperative analysis in rhinoplasty consists in analyzing individual anatomical and functional characteristics without losing sight of the initial requirements of the patient to which priority should be given. The examination is primarily clinical but it also uses preoperative photographs taken at specific accurate angles. Detecting functional disorders or associated general pathologies, which will reduce the risk of complications. All of these factors taken into account, the surgeon can work out a rhinoplasty plan which he or she will subsequently explain to the patient and obtain his or her approbation. Copyright © 2014 Elsevier Masson SAS. All rights reserved.

In-Situ Analysis Of Metal(loid)s In Plants: State Of The Art And Artefacts

EPA Science Inventory

Metals and metalloids play important roles in plant function and metabolism. Likewise, plants subsequently introduce vital dietary nutrition to people and animals. Understanding the transport, localisation and speciation of these elements is critical for understanding availabil...

The Effects of Presession Manipulations on Automatically Maintained Challenging Behavior and Task Responding

ERIC Educational Resources Information Center

Chung, Yi-Chieh; Cannella-Malone, Helen I.

2010-01-01

This study examined the effects of presession exposure to attention, response blocking, attention with response blocking, and noninteraction conditions on subsequent engagement in automatically maintained challenging behavior and correct responding in four individuals with significant intellectual disabilities. Following a functional analysis, the…

Concepts of Protein Sorting or Targeting Signals and Membrane Topology in Undergraduate Teaching

ERIC Educational Resources Information Center

Tang, Bor Luen; Teng, Felicia Yu Hsuan

2005-01-01

The process of protein biogenesis culminates in its correct targeting to specific subcellular locations where it serves a function. Contemporary molecular and cell biology investigations often involve the exogenous expression of epitope- or fluorescent protein-tagged recombinant molecules as well as subsequent analysis of protein-protein…

Theaters and Auditoriums. Second Edition.

ERIC Educational Resources Information Center

Burris-Meyer, Harold; Cole, Edward C.

Facilities for the performing arts are examined as to associated problems and possible design solutions. Also included are auditoriums which may not be directly related to theater functions but have similar problems and needs. Existing facilities serve as a basis for the subsequent critical analysis of certain areas and development of optimal…

Pichia stipitis genomics, transcriptomics, and gene clusters

Treesearch

Thomas W. Jeffries; Jennifer R. Headman Van Vleet

2009-01-01

Genome sequencing and subsequent global gene expression studies have advanced our understanding of the lignocellulose-fermenting yeast Pichia stipitis. These studies have provided an insight into its central carbon metabolism, and analysis of its genome has revealed numerous functional gene clusters and tandem repeats. Specialized physiological traits are often the...

Analysis of Compton continuum measurements

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

Gold, R.; Olson, I. K.

1970-01-01

Five computer programs: COMPSCAT, FEND, GABCO, DOSE, and COMPLOT, have been developed and used for the analysis and subsequent reduction of measured energy distributions of Compton recoil electrons to continuous gamma spectra. In addition to detailed descriptions of these computer programs, the relationship amongst these codes is stressed. The manner in which these programs function is illustrated by tracing a sample measurement through a complete cycle of the data-reduction process.

A Bayesian Approach to a Multiple-Group Latent Class-Profile Analysis: The Timing of Drinking Onset and Subsequent Drinking Behaviors among U.S. Adolescents

ERIC Educational Resources Information Center

Chung, Hwan; Anthony, James C.

2013-01-01

This article presents a multiple-group latent class-profile analysis (LCPA) by taking a Bayesian approach in which a Markov chain Monte Carlo simulation is employed to achieve more robust estimates for latent growth patterns. This article describes and addresses a label-switching problem that involves the LCPA likelihood function, which has…

The cognitive and neural basis of option generation and subsequent choice.

PubMed

Kaiser, Stefan; Simon, Joe J; Kalis, Annemarie; Schweizer, Sophie; Tobler, Philippe N; Mojzisch, Andreas

2013-12-01

Decision-making research has thoroughly investigated how people choose from a set of externally provided options. However, in ill-structured real-world environments, possible options for action are not defined by the situation but have to be generated by the agent. Here, we apply behavioral analysis (Study 1) and functional magnetic resonance imaging (Study 2) to investigate option generation and subsequent choice. For this purpose, we employ a new experimental task that requires participants to generate options for simple real-world scenarios and to subsequently decide among the generated options. Correlational analysis with a cognitive test battery suggests that retrieval of options from long-term memory is a relevant process during option generation. The results of the fMRI study demonstrate that option generation in simple real-world scenarios recruits the anterior prefrontal cortex. Furthermore, we show that choice behavior and its neural correlates differ between self-generated and externally provided options. Specifically, choice between self-generated options is associated with stronger recruitment of the dorsal anterior cingulate cortex. This impact of option generation on subsequent choice underlines the need for an expanded model of decision making to accommodate choice between self-generated options.

Open Reduction and Internal Fixation versus Non-Surgical Treatment in Displaced Midshaft Clavicle Fractures: A Meta-Analysis.

PubMed

Ahmed, Abdulaziz F; Salameh, Motasem; AlKhatib, Nidal; Elmhiregh, Aissam; Ahmed, Ghalib O

2018-04-17

To compare open reduction and internal fixation (ORIF) and non-surgical treatment outcomes in displaced midshaft clavicle fractures. PubMed, MEDLINE, EMBASE, Web of Science, Cochrane Library, and ClinicalTrials.gov were searched in September 2017. Inclusion criteria were randomized controlled trials reporting nonunion, shoulder functional outcomes, and subsequent surgery rates or pain scores. We excluded studies with patients younger than 16 years, maximum follow-up less than nine months, and inaccessible full text. Extracted data included the first author, publication year, number of patients, number of nonunions, Constant scores, disabilities of the arm, shoulder and hand (DASH) scores, number of subsequent surgeries, and pain measured using the visual analogue analog scale. The risk ratio (RR) of nonunion was 0.15 (95% confidence interval [CI], 0.08, 0.31) in ORIF compared with that of non-surgical treatment. Constant and DASH scores were significantly better in ORIF up to 6 months. The mean difference (MD) in DASH scores at 12 months was statistically insignificant in both treatments (MD, -4.19; 95% CI, -9.34, 0.96). Constant scores remained significant in ORIF (MD, 4.39; 95% CI, 1.03, 7.75). Subsequent surgeries and pain scores were similar in both treatments. Significant reduction in nonunions and favorable early functional outcomes are associated with ORIF. Nevertheless, late functional outcomes, subsequent surgeries, and pain scores are similar to those of non-surgical treatment. Although patients treated with ORIF mainly had subsequent elective plate removals; non-surgically treated patients had more surgical fixations for nonunions. As a result, there remains inconsistent evidence regarding the best treatment for displaced midshaft clavicle fractures. Therapeutic Level I.

Construction and Analysis of Functional Networks in the Gut Microbiome of Type 2 Diabetes Patients.

PubMed

Li, Lianshuo; Wang, Zicheng; He, Peng; Ma, Shining; Du, Jie; Jiang, Rui

2016-10-01

Although networks of microbial species have been widely used in the analysis of 16S rRNA sequencing data of a microbiome, the construction and analysis of a complete microbial gene network are in general problematic because of the large number of microbial genes in metagenomics studies. To overcome this limitation, we propose to map microbial genes to functional units, including KEGG orthologous groups and the evolutionary genealogy of genes: Non-supervised Orthologous Groups (eggNOG) orthologous groups, to enable the construction and analysis of a microbial functional network. We devised two statistical methods to infer pairwise relationships between microbial functional units based on a deep sequencing dataset of gut microbiome from type 2 diabetes (T2D) patients as well as healthy controls. Networks containing such functional units and their significant interactions were constructed subsequently. We conducted a variety of analyses of global properties, local properties, and functional modules in the resulting functional networks. Our data indicate that besides the observations consistent with the current knowledge, this study provides novel biological insights into the gut microbiome associated with T2D. Copyright © 2016. Production and hosting by Elsevier Ltd.

Six-month longitudinal associations between cognitive functioning and distress among the community-based elderly in Hong Kong: A cross-lagged panel analysis.

PubMed

Leung, Chantel Joanne; Cheng, Lewis; Yu, Junhong; Yiend, Jenny; Lee, Tatia M C

2018-07-01

Although previous studies have extensively documented the cross-sectional relationship between cognitive impairment and psychological distress, findings relating to their longitudinal associations remains mixed. The present study examines the longitudinal associations and mutual influence between cognitive functioning and psychological distress across six months among community-dwelling elderly in Hong Kong. A total of 162 older adults (40 males; M age  = 69.8 years, SD = 6.4) were administered objective and subjective measures of cognitive functioning, as well as self-reported ratings of distress, at two time points six months apart. Using structural equation modeling, we tested the cross-lagged relationships between cognitive functioning and distress. Our cross-lagged model indicated that cognitive functioning at baseline significantly predicted subsequent psychological distress. However, distress was not significantly associated with subsequent cognitive functioning. Additionally, the objective and subjective measures of cognitive functioning were not significantly correlated. These findings suggested that distress may occur as a consequence of poorer cognitive functioning in elderly, but not vice versa. The lack of correlation between objective and subjective cognitive measures suggested that the participants may not have adequate insight into their cognitive abilities. The implications of these findings are discussed. Copyright © 2018. Published by Elsevier B.V.

Incidence and rates of visual field progression after longitudinally measured optic disc change in glaucoma.

PubMed

Chauhan, Balwantray C; Nicolela, Marcelo T; Artes, Paul H

2009-11-01

To determine whether glaucoma patients with progressive optic disc change have subsequent visual field progression earlier and at a faster rate compared with those without disc change. Prospective, longitudinal, cohort study. Eighty-one patients with open-angle glaucoma. Patients underwent confocal scanning laser tomography and standard automated perimetry every 6 months. The complete follow-up was divided into initial and subsequent periods. Two initial periods-first 3 years (Protocol A) and first half of the total follow-up (Protocol B)-were used, with the respective remainder being the subsequent follow-up. Disc change during the initial follow-up was determined with liberal, moderate, or conservative criteria of the Topographic Change Analysis. Subsequent field progression was determined with significant pattern deviation change in >or=3 locations (criterion used in the Early Manifest Glaucoma Trial). As a control analysis, field change during the initial follow-up was determined with significant pattern deviation change in >or=1, >or=2, or >or=3 locations. Survival time to subsequent field progression, rates of mean deviation (MD) change, and positive and negative likelihood ratios. The median (interquartile range) total follow-up was 11.0 (8.0-12.0) years with 22 (18-24) examinations. More patients had disc changes during the initial follow-up compared with field changes. The mean time to field progression was consistently shorter (protocol A, 0.8-1.7 years; protocol B, 0.3-0.7 years) in patients with prior disc change. In the control analysis, patients with prior field change had statistically earlier subsequent field progression (protocol A, 2.9-3.0 years; protocol B, 0.7-0.9). Similarly, patients with either prior disc or field change always had worse mean rates of subsequent MD change, although the distributions overlapped widely. Patients with subsequent field progression were up to 3 times more likely to have prior disc change compared with those without, and up to 5 times more likely to have prior field change compared with those without. Longitudinally measured optic disc change is predictive of subsequent visual field progression and may be an efficacious end point for functional outcomes in clinical studies and trials in glaucoma.

Coaxial electrospinning of WO3 nanotubes functionalized with bio-inspired Pd catalysts and their superior hydrogen sensing performance

NASA Astrophysics Data System (ADS)

Choi, Seon-Jin; Chattopadhyay, Saptarshi; Kim, Jae Jin; Kim, Sang-Joon; Tuller, Harry L.; Rutledge, Gregory C.; Kim, Il-Doo

2016-04-01

Macroporous WO3 nanotubes (NTs) functionalized with nanoscale catalysts were fabricated using coaxial electrospinning combined with sacrificial templating and protein-encapsulated catalysts. The macroporous thin-walled nanotubular structures were obtained by introducing colloidal polystyrene (PS) particles to a shell solution of W precursor and poly(vinylpyrrolidone). After coaxial electrospinning with a core liquid of mineral oil and subsequent calcination, open pores with an average diameter of 173 nm were formed on the surface of WO3 NTs due to decomposition of the PS colloids. In addition, catalytic Pd nanoparticles (NPs) were synthesized using bio-inspired protein cages, i.e., apoferritin, and uniformly dispersed within the shell solution and subsequently on the WO3 NTs. The resulting Pd functionalized macroporous WO3 NTs were demonstrated to be high performance hydrogen (H2) sensors. In particular, Pd-functionalized macroporous WO3 NTs exhibited a very high H2 response (Rair/Rgas) of 17.6 at 500 ppm with a short response time. Furthermore, the NTs were shown to be highly selective for H2 compared to other gases such as carbon monoxide (CO), ammonia (NH3), and methane (CH4). The results demonstrate a new synthetic method to prepare highly porous nanotubular structures with well-dispersed nanoscale catalysts, which can provide improved microstructures for chemical sensing.Macroporous WO3 nanotubes (NTs) functionalized with nanoscale catalysts were fabricated using coaxial electrospinning combined with sacrificial templating and protein-encapsulated catalysts. The macroporous thin-walled nanotubular structures were obtained by introducing colloidal polystyrene (PS) particles to a shell solution of W precursor and poly(vinylpyrrolidone). After coaxial electrospinning with a core liquid of mineral oil and subsequent calcination, open pores with an average diameter of 173 nm were formed on the surface of WO3 NTs due to decomposition of the PS colloids. In addition, catalytic Pd nanoparticles (NPs) were synthesized using bio-inspired protein cages, i.e., apoferritin, and uniformly dispersed within the shell solution and subsequently on the WO3 NTs. The resulting Pd functionalized macroporous WO3 NTs were demonstrated to be high performance hydrogen (H2) sensors. In particular, Pd-functionalized macroporous WO3 NTs exhibited a very high H2 response (Rair/Rgas) of 17.6 at 500 ppm with a short response time. Furthermore, the NTs were shown to be highly selective for H2 compared to other gases such as carbon monoxide (CO), ammonia (NH3), and methane (CH4). The results demonstrate a new synthetic method to prepare highly porous nanotubular structures with well-dispersed nanoscale catalysts, which can provide improved microstructures for chemical sensing. Electronic supplementary information (ESI) available: Coaxial electrospinning with different feeding rates, additional TEM analysis for pore size analysis, XPS analysis of Pd-loaded macroporous WO3 NTs, and dynamic response transition properties of sensors. See DOI: 10.1039/c5nr06611e

Surface analysis of gold nanoparticles functionalized with thiol-modified glucose SAMs for biosensor applications.

NASA Astrophysics Data System (ADS)

Spampinato, Valentina; Parracino, Mariaantonietta; La Spina, Rita; Rossi, Francois; Ceccone, Giacomo

2016-02-01

In this work, Time of Flight Secondary Ion Mass Spectrometry (ToF-SIMS), Principal Component Analysis (PCA) and X-ray Photoelectron Spectroscopy (XPS) have been used to characterize the surface chemistry of gold substrates before and after functionalization with thiol-modified glucose self-assembled monolayers and subsequent biochemical specific recognition of maltose binding protein (MBP). The results indicate that the surface functionalization is achieved both on flat and nanoparticles gold substrates thus showing the potential of the developed system as biodetection platform. Moreover, the method presented here has been found to be a sound and valid approach to characterize the surface chemistry of nanoparticles functionalized with large molecules. Both techniques were proved to be very useful tools for monitoring all the functionalization steps, including the investigation of the biological behaviour of the glucose-modified particles in presence of the maltose binding protein.

Surface Analysis of Gold Nanoparticles Functionalized with Thiol-Modified Glucose SAMs for Biosensor Applications

PubMed Central

Spampinato, Valentina; Parracino, Maria Antonietta; La Spina, Rita; Rossi, Francois; Ceccone, Giacomo

2016-01-01

In this work, Time of Flight Secondary Ion Mass Spectrometry (ToF-SIMS), Principal Component Analysis (PCA) and X-ray Photoelectron Spectroscopy (XPS) have been used to characterize the surface chemistry of gold substrates before and after functionalization with thiol-modified glucose self-assembled monolayers and subsequent biochemical specific recognition of maltose binding protein (MBP). The results indicate that the surface functionalization is achieved both on flat and nanoparticles gold substrates thus showing the potential of the developed system as biodetection platform. Moreover, the method presented here has been found to be a sound and valid approach to characterize the surface chemistry of nanoparticles functionalized with large molecules. Both techniques were proved to be very useful tools for monitoring all the functionalization steps, including the investigation of the biological behavior of the glucose-modified particles in the presence of the maltose binding protein. PMID:26973830

Isolation of Mouse Hair Follicle Bulge Stem Cells and Their Functional Analysis in a Reconstitution Assay.

PubMed

Zheng, Ying; Hsieh, Jen-Chih; Escandon, Julia; Cotsarelis, George

2016-01-01

The hair follicle (HF) is a dynamic structure readily accessible within the skin, and contains various pools of stem cells that have a broad regenerative potential during normal homeostasis and in response to injury. Recent discoveries demonstrating the multipotent capabilities of hair follicle stem cells and the easy access to skin tissue make the HF an attractive source for isolating stem cells and their subsequent application in tissue engineering and regenerative medicine. Here, we describe the isolation and purification of hair follicle bulge stem cells from mouse skin, and hair reconstitution assays that allows the functional analysis of multipotent stem cells.

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.

Neuroimaging with functional near infrared spectroscopy: From formation to interpretation

NASA Astrophysics Data System (ADS)

Herrera-Vega, Javier; Treviño-Palacios, Carlos G.; Orihuela-Espina, Felipe

2017-09-01

Functional Near Infrared Spectroscopy (fNIRS) is gaining momentum as a functional neuroimaging modality to investigate the cerebral hemodynamics subsequent to neural metabolism. As other neuroimaging modalities, it is neuroscience's tool to understand brain systems functions at behaviour and cognitive levels. To extract useful knowledge from functional neuroimages it is critical to understand the series of transformations applied during the process of the information retrieval and how they bound the interpretation. This process starts with the irradiation of the head tissues with infrared light to obtain the raw neuroimage and proceeds with computational and statistical analysis revealing hidden associations between pixels intensities and neural activity encoded to end up with the explanation of some particular aspect regarding brain function.To comprehend the overall process involved in fNIRS there is extensive literature addressing each individual step separately. This paper overviews the complete transformation sequence through image formation, reconstruction and analysis to provide an insight of the final functional interpretation.

Dynamic Blowout Risk Analysis Using Loss Functions.

PubMed

Abimbola, Majeed; Khan, Faisal

2018-02-01

Most risk analysis approaches are static; failing to capture evolving conditions. Blowout, the most feared accident during a drilling operation, is a complex and dynamic event. The traditional risk analysis methods are useful in the early design stage of drilling operation while falling short during evolving operational decision making. A new dynamic risk analysis approach is presented to capture evolving situations through dynamic probability and consequence models. The dynamic consequence models, the focus of this study, are developed in terms of loss functions. These models are subsequently integrated with the probability to estimate operational risk, providing a real-time risk analysis. The real-time evolving situation is considered dependent on the changing bottom-hole pressure as drilling progresses. The application of the methodology and models are demonstrated with a case study of an offshore drilling operation evolving to a blowout. © 2017 Society for Risk Analysis.

Analysis of functional redundancies within the Arabidopsis TCP transcription factor family.

PubMed

Danisman, Selahattin; van Dijk, Aalt D J; Bimbo, Andrea; van der Wal, Froukje; Hennig, Lars; de Folter, Stefan; Angenent, Gerco C; Immink, Richard G H

2013-12-01

Analyses of the functions of TEOSINTE-LIKE1, CYCLOIDEA, and PROLIFERATING CELL FACTOR1 (TCP) transcription factors have been hampered by functional redundancy between its individual members. In general, putative functionally redundant genes are predicted based on sequence similarity and confirmed by genetic analysis. In the TCP family, however, identification is impeded by relatively low overall sequence similarity. In a search for functionally redundant TCP pairs that control Arabidopsis leaf development, this work performed an integrative bioinformatics analysis, combining protein sequence similarities, gene expression data, and results of pair-wise protein-protein interaction studies for the 24 members of the Arabidopsis TCP transcription factor family. For this, the work completed any lacking gene expression and protein-protein interaction data experimentally and then performed a comprehensive prediction of potential functional redundant TCP pairs. Subsequently, redundant functions could be confirmed for selected predicted TCP pairs by genetic and molecular analyses. It is demonstrated that the previously uncharacterized class I TCP19 gene plays a role in the control of leaf senescence in a redundant fashion with TCP20. Altogether, this work shows the power of combining classical genetic and molecular approaches with bioinformatics predictions to unravel functional redundancies in the TCP transcription factor family.

Analysis of functional redundancies within the Arabidopsis TCP transcription factor family

PubMed Central

Danisman, Selahattin; de Folter, Stefan; Immink, Richard G. H.

2013-01-01

Analyses of the functions of TEOSINTE-LIKE1, CYCLOIDEA, and PROLIFERATING CELL FACTOR1 (TCP) transcription factors have been hampered by functional redundancy between its individual members. In general, putative functionally redundant genes are predicted based on sequence similarity and confirmed by genetic analysis. In the TCP family, however, identification is impeded by relatively low overall sequence similarity. In a search for functionally redundant TCP pairs that control Arabidopsis leaf development, this work performed an integrative bioinformatics analysis, combining protein sequence similarities, gene expression data, and results of pair-wise protein–protein interaction studies for the 24 members of the Arabidopsis TCP transcription factor family. For this, the work completed any lacking gene expression and protein–protein interaction data experimentally and then performed a comprehensive prediction of potential functional redundant TCP pairs. Subsequently, redundant functions could be confirmed for selected predicted TCP pairs by genetic and molecular analyses. It is demonstrated that the previously uncharacterized class I TCP19 gene plays a role in the control of leaf senescence in a redundant fashion with TCP20. Altogether, this work shows the power of combining classical genetic and molecular approaches with bioinformatics predictions to unravel functional redundancies in the TCP transcription factor family. PMID:24129704

Statistics, Uncertainty, and Transmitted Variation

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

Wendelberger, Joanne Roth

2014-11-05

The field of Statistics provides methods for modeling and understanding data and making decisions in the presence of uncertainty. When examining response functions, variation present in the input variables will be transmitted via the response function to the output variables. This phenomenon can potentially have significant impacts on the uncertainty associated with results from subsequent analysis. This presentation will examine the concept of transmitted variation, its impact on designed experiments, and a method for identifying and estimating sources of transmitted variation in certain settings.

Automatic microscopy for mitotic cell location.

NASA Technical Reports Server (NTRS)

Herron, J.; Ranshaw, R.; Castle, J.; Wald, N.

1972-01-01

Advances are reported in the development of an automatic microscope with which to locate hematologic or other cells in mitosis for subsequent chromosome analysis. The system under development is designed to perform the functions of: slide scanning to locate metaphase cells; conversion of images of selected cells into binary form; and on-line computer analysis of the digitized image for significant cytogenetic data. Cell detection criteria are evaluated using a test sample of 100 mitotic cells and 100 artifacts.

Imposture, inauthenticity, and feeling fraudulent.

PubMed

Gediman, H K

1985-01-01

This paper deals with imposturous tendencies as ubiquitous and heterogeneous. They may enter into neurotic conflict and compromise, and also reflect an ego function disturbance involving multiple, shifting identities and subsequent problems in the subjective sense of reality of the self and objects. Imposture in a person undergoing analysis is, however, not only a function of individual character and psychopathology; it is also a function of certain inevitable requirements of the analytic situation which constitute a "pull" for its emergence. Vulnerable individuals will respond to this pull in revealing ways. Three case summaries illustrate the spectrum of imposturous tendencies.

Working memory overload: fronto-limbic interactions and effects on subsequent working memory function.

PubMed

Yun, Richard J; Krystal, John H; Mathalon, Daniel H

2010-03-01

The human working memory system provides an experimentally useful model for examination of neural overload effects on subsequent functioning of the overloaded system. This study employed functional magnetic resonance imaging in conjunction with a parametric working memory task to characterize the behavioral and neural effects of cognitive overload on subsequent cognitive performance, with particular attention to cognitive-limbic interactions. Overloading the working memory system was associated with varying degrees of subsequent decline in performance accuracy and reduced activation of brain regions central to both task performance and suppression of negative affect. The degree of performance decline was independently predicted by three separate factors operating during the overload condition: the degree of task failure, the degree of amygdala activation, and the degree of inverse coupling between the amygdala and dorsolateral prefrontal cortex. These findings suggest that vulnerability to overload effects in cognitive functioning may be mediated by reduced amygdala suppression and subsequent amygdala-prefrontal interaction.

Predictors of post-hospitalization recovery of renal function among patients with acute kidney injury requiring dialysis.

PubMed

Pajewski, Russell; Gipson, Patrick; Heung, Michael

2018-01-01

Acute kidney injury (AKI) requiring dialysis complicates 1% of all hospital admissions, and up to 30% of survivors will still require dialysis at hospital discharge. There is a paucity of data to describe the postdischarge outcomes or to guide evidence-based dialysis management of this vulnerable population. Single-center, retrospective analysis of 100 consecutive patients with AKI who survived to hospital discharge and required outpatient dialysis. Data collection included baseline characteristics, hospitalization characteristics, and outpatient dialysis treatment variables. Primary outcome was dialysis independence 90 days after discharge. Overall, 43% of patients recovered adequate renal function to discontinue dialysis, with the majority recovering within 30 days post discharge. Worse baseline renal function was associated with lower likelihood of renal recovery. In the first week postdischarge, patients with subsequent nonrecovery of renal function had greater net fluid removal (5.3 vs. 4.1 L, P = 0.037), higher ultrafiltration rates (6.0 vs. 4.7 mL/kg/h, P = 0.041) and more frequent intradialytic hypotension (24.6% vs. 9.3% with 3 or more episodes, P = 0.049) compared to patients that later recovered. A significant proportion of AKI survivors will recover renal function following discharge. Outpatient intradialytic factors may influence subsequent renal function recovery. © 2017 International Society for Hemodialysis.

Feasibility Analysis of Incorporating In-Vitro Toxicokinetic Data as a Surrogate for In-Vivo Data for Read-across Predictions (ASCCT meeting)

EPA Science Inventory

The underlying principle of read-across is that biological activity is a function of physical and structural properties of chemicals. Analogs are typically identified on the basis of structural similarity and subsequently evaluated for their use in read-across on the basis of the...

Molecular evolution of an Avirulence Homolog (Avh) gene subfamily in Phytophthora ramorum

Treesearch

GossErica M.; Caroline M. Press; Niklaus J. Grünwald

2008-01-01

Pathogen effectors can serve a virulence function on behalf of the pathogen or trigger a rapid defense response in resistant hosts. Sequencing of the Phytophthora ramorum genome and subsequent analysis identified a diverse superfamily of approximately 350 genes that are homologous to the four known avirulence genes in plant pathogenic oomycetes and...

Use of a latency-based demand assessment to identify potential demands for functional analyses.

PubMed

Call, Nathan A; Miller, Sarah J; Mintz, Joslyn Cynkus; Mevers, Joanna Lomas; Scheithauer, Mindy C; Eshelman, Julie E; Beavers, Gracie A

2016-12-01

Unlike potential tangible positive reinforcers, which are typically identified for inclusion in functional analyses empirically using preference assessments, demands are most often selected arbitrarily or based on caregiver report. The present study evaluated the use of a demand assessment with 12 participants who exhibited escape-maintained problem behavior. Participants were exposed to 10 demands, with aversiveness measured by average latency to the first instance of problem behavior. In subsequent functional analyses, results of a demand condition that included the demand with the shortest latency to problem behavior resulted in identification of an escape function for 11 of the participants. In contrast, a demand condition that included the demand with the longest latency resulted in identification of an escape function for only 5 participants. The implication of these findings is that for the remaining 7 participants, selection of the demand for the functional analysis without using the results of the demand assessment could have produced a false-negative finding. © 2016 Society for the Experimental Analysis of Behavior.

Grey Matter Alterations Co-Localize with Functional Abnormalities in Developmental Dyslexia: An ALE Meta-Analysis

PubMed Central

Linkersdörfer, Janosch; Lonnemann, Jan; Lindberg, Sven; Hasselhorn, Marcus; Fiebach, Christian J.

2012-01-01

The neural correlates of developmental dyslexia have been investigated intensively over the last two decades and reliable evidence for a dysfunction of left-hemispheric reading systems in dyslexic readers has been found in functional neuroimaging studies. In addition, structural imaging studies using voxel-based morphometry (VBM) demonstrated grey matter reductions in dyslexics in several brain regions. To objectively assess the consistency of these findings, we performed activation likelihood estimation (ALE) meta-analysis on nine published VBM studies reporting 62 foci of grey matter reduction in dyslexic readers. We found six significant clusters of convergence in bilateral temporo-parietal and left occipito-temporal cortical regions and in the cerebellum bilaterally. To identify possible overlaps between structural and functional deviations in dyslexic readers, we conducted additional ALE meta-analyses of imaging studies reporting functional underactivations (125 foci from 24 studies) or overactivations (95 foci from 11 studies ) in dyslexics. Subsequent conjunction analyses revealed overlaps between the results of the VBM meta-analysis and the meta-analysis of functional underactivations in the fusiform and supramarginal gyri of the left hemisphere. An overlap between VBM results and the meta-analysis of functional overactivations was found in the left cerebellum. The results of our study provide evidence for consistent grey matter variations bilaterally in the dyslexic brain and substantial overlap of these structural variations with functional abnormalities in left hemispheric regions. PMID:22916214

Cognitively Stimulating Leisure Activity and Subsequent Cognitive Function: A SHARE-based Analysis.

PubMed

Litwin, Howard; Schwartz, Ella; Damri, Noam

2017-10-01

The aim of the inquiry was to examine whether cognitively stimulating leisure activity (CSLA) can delay or reduce cognitive decline in late life and whether its effect is moderated by education, age, or activity pattern. Employing secondary analysis of data on respondents aged 65 and older from the 4th and 5th waves of the Survey of Health, Ageing and Retirement in Europe (N = 16,572), the inquiry regressed cognitive function (memory, numeracy, and fluency) at Time 2 on frequency of engagement in CSLA at baseline, controlling for cognitive function scores at baseline and a range of confounders. The study also considered education by CSLA and age by CSLA interactions, as well as the effect of CSLA patterns. CSLA frequency was found to be positively related to subsequent cognitive functioning on all measures, 2 years later. The effect of CSLA on memory and fluency was stronger among those with lower education, whereas the age by CSLA interaction was not significant. Respondents who started CSLA after baseline showed better cognitive functioning at Time 2 than those who did not engage in CSLA at all and those who had engaged in such activity at baseline but stopped. The study documents that CSLAs constitute a potential source for the delay or reduction of cognitive decline, regardless of one's age. As such, practitioners should recognize the value of this medium and encourage its greater use in appropriate settings. © The Author 2016. Published by Oxford University Press on behalf of The Gerontological Society of America. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Expediting Combinatorial Data Set Analysis by Combining Human and Algorithmic Analysis.

PubMed

Stein, Helge Sören; Jiao, Sally; Ludwig, Alfred

2017-01-09

A challenge in combinatorial materials science remains the efficient analysis of X-ray diffraction (XRD) data and its correlation to functional properties. Rapid identification of phase-regions and proper assignment of corresponding crystal structures is necessary to keep pace with the improved methods for synthesizing and characterizing materials libraries. Therefore, a new modular software called htAx (high-throughput analysis of X-ray and functional properties data) is presented that couples human intelligence tasks used for "ground-truth" phase-region identification with subsequent unbiased verification by an algorithm to efficiently analyze which phases are present in a materials library. Identified phases and phase-regions may then be correlated to functional properties in an expedited manner. For the functionality of htAx to be proven, two previously published XRD benchmark data sets of the materials systems Al-Cr-Fe-O and Ni-Ti-Cu are analyzed by htAx. The analysis of ∼1000 XRD patterns takes less than 1 day with htAx. The proposed method reliably identifies phase-region boundaries and robustly identifies multiphase structures. The method also addresses the problem of identifying regions with previously unpublished crystal structures using a special daisy ternary plot.

Serum Micronutrient Concentrations and Decline in Physical Function Among Older Persons

PubMed Central

Bartali, Benedetta; Frongillo, Edward A.; Guralnik, Jack M.; Stipanuk, Martha H.; Allore, Heather G.; Cherubini, Antonio; Bandinelli, Stefania; Ferrucci, Luigi; Gill, Thomas M.

2009-01-01

Context Maintaining independence of older persons is a public health priority, and identifying the factors that contribute to decline in physical function is needed to prevent or postpone the disablement process. The potential deleterious effect of poor nutrition on decline in physical function in older persons is unclear. Objective To determine whether a low serum concentration of micronutrients is associated with subsequent decline in physical function among older men and women living in the community. Design, Setting, and Participants Longitudinal study of 698 community-living persons 65 years or older who were randomly selected from a population registry in Tuscany, Italy. Participants completed the baseline examination from November 1, 1998, through May 28, 2000, and the 3-year follow-up assessments from November 1, 2001, through March 30, 2003. Main Outcome Measure Decline in physical function was defined as a loss of at least 1 point in the Short Physical Performance Battery during the 3-year follow-up. Odds ratios (ORs) were calculated for the lowest quartile of each nutrient using the other 3 quartiles combined as the reference group. Two additional and complementary analytical approaches were used to confirm the validity of the results. Results The mean decline in the Short Physical Performance Battery score was 1.1 point. In a logistic regression analysis that was adjusted for potential confounders, only a low concentration of vitamin E (<1.1 μg/mL [<24.9 μmol/L]) was significantly associated with subsequent decline in physical function (OR, 1.62; 95% confidence interval, 1.11-2.36; P=.01 for association of lowest α-tocopherol quartile with at least a 1-point decline in physical function). In a general linear model, the concentration of vitamin E at baseline, when analyzed as a continuous measure, was significantly associated with the Short Physical Performance Battery score at follow-up after adjustment for potential confounders and Short Physical Performance Battery score at baseline (β=.023; P=.01). In a classification and regression tree analysis, age older than 81 years and vitamin E (in participants aged 70-80 years) were identified as the strongest determinants of decline in physical function (physical decline in 84% and 60%, respectively; misclassification error rate, 0.33). Conclusions These results provide empirical evidence that a low serum concentration of vitamin E is associated with subsequent decline in physical function among community-living older adults. Clinical trials may be warranted to determine whether an optimal concentration of vitamin E reduces functional decline and the onset of disability in older persons. PMID:18212315

TUBEs-Mass Spectrometry for Identification and Analysis of the Ubiquitin-Proteome.

PubMed

Azkargorta, Mikel; Escobes, Iraide; Elortza, Felix; Matthiesen, Rune; Rodríguez, Manuel S

2016-01-01

Mass spectrometry (MS) has become the method of choice for the large-scale analysis of protein ubiquitylation. There exist a number of proposed methods for mapping ubiquitin sites, each with different pros and cons. We present here a protocol for the MS analysis of the ubiquitin-proteome captured by TUBEs and subsequent data analysis. Using dedicated software and algorithms, specific information on the presence of ubiquitylated peptides can be obtained from the MS search results. In addition, a quantitative and functional analysis of the ubiquitylated proteins and their interacting partners helps to unravel the biological and molecular processes they are involved in.

On the Regularities of the Polar Profiles of Proteins Related to Ebola Virus Infection and their Functional Domains.

PubMed

Polanco, Carlos; Samaniego Mendoza, José Lino; Buhse, Thomas; Uversky, Vladimir N; Bañuelos Chao, Ingrid Paola; Bañuelos Cedano, Marcela Angola; Tavera, Fernando Michel; Tavera, Daniel Michel; Falconi, Manuel; Ponce de León, Abelardo Vela

2018-03-06

The number of fatalities and economic losses caused by the Ebola virus infection across the planet culminated in the havoc that occurred between August and November 2014. However, little is known about the molecular protein profile of this devastating virus. This work represents a thorough bioinformatics analysis of the regularities of charge distribution (polar profiles) in two groups of proteins and their functional domains associated with Ebola virus disease: Ebola virus proteins and Human proteins interacting with Ebola virus. Our analysis reveals that a fragment exists in each of these proteins-one named the "functional domain"-with the polar profile similar to the polar profile of the protein that contains it. Each protein is formed by a group of short sub-sequences, where each fragment has a different and distinctive polar profile and where the polar profile between adjacent short sub-sequences changes orderly and gradually to coincide with the polar profile of the whole protein. When using the charge distribution as a metric, it was observed that it effectively discriminates the proteins from their functional domains. As a counterexample, the same test was applied to a set of synthetic proteins built for that purpose, revealing that any of the regularities reported here for the Ebola virus proteins and human proteins interacting with Ebola virus were not present in the synthetic proteins. Our results indicate that the polar profile of each protein studied and its corresponding functional domain are similar. Thus, when building each protein from its functional domai-adding one amino acid at a time and plotting each time its polar profile-it was observed that the resulting graphs can be divided into groups with similar polar profiles.

Assessment of protein set coherence using functional annotations

PubMed Central

Chagoyen, Monica; Carazo, Jose M; Pascual-Montano, Alberto

2008-01-01

Background Analysis of large-scale experimental datasets frequently produces one or more sets of proteins that are subsequently mined for functional interpretation and validation. To this end, a number of computational methods have been devised that rely on the analysis of functional annotations. Although current methods provide valuable information (e.g. significantly enriched annotations, pairwise functional similarities), they do not specifically measure the degree of homogeneity of a protein set. Results In this work we present a method that scores the degree of functional homogeneity, or coherence, of a set of proteins on the basis of the global similarity of their functional annotations. The method uses statistical hypothesis testing to assess the significance of the set in the context of the functional space of a reference set. As such, it can be used as a first step in the validation of sets expected to be homogeneous prior to further functional interpretation. Conclusion We evaluate our method by analysing known biologically relevant sets as well as random ones. The known relevant sets comprise macromolecular complexes, cellular components and pathways described for Saccharomyces cerevisiae, which are mostly significantly coherent. Finally, we illustrate the usefulness of our approach for validating 'functional modules' obtained from computational analysis of protein-protein interaction networks. Matlab code and supplementary data are available at PMID:18937846

[Method of recording impulses from an implanted cardiostimulator].

PubMed

Vetkin, A N; Osipov, V P

1976-01-01

An analysis of pulses from an implanted cardiostimulator recorded from the surface of the patient's body is one of the methods permitting it to pass judgment as to its functioning. Because of the possibility of the recording electrodes location coinciding with the equipotential line an erroneous interpretation of the cardiostimulator's condition is not to be ruled out. It is recommended that the pulses should be recorded with their subsequent analysis in no less than 2 standard ECG leads from the limbs.

Aberrant functional connectivity for diagnosis of major depressive disorder: a discriminant analysis.

PubMed

Cao, Longlong; Guo, Shuixia; Xue, Zhimin; Hu, Yong; Liu, Haihong; Mwansisya, Tumbwene E; Pu, Weidan; Yang, Bo; Liu, Chang; Feng, Jianfeng; Chen, Eric Y H; Liu, Zhening

2014-02-01

Aberrant brain functional connectivity patterns have been reported in major depressive disorder (MDD). It is unknown whether they can be used in discriminant analysis for diagnosis of MDD. In the present study we examined the efficiency of discriminant analysis of MDD by individualized computer-assisted diagnosis. Based on resting-state functional magnetic resonance imaging data, a new approach was adopted to investigate functional connectivity changes in 39 MDD patients and 37 well-matched healthy controls. By using the proposed feature selection method, we identified significant altered functional connections in patients. They were subsequently applied to our analysis as discriminant features using a support vector machine classification method. Furthermore, the relative contribution of functional connectivity was estimated. After subset selection of high-dimension features, the support vector machine classifier reached up to approximately 84% with leave-one-out training during the discrimination process. Through summarizing the classification contribution of functional connectivities, we obtained four obvious contribution modules: inferior orbitofrontal module, supramarginal gyrus module, inferior parietal lobule-posterior cingulated gyrus module and middle temporal gyrus-inferior temporal gyrus module. The experimental results demonstrated that the proposed method is effective in discriminating MDD patients from healthy controls. Functional connectivities might be useful as new biomarkers to assist clinicians in computer auxiliary diagnosis of MDD. © 2013 The Authors. Psychiatry and Clinical Neurosciences © 2013 Japanese Society of Psychiatry and Neurology.

Association between the Type of Workplace and Lung Function in Copper Miners

PubMed Central

Gruszczyński, Leszek; Wojakowska, Anna; Ścieszka, Marek; Turczyn, Barbara; Schmidt, Edward

2016-01-01

The aim of the analysis was to retrospectively assess changes in lung function in copper miners depending on the type of workplace. In the groups of 225 operators, 188 welders, and 475 representatives of other jobs, spirometry was performed at the start of employment and subsequently after 10, 20, and 25 years of work. Spirometry Longitudinal Data Analysis software was used to estimate changes in group means for FEV1 and FVC. Multiple linear regression analysis was used to assess an association between workplace and lung function. Lung function assessed on the basis of calculation of longitudinal FEV1 (FVC) decline was similar in all studied groups. However, multiple linear regression model used in cross-sectional analysis revealed an association between workplace and lung function. In the group of welders, FEF75 was lower in comparison to operators and other miners as early as after 10 years of work. Simultaneously, in smoking welders, the FEV1/FVC ratio was lower than in nonsmokers (p < 0,05). The interactions between type of workplace and smoking (p < 0,05) in their effect on FVC, FEV1, PEF, and FEF50 were shown. Among underground working copper miners, the group of smoking welders is especially threatened by impairment of lung ventilatory function. PMID:27274987

Unified functional network and nonlinear time series analysis for complex systems science: The pyunicorn package

NASA Astrophysics Data System (ADS)

Donges, Jonathan F.; Heitzig, Jobst; Beronov, Boyan; Wiedermann, Marc; Runge, Jakob; Feng, Qing Yi; Tupikina, Liubov; Stolbova, Veronika; Donner, Reik V.; Marwan, Norbert; Dijkstra, Henk A.; Kurths, Jürgen

2015-11-01

We introduce the pyunicorn (Pythonic unified complex network and recurrence analysis toolbox) open source software package for applying and combining modern methods of data analysis and modeling from complex network theory and nonlinear time series analysis. pyunicorn is a fully object-oriented and easily parallelizable package written in the language Python. It allows for the construction of functional networks such as climate networks in climatology or functional brain networks in neuroscience representing the structure of statistical interrelationships in large data sets of time series and, subsequently, investigating this structure using advanced methods of complex network theory such as measures and models for spatial networks, networks of interacting networks, node-weighted statistics, or network surrogates. Additionally, pyunicorn provides insights into the nonlinear dynamics of complex systems as recorded in uni- and multivariate time series from a non-traditional perspective by means of recurrence quantification analysis, recurrence networks, visibility graphs, and construction of surrogate time series. The range of possible applications of the library is outlined, drawing on several examples mainly from the field of climatology.

Self-esteem modulates amygdala-ventrolateral prefrontal cortex connectivity in response to mortality threats.

PubMed

Yanagisawa, Kuniaki; Abe, Nobuhito; Kashima, Emiko S; Nomura, Michio

2016-03-01

Reminders of death often elicit defensive responses in individuals, especially among those with low self-esteem. Although empirical evidence indicates that self-esteem serves as a buffer against mortality threats, the precise neural mechanism underlying this effect remains unknown. We used functional magnetic resonance imaging (fMRI) to test the hypothesis that self-esteem modulates neural responses to death-related stimuli, especially functional connectivity within the limbic-frontal circuitry, thereby affecting subsequent defensive reactions. As predicted, individuals with high self-esteem subjected to a mortality threat exhibited increased amygdala-ventrolateral prefrontal cortex (VLPFC) connectivity during the processing of death-related stimuli compared with individuals who have low self-esteem. Further analysis revealed that stronger functional connectivity between the amygdala and the VLPFC predicted a subsequent decline in responding defensively to those who threaten one's beliefs. These results suggest that the amygdala-VLPFC interaction, which is modulated by self-esteem, can reduce the defensiveness caused by death-related stimuli, thereby providing a neural explanation for why individuals with high self-esteem exhibit less defensive reactions to mortality threats. (c) 2016 APA, all rights reserved).

Digital fabrication of multi-material biomedical objects.

PubMed

Cheung, H H; Choi, S H

2009-12-01

This paper describes a multi-material virtual prototyping (MMVP) system for modelling and digital fabrication of discrete and functionally graded multi-material objects for biomedical applications. The MMVP system consists of a DMMVP module, an FGMVP module and a virtual reality (VR) simulation module. The DMMVP module is used to model discrete multi-material (DMM) objects, while the FGMVP module is for functionally graded multi-material (FGM) objects. The VR simulation module integrates these two modules to perform digital fabrication of multi-material objects, which can be subsequently visualized and analysed in a virtual environment to optimize MMLM processes for fabrication of product prototypes. Using the MMVP system, two biomedical objects, including a DMM human spine and an FGM intervertebral disc spacer are modelled and digitally fabricated for visualization and analysis in a VR environment. These studies show that the MMVP system is a practical tool for modelling, visualization, and subsequent fabrication of biomedical objects of discrete and functionally graded multi-materials for biomedical applications. The system may be adapted to control MMLM machines with appropriate hardware for physical fabrication of biomedical objects.

Predictive assessment of kidney functional recovery following ischemic injury using optical spectroscopy

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

Raman, Rajesh N.; Pivetti, Christopher D.; Ramsamooj, Rajendra

Functional changes in rat kidneys during the induced ischemic injury and recovery phases were explored using multimodal autofluorescence and light scattering imaging. We aim to evaluate the use of noncontact optical signatures for rapid assessment of tissue function and viability. Specifically, autofluorescence images were acquired in vivo under 355, 325, and 266 nm illumination while light scattering images were collected at the excitation wavelengths as well as using relatively narrowband light centered at 500 nm. The images were simultaneously recorded using a multimodal optical imaging system. We also analyzed to obtain time constants, which were correlated to kidney dysfunction asmore » determined by a subsequent survival study and histopathological analysis. This analysis of both the light scattering and autofluorescence images suggests that changes in tissue microstructure, fluorophore emission, and blood absorption spectral characteristics, coupled with vascular response, contribute to the behavior of the observed signal, which may be used to obtain tissue functional information and offer the ability to predict posttransplant kidney function.« less

Influence of the fiber from agro-industrial co-products as functional food ingredient on the acceptance, neophobia and sensory characteristics of cooked sausages.

PubMed

Díaz-Vela, Juan; Totosaus, Alfonso; Escalona-Buendía, Héctor B; Pérez-Chabela, M Lourdes

2017-02-01

The sensory analysis of new products is essential for subsequent acceptance by consumers, moreover in the functional food market. The acceptance and food neophobia of cooked sausages formulated with cactus pear fiber or pineapple pear fiber, as functional ingredient, was complemented with a sensory characterization by R-index and qualitative descriptive analysis (QDA). Female consumers aged between 40 and 50 years showed greater interest in the consumption of healthy foods, with a higher level of food neophobia towards pineapple fiber sausages. R-index for taste was higher in pineapple fiber samples. Cactus pear fiber samples presented higher R-index score for texture. In QDA, color, sweet, astringent and bitter flavors, pork meat smell and a firm and plastic texture were significant, with a good relationship (38%) between the evaluated attributes. Sensory attributes are important on the acceptance and neophobia of functional foods like cooked sausages with fruit peel fiber as functional ingredient.

Predictive assessment of kidney functional recovery following ischemic injury using optical spectroscopy

DOE PAGES

Raman, Rajesh N.; Pivetti, Christopher D.; Ramsamooj, Rajendra; ...

2017-05-03

Functional changes in rat kidneys during the induced ischemic injury and recovery phases were explored using multimodal autofluorescence and light scattering imaging. We aim to evaluate the use of noncontact optical signatures for rapid assessment of tissue function and viability. Specifically, autofluorescence images were acquired in vivo under 355, 325, and 266 nm illumination while light scattering images were collected at the excitation wavelengths as well as using relatively narrowband light centered at 500 nm. The images were simultaneously recorded using a multimodal optical imaging system. We also analyzed to obtain time constants, which were correlated to kidney dysfunction asmore » determined by a subsequent survival study and histopathological analysis. This analysis of both the light scattering and autofluorescence images suggests that changes in tissue microstructure, fluorophore emission, and blood absorption spectral characteristics, coupled with vascular response, contribute to the behavior of the observed signal, which may be used to obtain tissue functional information and offer the ability to predict posttransplant kidney function.« less

Advanced functional network analysis in the geosciences: The pyunicorn package

NASA Astrophysics Data System (ADS)

Donges, Jonathan F.; Heitzig, Jobst; Runge, Jakob; Schultz, Hanna C. H.; Wiedermann, Marc; Zech, Alraune; Feldhoff, Jan; Rheinwalt, Aljoscha; Kutza, Hannes; Radebach, Alexander; Marwan, Norbert; Kurths, Jürgen

2013-04-01

Functional networks are a powerful tool for analyzing large geoscientific datasets such as global fields of climate time series originating from observations or model simulations. pyunicorn (pythonic unified complex network and recurrence analysis toolbox) is an open-source, fully object-oriented and easily parallelizable package written in the language Python. It allows for constructing functional networks (aka climate networks) representing the structure of statistical interrelationships in large datasets and, subsequently, investigating this structure using advanced methods of complex network theory such as measures for networks of interacting networks, node-weighted statistics or network surrogates. Additionally, pyunicorn allows to study the complex dynamics of geoscientific systems as recorded by time series by means of recurrence networks and visibility graphs. The range of possible applications of the package is outlined drawing on several examples from climatology.

Technological advances and genomics in metazoan parasites.

PubMed

Knox, D P

2004-02-01

Molecular biology has provided the means to identify parasite proteins, to define their function, patterns of expression and the means to produce them in quantity for subsequent functional analyses. Whole genome and expressed sequence tag programmes, and the parallel development of powerful bioinformatics tools, allow the execution of genome-wide between stage or species comparisons and meaningful gene-expression profiling. The latter can be undertaken with several new technologies such as DNA microarray and serial analysis of gene expression. Proteome analysis has come to the fore in recent years providing a crucial link between the gene and its protein product. RNA interference and ballistic gene transfer are exciting developments which can provide the means to precisely define the function of individual genes and, of importance in devising novel parasite control strategies, the effect that gene knockdown will have on parasite survival.

Time Course of Changes in Maternal Left Ventricular Function during Subsequent Pregnancy in Women with a History of Gestational Hypertensive Disorders.

PubMed

Hieda, Michinari; Yoo, Jeung-Ki; Sun, Dan-Dan; Okada, Yoshiyuki; Parker, Rosemary S; Roberts-Reeves, Monique A; Adams-Huet, Beverley; Nelson, David B; Levine, Benjamin D; Fu, Qi

2018-06-13

Women with a history of gestational hypertensive disorders (GHD) are at increased risk for developing perinatal cardiovascular complications (e.g., gestational hypertension, preeclampsia, etc.) in subsequent pregnancies. The underlying mechanisms remain uncertain, but impaired maternal left ventricular function may be one contributing factor for these complications. We evaluated the time course of changes in left ventricular function before, during and after pregnancy in women with prior GHD. Sixteen women with a history of GHD (the high-risk group), and 25 women without such a history (controls) were enrolled. Resting hemodynamic and echocardiographic measurements were longitudinally performed prior to pregnancy, during early (4-8 weeks of gestation), late pregnancy (32-36 weeks), and postpartum (6-10 weeks after delivery). Pregnancy outcomes were obtained after delivery. At pre-pregnancy, there was no difference in blood pressure and heart rate between the groups. Corrected isovolumetric relaxation time was longer, E/e' was larger, and Tei-index was greater in the high-risk group than controls. Moreover, the rate of GHD during the study was significantly greater in the high-risk group than controls (Odds Ratio: 8.94 [95% CI: 1.55-51.5], P=0.007). Multiple logistic regression analysis adjusted for age demonstrated that pre-pregnancy E/e' was an independent predictor for GHD (P=0.017). Thus, women with a history of GHD have modestly impaired cardiac function pre-pregnancy compared to controls, which identifies an increased susceptibility to developing cardiovascular complications during a subsequent pregnancy.

Analysis of Glycoproteins in Human Serum by Means of Glycospecific Magnetic Bead Separation and LC-MALDI-TOF/TOF Analysis with Automated Glycopeptide Detection

PubMed Central

Sparbier, Katrin; Asperger, Arndt; Resemann, Anja; Kessler, Irina; Koch, Sonja; Wenzel, Thomas; Stein, Günter; Vorwerg, Lars; Suckau, Detlev; Kostrzewa, Markus

2007-01-01

Comprehensive proteomic analyses require efficient and selective pre-fractionation to facilitate analysis of post-translationally modified peptides and proteins, and automated analysis workflows enabling the detection, identification, and structural characterization of the corresponding peptide modifications. Human serum contains a high number of glycoproteins, comprising several orders of magnitude in concentration. Thereby, isolation and subsequent identification of low-abundant glycoproteins from serum is a challenging task. selective capturing of glycopeptides and -proteins was attained by means of magnetic particles specifically functionalized with lectins or boronic acids that bind to various structural motifs. Human serum was incubated with differentially functionalized magnetic micro-particles (lectins or boronic acids), and isolated proteins were digested with trypsin. Subsequently, the resulting complex mixture of peptides and glycopeptides was subjected to LC-MALDI analysis and database searching. In parallel, a second magnetic bead capturing was performed on the peptide level to separate and analyze by LC-MALDI intact glycopeptides, both peptide sequence and glycan structure. Detection of glycopeptides was achieved by means of a software algorithm that allows extraction and characterization of potential glycopeptide candidates from large LC-MALDI-MS/MS data sets, based on N-glycopeptide-specific fragmentation patterns and characteristic fragment mass peaks, respectively. By means of fast and simple glycospecific capturing applied in conjunction with extensive LC-MALDI-MS/MS analysis and novel data analysis tools, a high number of low-abundant proteins were identified, comprising known or predicted glycosylation sites. According to the specific binding preferences of the different types of beads, complementary results were obtained from the experiments using either magnetic ConA-, LCA-, WGA-, and boronic acid beads, respectively. PMID:17916798

Protein functional landscapes, dynamics, allostery: a tortuous path towards a universal theoretical framework.

PubMed

Zhuravlev, Pavel I; Papoian, Garegin A

2010-08-01

Energy landscape theories have provided a common ground for understanding the protein folding problem, which once seemed to be overwhelmingly complicated. At the same time, the native state was found to be an ensemble of interconverting states with frustration playing a more important role compared to the folding problem. The landscape of the folded protein - the native landscape - is glassier than the folding landscape; hence, a general description analogous to the folding theories is difficult to achieve. On the other hand, the native basin phase volume is much smaller, allowing a protein to fully sample its native energy landscape on the biological timescales. Current computational resources may also be used to perform this sampling for smaller proteins, to build a 'topographical map' of the native landscape that can be used for subsequent analysis. Several major approaches to representing this topographical map are highlighted in this review, including the construction of kinetic networks, hierarchical trees and free energy surfaces with subsequent structural and kinetic analyses. In this review, we extensively discuss the important question of choosing proper collective coordinates characterizing functional motions. In many cases, the substates on the native energy landscape, which represent different functional states, can be used to obtain variables that are well suited for building free energy surfaces and analyzing the protein's functional dynamics. Normal mode analysis can provide such variables in cases where functional motions are dictated by the molecule's architecture. Principal component analysis is a more expensive way of inferring the essential variables from the protein's motions, one that requires a long molecular dynamics simulation. Finally, the two popular models for the allosteric switching mechanism, 'preexisting equilibrium' and 'induced fit', are interpreted within the energy landscape paradigm as extreme points of a continuum of transition mechanisms. Some experimental evidence illustrating each of these two models, as well as intermediate mechanisms, is presented and discussed.

Greater neural pattern similarity across repetitions is associated with better memory.

PubMed

Xue, Gui; Dong, Qi; Chen, Chuansheng; Lu, Zhonglin; Mumford, Jeanette A; Poldrack, Russell A

2010-10-01

Repeated study improves memory, but the underlying neural mechanisms of this improvement are not well understood. Using functional magnetic resonance imaging and representational similarity analysis of brain activity, we found that, compared with forgotten items, subsequently remembered faces and words showed greater similarity in neural activation across multiple study in many brain regions, including (but not limited to) the regions whose mean activities were correlated with subsequent memory. This result addresses a longstanding debate in the study of memory by showing that successful episodic memory encoding occurs when the same neural representations are more precisely reactivated across study episodes, rather than when patterns of activation are more variable across time.

The smart cluster method. Adaptive earthquake cluster identification and analysis in strong seismic regions

NASA Astrophysics Data System (ADS)

Schaefer, Andreas M.; Daniell, James E.; Wenzel, Friedemann

2017-07-01

Earthquake clustering is an essential part of almost any statistical analysis of spatial and temporal properties of seismic activity. The nature of earthquake clusters and subsequent declustering of earthquake catalogues plays a crucial role in determining the magnitude-dependent earthquake return period and its respective spatial variation for probabilistic seismic hazard assessment. This study introduces the Smart Cluster Method (SCM), a new methodology to identify earthquake clusters, which uses an adaptive point process for spatio-temporal cluster identification. It utilises the magnitude-dependent spatio-temporal earthquake density to adjust the search properties, subsequently analyses the identified clusters to determine directional variation and adjusts its search space with respect to directional properties. In the case of rapid subsequent ruptures like the 1992 Landers sequence or the 2010-2011 Darfield-Christchurch sequence, a reclassification procedure is applied to disassemble subsequent ruptures using near-field searches, nearest neighbour classification and temporal splitting. The method is capable of identifying and classifying earthquake clusters in space and time. It has been tested and validated using earthquake data from California and New Zealand. A total of more than 1500 clusters have been found in both regions since 1980 with M m i n = 2.0. Utilising the knowledge of cluster classification, the method has been adjusted to provide an earthquake declustering algorithm, which has been compared to existing methods. Its performance is comparable to established methodologies. The analysis of earthquake clustering statistics lead to various new and updated correlation functions, e.g. for ratios between mainshock and strongest aftershock and general aftershock activity metrics.

Disorganized Symptoms Predicted Worse Functioning Outcome in Schizophrenia Patients with Established Illness.

PubMed

Ortiz, Bruno Bertolucci; Gadelha, Ary; Higuchi, Cinthia Hiroko; Noto, Cristiano; Medeiros, Daiane; Pitta, José Cássio do Nascimento; de Araújo Filho, Gerardo Maria; Hallak, Jaime Eduardo Cecílio; Bressan, Rodrigo Affonseca

Most patients with schizophrenia will have subsequent relapses of the disorder, with continuous impairments in functioning. However, evidence is lacking on how symptoms influence functioning at different phases of the disease. This study aims to investigate the relationship between symptom dimensions and functioning at different phases: acute exacerbation, nonremission and remission. Patients with schizophrenia were grouped into acutely ill (n=89), not remitted (n=89), and remitted (n=69). Three exploratory stepwise linear regression analyses were performed for each phase of schizophrenia, in which the five PANSS factors and demographic variables were entered as the independent variables and the total Global Assessment of Functioning Scale (GAF) score was entered as the dependent variable. An additional exploratory stepwise logistic regression analysis was performed to predict subsequent remission at discharge in the inpatient population. The Disorganized factor was the most significant predictor for acutely ill patients (p<0.001), while the Hostility factor was the most significant for not-remitted patients and the Negative factor was the most significant for remitted patients (p=0.001 and p<0.001, respectively). In the logistic regression, the Disorganized factor score presented a significant negative association with remission (p=0.007). Higher disorganization symptoms showed the greatest impact in functioning at acute phase, and prevented patients from achieving remission, suggesting it may be a marker of symptom severity and worse outcome in schizophrenia.

Response surface method in geotechnical/structural analysis, phase 1

NASA Astrophysics Data System (ADS)

Wong, F. S.

1981-02-01

In the response surface approach, an approximating function is fit to a long running computer code based on a limited number of code calculations. The approximating function, called the response surface, is then used to replace the code in subsequent repetitive computations required in a statistical analysis. The procedure of the response surface development and feasibility of the method are shown using a sample problem in slop stability which is based on data from centrifuge experiments of model soil slopes and involves five random soil parameters. It is shown that a response surface can be constructed based on as few as four code calculations and that the response surface is computationally extremely efficient compared to the code calculation. Potential applications of this research include probabilistic analysis of dynamic, complex, nonlinear soil/structure systems such as slope stability, liquefaction, and nuclear reactor safety.

Lack of effectiveness of laser therapy applied to the nerve course and the correspondent medullary roots

PubMed Central

Sousa, Fausto Fernandes de Almeida; Ribeiro, Thaís Lopes; Fazan, Valéria Paula Sassoli; Barbieri, Claudio Henrique

2013-01-01

OBJECTIVE: To investigate the influence of low intensity laser irradiation on the regeneration of the fibular nerve of rats after crush injury. METHODS: Twenty-five rats were used, divided into three groups: 1) intact nerve, no treatment; 2) crushed nerve, no treatment; 3) crush injury, laser irradiation applied on the medullary region corresponding to the roots of the sciatic nerve and subsequently on the course of the damaged nerve. Laser irradiation was carried out for 14 consecutive days. RESULTS: Animals were evaluated by functional gait analysis with the peroneal functional index and by histomorphometric analysis using the total number of myelinated nerve fibers and their density, total number of Schwann cells, total number of blood vessels and the occupied area, minimum diameter of the fiber diameter and G-quotient. CONCLUSION: According to the statistical analysis there was no significant difference among groups and the authors conclude that low intensity laser irradiation has little or no influence on nerve regeneration and functional recovery. Laboratory investigation. PMID:24453650

A basic analysis toolkit for biological sequences

PubMed Central

Giancarlo, Raffaele; Siragusa, Alessandro; Siragusa, Enrico; Utro, Filippo

2007-01-01

This paper presents a software library, nicknamed BATS, for some basic sequence analysis tasks. Namely, local alignments, via approximate string matching, and global alignments, via longest common subsequence and alignments with affine and concave gap cost functions. Moreover, it also supports filtering operations to select strings from a set and establish their statistical significance, via z-score computation. None of the algorithms is new, but although they are generally regarded as fundamental for sequence analysis, they have not been implemented in a single and consistent software package, as we do here. Therefore, our main contribution is to fill this gap between algorithmic theory and practice by providing an extensible and easy to use software library that includes algorithms for the mentioned string matching and alignment problems. The library consists of C/C++ library functions as well as Perl library functions. It can be interfaced with Bioperl and can also be used as a stand-alone system with a GUI. The software is available at under the GNU GPL. PMID:17877802

Second Generation International Space Station (ISS) Total Organic Carbon Analyzer (TOCA) Verification Testing and On-Orbit Performance Results

NASA Technical Reports Server (NTRS)

Bentley, Nicole L.; Thomas, Evan A.; VanWie, Michael; Morrison, Chad; Stinson, Richard G.

2010-01-01

The Total Organic Carbon Analyzer (TOGA) is designed to autonomously determine recovered water quality as a function of TOC. The current TOGA has been on the International Space Station since November 2008. Functional checkout and operations revealed complex operating considerations. Specifically, failure of the hydrogen catalyst resulted in the development of an innovative oxidation analysis method. This method reduces the activation time and limits the hydrogen produced during analysis, while retaining the ability to indicate TOC concentrations within 25% accuracy. Subsequent testing and comparison to archived samples returned from the Station and tested on the ground yield high confidence in this method, and in the quality of the recovered water.

Urinary type IV collagen excretion predicts subsequent declining renal function in type 2 diabetic patients with proteinuria.

PubMed

Katavetin, Pisut; Katavetin, Paravee; Susantitaphong, Paweena; Townamchai, Natavudh; Tiranathanagul, Khajohn; Tungsanga, Kriang; Eiam-Ong, Somchai

2010-08-01

Baseline urinary type IV collagen excretion was negatively correlated with the subsequent GFR change (r(s)=-0.39, p=0.04) in our cohort of 30 type 2 diabetic patients with proteinuria. Therefore, it could be used to predict subsequent declining renal function in type 2 diabetic patients with proteinuria. Copyright 2010 Elsevier Ireland Ltd. All rights reserved.

Generalized Least Squares Estimators in the Analysis of Covariance Structures.

ERIC Educational Resources Information Center

Browne, Michael W.

This paper concerns situations in which a p x p covariance matrix is a function of an unknown q x 1 parameter vector y-sub-o. Notation is defined in the second section, and some algebraic results used in subsequent sections are given. Section 3 deals with asymptotic properties of generalized least squares (G.L.S.) estimators of y-sub-o. Section 4…

Factors Associated with Postpartum Maternal Functioning in Women with Positive Screens for Depression.

PubMed

Barkin, Jennifer L; Wisner, Katherine L; Bromberger, Joyce T; Beach, Scott R; Wisniewski, Stephen R

2016-07-01

Functional assessment may represent a valuable addition to postpartum depression screening, providing a more thorough characterization of the mother's health and quality of life. To the authors' knowledge, this analysis represents the first examination of postpartum maternal functioning, as measured by a patient-centered validated tool aimed at ascertainment of functional status explicitly, and its clinical and sociodemographic correlates. A total of 189 women recruited from a large, urban women's hospital in the northeastern United States who both (1) screened positive for depression between 4 and 6 weeks postpartum and (2) completed a subsequent home (baseline) visit between October 1, 2008, and September 4, 2009, were included in this analysis. Multiple linear regression was conducted to ascertain which clinical and sociodemographic variables were independently associated with maternal functioning. The multivariate analysis revealed independent associations between bipolar status, atypical depression, depression score (17-item Hamilton Rating Scale for Depression), and insurance type with postpartum maternal functioning. The beta coefficient for bipolar status indicates that on average we would expect those with bipolar disorder to have maternal functioning scores that are 5.6 points less than those without bipolar disorder. Healthcare providers treating postpartum women with complicating mental health conditions should be cognizant of the potential ramifications on maternal functioning. Impaired functioning in the maternal role is likely to impact child development, although the precise nature of this relationship is yet to be elucidated.

Circular RNAs: analysis, expression and potential functions

PubMed Central

Salzman, Julia

2016-01-01

Just a few years ago, it had been assumed that the dominant RNA isoforms produced from eukaryotic genes were variants of messenger RNA, functioning as intermediates in gene expression. In early 2012, however, a surprising discovery was made: circular RNA (circRNA) was shown to be a transcriptional product in thousands of human and mouse genes and in hundreds of cases constituted the dominant RNA isoform. Subsequent studies revealed that the expression of circRNAs is developmentally regulated, tissue and cell-type specific, and shared across the eukaryotic tree of life. These features suggest important functions for these molecules. Here, we describe major advances in the field of circRNA biology, focusing on the regulation of and functional roles played by these molecules. PMID:27246710

The increase in medial prefrontal glutamate/glutamine concentration during memory encoding is associated with better memory performance and stronger functional connectivity in the human medial prefrontal–thalamus–hippocampus network

PubMed Central

Hong, Donghyun; Rohani Rankouhi, Seyedmorteza; Wiltfang, Jens; Fernández, Guillén; Norris, David G.; Tendolkar, Indira

2018-01-01

Abstract The classical model of the declarative memory system describes the hippocampus and its interactions with representational brain areas in posterior neocortex as being essential for the formation of long‐term episodic memories. However, new evidence suggests an extension of this classical model by assigning the medial prefrontal cortex (mPFC) a specific, yet not fully defined role in episodic memory. In this study, we utilized 1H magnetic resonance spectroscopy (MRS) and psychophysiological interaction (PPI) analysis to lend further support for the idea of a mnemonic role of the mPFC in humans. By using MRS, we measured mPFC γ‐aminobutyric acid (GABA) and glutamate/glutamine (GLx) concentrations before and after volunteers memorized face–name association. We demonstrate that mPFC GLx but not GABA levels increased during the memory task, which appeared to be related to memory performance. Regarding functional connectivity, we used the subsequent memory paradigm and found that the GLx increase was associated with stronger mPFC connectivity to thalamus and hippocampus for associations subsequently recognized with high confidence as opposed to subsequently recognized with low confidence/forgotten. Taken together, we provide new evidence for an mPFC involvement in episodic memory by showing a memory‐related increase in mPFC excitatory neurotransmitter levels that was associated with better memory and stronger memory‐related functional connectivity in a medial prefrontal–thalamus–hippocampus network. PMID:29488277

Quantitative proteomics and systems analysis of cultured H9C2 cardiomyoblasts during differentiation over time supports a 'function follows form' model of differentiation.

PubMed

Kankeu, Cynthia; Clarke, Kylie; Van Haver, Delphi; Gevaert, Kris; Impens, Francis; Dittrich, Anna; Roderick, H Llewelyn; Passante, Egle; Huber, Heinrich J

2018-05-17

The rat cardiomyoblast cell line H9C2 has emerged as a valuable tool for studying cardiac development, mechanisms of disease and toxicology. We present here a rigorous proteomic analysis that monitored the changes in protein expression during differentiation of H9C2 cells into cardiomyocyte-like cells over time. Quantitative mass spectrometry followed by gene ontology (GO) enrichment analysis revealed that early changes in H9C2 differentiation are related to protein pathways of cardiac muscle morphogenesis and sphingolipid synthesis. These changes in the proteome were followed later in the differentiation time-course by alterations in the expression of proteins involved in cation transport and beta-oxidation. Studying the temporal profile of the H9C2 proteome during differentiation in further detail revealed eight clusters of co-regulated proteins that can be associated with early, late, continuous and transient up- and downregulation. Subsequent reactome pathway analysis based on these eight clusters further corroborated and detailed the results of the GO analysis. Specifically, this analysis confirmed that proteins related to pathways in muscle contraction are upregulated early and transiently, and proteins relevant to extracellular matrix organization are downregulated early. In contrast, upregulation of proteins related to cardiac metabolism occurs at later time points. Finally, independent validation of the proteomics results by immunoblotting confirmed hereto unknown regulators of cardiac structure and ionic metabolism. Our results are consistent with a 'function follows form' model of differentiation, whereby early and transient alterations of structural proteins enable subsequent changes that are relevant to the characteristic physiology of cardiomyocytes.

Statistical significance of task related deep brain EEG dynamic changes in the time-frequency domain.

PubMed

Chládek, J; Brázdil, M; Halámek, J; Plešinger, F; Jurák, P

2013-01-01

We present an off-line analysis procedure for exploring brain activity recorded from intra-cerebral electroencephalographic data (SEEG). The objective is to determine the statistical differences between different types of stimulations in the time-frequency domain. The procedure is based on computing relative signal power change and subsequent statistical analysis. An example of characteristic statistically significant event-related de/synchronization (ERD/ERS) detected across different frequency bands following different oddball stimuli is presented. The method is used for off-line functional classification of different brain areas.

Correlation analysis of targeted proteins and metabolites to assess and engineer microbial isopentenol production.

PubMed

George, Kevin W; Chen, Amy; Jain, Aakriti; Batth, Tanveer S; Baidoo, Edward E K; Wang, George; Adams, Paul D; Petzold, Christopher J; Keasling, Jay D; Lee, Taek Soon

2014-08-01

The ability to rapidly assess and optimize heterologous pathway function is critical for effective metabolic engineering. Here, we develop a systematic approach to pathway analysis based on correlations between targeted proteins and metabolites and apply it to the microbial production of isopentenol, a promising biofuel. Starting with a seven-gene pathway, we performed a correlation analysis to reduce pathway complexity and identified two pathway proteins as the primary determinants of efficient isopentenol production. Aided by the targeted quantification of relevant pathway intermediates, we constructed and subsequently validated a conceptual model of isopentenol pathway function. Informed by our analysis, we assembled a strain which produced isopentenol at a titer 1.5 g/L, or 46% of theoretical yield. Our engineering approach allowed us to accurately identify bottlenecks and determine appropriate pathway balance. Paired with high-throughput cloning techniques and analytics, this strategy should prove useful for the analysis and optimization of increasingly complex heterologous pathways. © 2014 Wiley Periodicals, Inc.

ISRNA: an integrative online toolkit for short reads from high-throughput sequencing data.

PubMed

Luo, Guan-Zheng; Yang, Wei; Ma, Ying-Ke; Wang, Xiu-Jie

2014-02-01

Integrative Short Reads NAvigator (ISRNA) is an online toolkit for analyzing high-throughput small RNA sequencing data. Besides the high-speed genome mapping function, ISRNA provides statistics for genomic location, length distribution and nucleotide composition bias analysis of sequence reads. Number of reads mapped to known microRNAs and other classes of short non-coding RNAs, coverage of short reads on genes, expression abundance of sequence reads as well as some other analysis functions are also supported. The versatile search functions enable users to select sequence reads according to their sub-sequences, expression abundance, genomic location, relationship to genes, etc. A specialized genome browser is integrated to visualize the genomic distribution of short reads. ISRNA also supports management and comparison among multiple datasets. ISRNA is implemented in Java/C++/Perl/MySQL and can be freely accessed at http://omicslab.genetics.ac.cn/ISRNA/.

Cognitive Impairment Precedes and Predicts Functional Impairment in Mild Alzheimer's Disease.

PubMed

Liu-Seifert, Hong; Siemers, Eric; Price, Karen; Han, Baoguang; Selzler, Katherine J; Henley, David; Sundell, Karen; Aisen, Paul; Cummings, Jeffrey; Raskin, Joel; Mohs, Richard

2015-01-01

The temporal relationship of cognitive deficit and functional impairment in Alzheimer's disease (AD) is not well characterized. Recent analyses suggest cognitive decline predicts subsequent functional decline throughout AD progression. To better understand the relationship between cognitive and functional decline in mild AD using autoregressive cross-lagged (ARCL) panel analyses in several clinical trials. Data included placebo patients with mild AD pooled from two multicenter, double-blind, Phase 3 solanezumab (EXPEDITION/2) or semagacestat (IDENTITY/2) studies, and from AD patients participating in the Alzheimer's Disease Neuroimaging Initiative (ADNI). Cognitive and functional outcomes were assessed using AD Assessment Scale-Cognitive subscale (ADAS-Cog), AD Cooperative Study-Activities of Daily Living instrumental subscale (ADCS-iADL), or Functional Activities Questionnaire (FAQ), respectively. ARCL panel analyses evaluated relationships between cognitive and functional impairment over time. In EXPEDITION, ARCL panel analyses demonstrated cognitive scores significantly predicted future functional impairment at 5 of 6 time points, while functional scores predicted subsequent cognitive scores in only 1 of 6 time points. Data from IDENTITY and ADNI programs yielded consistent results whereby cognition predicted subsequent function, but not vice-versa. Analyses from three databases indicated cognitive decline precedes and predicts subsequent functional decline in mild AD dementia, consistent with previously proposed hypotheses, and corroborate recent publications using similar methodologies. Cognitive impairment may be used as a predictor of future functional impairment in mild AD dementia and can be considered a critical target for prevention strategies to limit future functional decline in the dementia process.

Large-scale network integration in the human brain tracks temporal fluctuations in memory encoding performance.

PubMed

Keerativittayayut, Ruedeerat; Aoki, Ryuta; Sarabi, Mitra Taghizadeh; Jimura, Koji; Nakahara, Kiyoshi

2018-06-18

Although activation/deactivation of specific brain regions have been shown to be predictive of successful memory encoding, the relationship between time-varying large-scale brain networks and fluctuations of memory encoding performance remains unclear. Here we investigated time-varying functional connectivity patterns across the human brain in periods of 30-40 s, which have recently been implicated in various cognitive functions. During functional magnetic resonance imaging, participants performed a memory encoding task, and their performance was assessed with a subsequent surprise memory test. A graph analysis of functional connectivity patterns revealed that increased integration of the subcortical, default-mode, salience, and visual subnetworks with other subnetworks is a hallmark of successful memory encoding. Moreover, multivariate analysis using the graph metrics of integration reliably classified the brain network states into the period of high (vs. low) memory encoding performance. Our findings suggest that a diverse set of brain systems dynamically interact to support successful memory encoding. © 2018, Keerativittayayut et al.

Detection of Functional Change Using Cluster Trend Analysis in Glaucoma.

PubMed

Gardiner, Stuart K; Mansberger, Steven L; Demirel, Shaban

2017-05-01

Global analyses using mean deviation (MD) assess visual field progression, but can miss localized changes. Pointwise analyses are more sensitive to localized progression, but more variable so require confirmation. This study assessed whether cluster trend analysis, averaging information across subsets of locations, could improve progression detection. A total of 133 test-retest eyes were tested 7 to 10 times. Rates of change and P values were calculated for possible re-orderings of these series to generate global analysis ("MD worsening faster than x dB/y with P < y"), pointwise and cluster analyses ("n locations [or clusters] worsening faster than x dB/y with P < y") with specificity exactly 95%. These criteria were applied to 505 eyes tested over a mean of 10.5 years, to find how soon each detected "deterioration," and compared using survival models. This was repeated including two subsequent visual fields to determine whether "deterioration" was confirmed. The best global criterion detected deterioration in 25% of eyes in 5.0 years (95% confidence interval [CI], 4.7-5.3 years), compared with 4.8 years (95% CI, 4.2-5.1) for the best cluster analysis criterion, and 4.1 years (95% CI, 4.0-4.5) for the best pointwise criterion. However, for pointwise analysis, only 38% of these changes were confirmed, compared with 61% for clusters and 76% for MD. The time until 25% of eyes showed subsequently confirmed deterioration was 6.3 years (95% CI, 6.0-7.2) for global, 6.3 years (95% CI, 6.0-7.0) for pointwise, and 6.0 years (95% CI, 5.3-6.6) for cluster analyses. Although the specificity is still suboptimal, cluster trend analysis detects subsequently confirmed deterioration sooner than either global or pointwise analyses.

Impact of transient emotions on functional connectivity during subsequent resting state: a wavelet correlation approach.

PubMed

Eryilmaz, Hamdi; Van De Ville, Dimitri; Schwartz, Sophie; Vuilleumier, Patrik

2011-02-01

The functional properties of resting brain activity are poorly understood, but have generally been related to self-monitoring and introspective processes. Here we investigated how emotionally positive and negative information differentially influenced subsequent brain activity at rest. We acquired fMRI data in 15 participants during rest periods following fearful, joyful, and neutral movies. Several brain regions were more active during resting than during movie-watching, including posterior/anterior cingulate cortices (PCC, ACC), bilateral insula and inferior parietal lobules (IPL). Functional connectivity at different frequency bands was also assessed using a wavelet correlation approach and small-world network analysis. Resting activity in ACC and insula as well as their coupling were strongly enhanced by preceding emotions, while coupling between ventral-medial prefrontal cortex and amygdala was selectively reduced. These effects were more pronounced after fearful than joyful movies for higher frequency bands. Moreover, the initial suppression of resting activity in ACC and insula after emotional stimuli was followed by a gradual restoration over time. Emotions did not affect IPL average activity but increased its connectivity with other regions. These findings reveal specific neural circuits recruited during the recovery from emotional arousal and highlight the complex functional dynamics of default mode networks in emotionally salient contexts. Copyright © 2010 Elsevier Inc. All rights reserved.

Loneliness and Cognitive Function in Older Adults: Findings From the Chinese Longitudinal Healthy Longevity Survey

PubMed Central

Chen, Shu-Lin; Tu, Xin; Conwell, Yeates

2017-01-01

Objectives: To examine the relationship between loneliness and cognitive function and to explore the mediating role of physical health on the loneliness–cognition relationship in Chinese older adults (OAs). Method: Data came from a nationally representative sample of 14,199 Chinese OAs (aged 65+) from 2002, 2005, 2008, and 2011 waves of the Chinese Longitudinal Healthy Longevity Survey. A latent variable cross-lagged panel model combined with mediation analysis was used to determine the relationship between loneliness and cognitive function and the mediating effect of increase in the number of chronic conditions (ΔNCCs) on the ascertained loneliness–cognition relationship. Results: Severe loneliness at prior assessment points was significantly associated with poorer cognitive function at subsequent assessments, and vice versa. The ΔNCCs partially mediated this prospective reciprocal relationships, accounting for 2.58% of the total effect of loneliness on cognition and 4.44% of the total effect of cognition on loneliness, respectively. Discussion: Loneliness may predict subsequent cognitive decline, and vice versa. This loneliness–cognition relationship is partially explained by their impact on physical health. Multidisciplinary interventions aimed at reducing loneliness and cognitive decline per se and their associated risk factors as well as improving chronic illness management would be beneficial for emotional well-being and cognitive health in OAs. PMID:27013536

Non-functional Avionics Requirements

NASA Astrophysics Data System (ADS)

Paulitsch, Michael; Ruess, Harald; Sorea, Maria

Embedded systems in aerospace become more and more integrated in order to reduce weight, volume/size, and power of hardware for more fuel-effi ciency. Such integration tendencies change architectural approaches of system ar chi tec tures, which subsequently change non-functional requirements for plat forms. This paper provides some insight into state-of-the-practice of non-func tional requirements for developing ultra-critical embedded systems in the aero space industry, including recent changes and trends. In particular, formal requi re ment capture and formal analysis of non-functional requirements of avionic systems - including hard-real time, fault-tolerance, reliability, and per for mance - are exemplified by means of recent developments in SAL and HiLiTE.

Application of a data-mining method based on Bayesian networks to lesion-deficit analysis

NASA Technical Reports Server (NTRS)

Herskovits, Edward H.; Gerring, Joan P.

2003-01-01

Although lesion-deficit analysis (LDA) has provided extensive information about structure-function associations in the human brain, LDA has suffered from the difficulties inherent to the analysis of spatial data, i.e., there are many more variables than subjects, and data may be difficult to model using standard distributions, such as the normal distribution. We herein describe a Bayesian method for LDA; this method is based on data-mining techniques that employ Bayesian networks to represent structure-function associations. These methods are computationally tractable, and can represent complex, nonlinear structure-function associations. When applied to the evaluation of data obtained from a study of the psychiatric sequelae of traumatic brain injury in children, this method generates a Bayesian network that demonstrates complex, nonlinear associations among lesions in the left caudate, right globus pallidus, right side of the corpus callosum, right caudate, and left thalamus, and subsequent development of attention-deficit hyperactivity disorder, confirming and extending our previous statistical analysis of these data. Furthermore, analysis of simulated data indicates that methods based on Bayesian networks may be more sensitive and specific for detecting associations among categorical variables than methods based on chi-square and Fisher exact statistics.

Polymer surface functionalities that control human embryoid body cell adhesion revealed by high throughput surface characterization of combinatorial material microarrays

PubMed Central

Yang, Jing; Mei, Ying; Hook, Andrew L.; Taylor, Michael; Urquhart, Andrew J.; Bogatyrev, Said R.; Langer, Robert; Anderson, Daniel G.; Davies, Martyn C.; Alexander, Morgan R.

2010-01-01

High throughput materials discovery using combinatorial polymer microarrays to screen for new biomaterials with new and improved function is established as a powerful strategy. Here we combine this screening approach with high throughput surface characterisation (HT-SC) to identify surface structure-function relationships. We explore how this combination can help to identify surface chemical moieties that control protein adsorption and subsequent cellular response. The adhesion of human embryoid body (hEB) cells to a large number (496) of different acrylate polymers synthesized in a microarray format is screened using a high throughput procedure. To determine the role of the polymer surface properties on hEB cell adhesion, detailed HT-SC of these acrylate polymers is carried out using time of flight secondary ion mass spectrometry (ToF SIMS), x-ray photoelectron spectroscopy (XPS), pico litre drop sessile water contact angle (WCA) measurement and atomic force microscopy (AFM). A structure-function relationship is identified between the ToF SIMS analysis of the surface chemistry after a fibronectin (Fn) pre-conditioning step and the cell adhesion to each spot using the multivariate analysis technique partial least squares (PLS) regression. Secondary ions indicative of the adsorbed Fn correlate with increased cell adhesion whereas glycol and other functionalities from the polymers are identified that reduce cell adhesion. Furthermore, a strong relationship between the ToF SIMS spectra of bare polymers and the cell adhesion to each spot is identified using PLS regression. This identifies a role for both the surface chemistry of the bare polymer and the pre-adsorbed Fn, as-represented in the ToF SIMS spectra, in controlling cellular adhesion. In contrast, no relationship is found between cell adhesion and wettability, surface roughness, elemental or functional surface composition. The correlation between ToF SIMS data of the surfaces and the cell adhesion demonstrates the ability of identifying surface moieties that control protein adsorption and subsequent cell adhesion using ToF SIMS and multivariate analysis. PMID:20832108

Sonochemical surface functionalization of exfoliated LDH: Effect on textural properties, CO2 adsorption, cyclic regeneration capacities and subsequent gas uptake for simultaneous methanol synthesis.

PubMed

Ezeh, Collins I; Huang, Xiani; Yang, Xiaogang; Sun, Cheng-Gong; Wang, Jiawei

2017-11-01

To improve CO 2 adsorption, amine modified Layered double hydroxide (LDH) were prepared via a two stage process, SDS/APTS intercalation was supported by ultrasonic irradiation and then followed by MEA extraction. The prepared samples were characterised using Scanning electron microscope-Energy dispersive X-ray spectroscopy (SEM-EDX), X-ray Photoelectron Spectroscopy (XPS), X-ray diffraction (XRD), Temperature Programmed Desorption (TPD), Brunauer-Emmett-Teller (BET), and Thermogravimetric analysis (TGA), respectively. The characterisation results were compared with those obtained using the conventional preparation method with consideration to the effect of sonochemical functionalization on textural properties, adsorption capacity, regeneration and lifetime of the LDH adsorbent. It is found that LDHs prepared by sonochemical modification had improved pore structure and CO 2 adsorption capacity, depending on sonic intensity. This is attributed to the enhanced deprotonation of activated amino functional groups via the sonochemical process. Subsequently, this improved the amine loading and effective amine efficiency by 60% of the conventional. In addition, the sonochemical process improved the thermal stability of the adsorbent and also, reduced the irreversible CO 2 uptake, CUirrev, from 0.18mmol/g to 0.03mmol/g. Subsequently, improving the lifetime and ease of regenerating the adsorbent respectively. This is authenticated by subjecting the prepared adsorbents to series of thermal swing adsorption (TSA) cycles until its adsorption capacity goes below 60% of the original CO 2 uptake. While the conventional adsorbent underwent a 10 TSA cycles before breaking down, the sonochemically functionalized LDH went further than 30 TSA cycles. Copyright © 2017 Elsevier B.V. All rights reserved.

Importance of Hydrophobic Cavities in Allosteric Regulation of Formylglycinamide Synthetase: Insight from Xenon Trapping and Statistical Coupling Analysis

PubMed Central

Choudhary, Deepanshu; Panjikar, Santosh; Anand, Ruchi

2013-01-01

Formylglycinamide ribonucleotide amidotransferase (FGAR-AT) is a 140 kDa bi-functional enzyme involved in a coupled reaction, where the glutaminase active site produces ammonia that is subsequently utilized to convert FGAR to its corresponding amidine in an ATP assisted fashion. The structure of FGAR-AT has been previously determined in an inactive state and the mechanism of activation remains largely unknown. In the current study, hydrophobic cavities were used as markers to identify regions involved in domain movements that facilitate catalytic coupling and subsequent activation of the enzyme. Three internal hydrophobic cavities were located by xenon trapping experiments on FGAR-AT crystals and further, these cavities were perturbed via site-directed mutagenesis. Biophysical characterization of the mutants demonstrated that two of these three voids are crucial for stability and function of the protein, although being ∼20 Å from the active centers. Interestingly, correlation analysis corroborated the experimental findings, and revealed that amino acids lining the functionally important cavities form correlated sets (co-evolving residues) that connect these regions to the amidotransferase active center. It was further proposed that the first cavity is transient and allows for breathing motion to occur and thereby serves as an allosteric hotspot. In contrast, the third cavity which lacks correlated residues was found to be highly plastic and accommodated steric congestion by local adjustment of the structure without affecting either stability or activity. PMID:24223728

Preparation of sumoylated substrates for biochemical analysis.

PubMed

Knipscheer, Puck; Klug, Helene; Sixma, Titia K; Pichler, Andrea

2009-01-01

Covalent modification of proteins with SUMO (small ubiquitin related modifier) affects many cellular processes like transcription, nuclear transport, DNA repair and cell cycle progression. Although hundreds of SUMO targets have been identified, for several of them the function remains obscure. In the majority of cases sumoylation is investigated via "loss of modification" analysis by mutating the relevant target lysine. However, in other cases this approach is not successful since mapping of the modification site is problematic or mutation does not cause an obvious phenotype. These latter cases ask for different approaches to investigate the target modification. One possibility is to choose the opposite approach, a "gain in modification" analysis by producing both SUMO modified and unmodified protein in vitro and comparing them in functional assays. Here, we describe the purification of the ubiquitin conjugating enzyme E2-25K, its in vitro sumoylation with recombinant enzymes and the subsequent separation and purification of the modified and the unmodified forms.

Efficient Enrichment and Analysis of Vicinal-Diol-Containing Flavonoid Molecules Using Boronic-Acid-Functionalized Particles and Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry.

PubMed

Kim, Eunjin; Kang, Hyunook; Choi, Insung; Song, Jihyeon; Mok, Hyejung; Jung, Woong; Yeo, Woon-Seok

2018-05-09

Detection and quantitation of flavonoids are relatively difficult compared to those of other small-molecule analytes because flavonoids undergo rapid metabolic processes, resulting in their elimination from the body. Here, we report an efficient enrichment method for facilitating the analysis of vicinal-diol-containing flavonoid molecules using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. In our strategy, boronic-acid-functionalized polyacrylamide particles were used, where boronic acids bound to vicinal diols to form boronate monoesters at basic pH. This complex remained intact during the enrichment processes, and the vicinal-diol-containing flavonoids were easily separated by centrifugation and subsequent acidic treatments. The selectivity and limit of detection of our strategy were confirmed by mass spectrometry analysis, and the validity was assessed by performing the detection and quantitation of quercetin in mouse organs.

Model-OA wind turbine generator - Failure modes and effects analysis

NASA Technical Reports Server (NTRS)

Klein, William E.; Lali, Vincent R.

1990-01-01

The results failure modes and effects analysis (FMEA) conducted for wind-turbine generators are presented. The FMEA was performed for the functional modes of each system, subsystem, or component. The single-point failures were eliminated for most of the systems. The blade system was the only exception. The qualitative probability of a blade separating was estimated at level D-remote. Many changes were made to the hardware as a result of this analysis. The most significant change was the addition of the safety system. Operational experience and need to improve machine availability have resulted in subsequent changes to the various systems, which are also reflected in this FMEA.

Error rate information in attention allocation pilot models

NASA Technical Reports Server (NTRS)

Faulkner, W. H.; Onstott, E. D.

1977-01-01

The Northrop urgency decision pilot model was used in a command tracking task to compare the optimized performance of multiaxis attention allocation pilot models whose urgency functions were (1) based on tracking error alone, and (2) based on both tracking error and error rate. A matrix of system dynamics and command inputs was employed, to create both symmetric and asymmetric two axis compensatory tracking tasks. All tasks were single loop on each axis. Analysis showed that a model that allocates control attention through nonlinear urgency functions using only error information could not achieve performance of the full model whose attention shifting algorithm included both error and error rate terms. Subsequent to this analysis, tracking performance predictions for the full model were verified by piloted flight simulation. Complete model and simulation data are presented.

Successful Aging in the Context of the Disablement Process: Working and Volunteering as Moderators on the Association Between Chronic Conditions and Subsequent Functional Limitations.

PubMed

Kail, Ben Lennox; Carr, Dawn C

2017-03-01

This study evaluated the successful aging model by assessing the impact of two forms of productive engagement-working and volunteering-as potential interventions in the process of disablement. The Health and Retirement Study was used to (a) estimate two-stage selection equations of (i) currently working part time and full time and (ii) currently volunteering less than 100 hours and volunteering 100 hours or more per year (net of chronic health problems) and (b) assess whether, net of selection, working, and volunteering moderate the association between chronic conditions and subsequent functional limitations. Chronic conditions were associated with elevated levels of subsequent functional limitations, whereas both working and volunteering were associated with lower levels of subsequent functional limitations. Moreover, workers and volunteers of less than 100 hours per year experienced a reduction in the association of chronic conditions on subsequent functional limitations. This research highlights the role of productive engagement as a key element in successful aging. Not only do work and volunteering have direct associations with health outcomes themselves, but they also act as potential interventions in the process of disablement by attenuating the way in which chronic conditions are translated into subsequent functional limitations. This suggests that (a) future research should apply successful aging models to health processes as well as health outcomes and (b) policy makers should support social institutions that foster late-life productive engagement. © The Author 2016. Published by Oxford University Press on behalf of The Gerontological Society of America. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Identification and characterization of kidney transplants with good glomerular filtration rate at 1 year but subsequent progressive loss of renal function.

PubMed

Park, Walter D; Larson, Timothy S; Griffin, Matthew D; Stegall, Mark D

2012-11-15

After the first year after kidney transplantation, 3% to 5% of grafts fail each year but detailed studies of how grafts progress to failure are lacking. This study aimed to analyze the functional stability of kidney transplants between 1 and 5 years after transplantation and to identify initially well-functioning grafts with progressive decline in allograft function. The study included 788 adult conventional kidney transplants performed at the Mayo Clinic Rochester between January 2000 and December 2005 with a minimum graft survival and follow-up of 2.6 years. The modification of diet in renal disease equation for estimating glomerular filtration rate (eGFR(MDRD)) was used to calculate the slope of renal function over time using all available serum creatinine values between 1 and 5 years after transplantation. Most transplants demonstrated good function (eGFR(MDRD) ≥40 mL/min) at 1 year with positive eGFR(MDRD) slope between 1 and 5 years after transplantation. However, a subset of grafts with 1-year eGFR(MDRD) ≥40 mL/min exhibited strongly negative eGFR(MDRD) slope between 1 and 5 years suggestive of progressive loss of graft function. Forty-one percent of this subset reached graft failure during follow-up, accounting for 69% of allograft failures occurring after 2.5 years after transplantation. This pattern of progressive decline in estimated glomerular filtration rate despite good early function was associated with but not fully attributable to factors suggestive of enhanced antidonor immunity. Longitudinal analysis of serial estimated glomerular filtration ratemeasurements identifies initially well-functioning kidney transplants at high risk for subsequent graft loss. For this subset, further studies are needed to identify modifiable causes of functional decline.

Further evaluation of leisure items in the attention condition of functional analyses.

PubMed

Roscoe, Eileen M; Carreau, Abbey; MacDonald, Jackie; Pence, Sacha T

2008-01-01

Research suggests that including leisure items in the attention condition of a functional analysis may produce engagement that masks sensitivity to attention. In this study, 4 individuals' initial functional analyses indicated that behavior was maintained by nonsocial variables (n = 3) or by attention (n = 1). A preference assessment was used to identify items for subsequent functional analyses. Four conditions were compared, attention with and without leisure items and control with and without leisure items. Following this, either high- or low-preference items were included in the attention condition. Problem behavior was more probable during the attention condition when no leisure items or low-preference items were included, and lower levels of problem behavior were observed during the attention condition when high-preference leisure items were included. These findings suggest how preferred items may hinder detection of behavioral function.

Transactional Relations Between Marital Functioning and Depressive Symptoms

PubMed Central

Kouros, Chrystyna D.; Cummings, E. Mark

2012-01-01

The present study investigated dynamic, longitudinal associations between depressive symptoms and marital processes. Two hundred ninety-six couples reported on marital satisfaction, marital conflict, and depressive symptoms yearly for three years. Observational measures of marital conflict were also collected. Results suggested that different domains of marital functioning related to husbands’ versus wives’ symptoms. For husbands, transactional relations between marital satisfaction and depressive symptoms were identified: high levels of depressive symptoms predicted subsequent decreases in marital satisfaction, and decreased marital satisfaction predicted subsequent elevations in symptoms over time. For wives, high levels of marital conflict predicted subsequent elevations in symptoms over time. Cross-partner results indicated that husbands’ depressive symptoms were also related to subsequent declines in wives’ marital satisfaction. Results are discussed with regard to theoretical perspectives on the marital functioning-depression link and directions for future research are outlined. PMID:21219284

A novel microfluidic platform for size and deformability based separation and the subsequent molecular characterization of viable circulating tumor cells.

PubMed

Hvichia, G E; Parveen, Z; Wagner, C; Janning, M; Quidde, J; Stein, A; Müller, V; Loges, S; Neves, R P L; Stoecklein, N H; Wikman, H; Riethdorf, S; Pantel, K; Gorges, T M

2016-06-15

Circulating tumor cells (CTCs) were introduced as biomarkers more than 10 years ago, but capture of viable CTCs at high purity from peripheral blood of cancer patients is still a major technical challenge. Here, we report a novel microfluidic platform designed for marker independent capture of CTCs. The Parsortix™ cell separation system provides size and deformability-based enrichment with automated staining for cell identification, and subsequent recovery (harvesting) of cells from the device. Using the Parsortix™ system, average cell capture inside the device ranged between 42% and 70%. Subsequent harvest of cells from the device ranged between 54% and 69% of cells captured. Most importantly, 99% of the isolated tumor cells were viable after processing in spiking experiments as well as after harvesting from patient samples and still functional for downstream molecular analysis as demonstrated by mRNA characterization and array-based comparative genomic hybridization. Analyzing clinical blood samples from metastatic (n = 20) and nonmetastatic (n = 6) cancer patients in parallel with CellSearch(®) system, we found that there was no statistically significant difference between the quantitative behavior of the two systems in this set of twenty six paired separations. In conclusion, the epitope independent Parsortix™ system enables the isolation of viable CTCs at a very high purity. Using this system, viable tumor cells are easily accessible and ready for molecular and functional analysis. The system's ability for enumeration and molecular characterization of EpCAM-negative CTCs will help to broaden research into the mechanisms of cancer as well as facilitating the use of CTCs as "liquid biopsies." © 2016 The Authors International Journal of Cancer published by John Wiley & Sons Ltd on behalf of UICC.

Ghrelin Promotes Functional Angiogenesis in a Mouse Model of Critical Limb Ischemia Through Activation of Proangiogenic MicroRNAs.

PubMed

Katare, Rajesh; Rawal, Shruti; Munasinghe, Pujika Emani; Tsuchimochi, Hirotsugu; Inagaki, Tadakatsu; Fujii, Yutaka; Dixit, Parul; Umetani, Keiji; Kangawa, Kenji; Shirai, Mikiyasu; Schwenke, Daryl O

2016-02-01

Current therapeutic strategies for the treatment of critical limb ischemia (CLI) have only limited success. Recent in vitro evidence in the literature, using cell lines, proposes that the peptide hormone ghrelin may have angiogenic properties. In this study, we aim to investigate if ghrelin could promote postischemic angiogenesis in a mouse model of CLI and, further, identify the mechanistic pathway(s) that underpin ghrelin's proangiogenic properties. CLI was induced in male CD1 mice by femoral artery ligation. Animals were then randomized to receive either vehicle or acylated ghrelin (150 μg/kg sc) for 14 consecutive days. Subsequently, synchrotron radiation microangiography was used to assess hindlimb perfusion. Subsequent tissue samples were collected for molecular and histological analysis. Ghrelin treatment markedly improved limb perfusion by promoting the generation of new capillaries and arterioles (internal diameter less than 50 μm) within the ischemic hindlimb that were both structurally and functionally normal; evident by robust endothelium-dependent vasodilatory responses to acetylcholine. Molecular analysis revealed that ghrelin's angiogenic properties were linked to activation of prosurvival Akt/vascular endothelial growth factor/Bcl-2 signaling cascade, thus reducing the apoptotic cell death and subsequent fibrosis. Further, ghrelin treatment activated proangiogenic (miR-126 and miR-132) and antifibrotic (miR-30a) microRNAs (miRs) while inhibiting antiangiogenic (miR-92a and miR-206) miRs. Importantly, in vitro knockdown of key proangiogenic miRs (miR-126 and miR-132) inhibited the angiogenic potential of ghrelin. These results therefore suggest that clinical use of ghrelin for the early treatment of CLI may be a promising and potent inducer of reparative vascularization through modulation of key molecular factors.

Structural and magnetic characterization of copper sulfonated phthalocyanine grafted onto treated polyethylene

NASA Astrophysics Data System (ADS)

Reznickova, A.; Kolska, Z.; Orendac, M.; Cizmar, E.; Sajdl, P.; Svorcik, V.

2016-08-01

This study focuses on high density polyethylene (HDPE) activated by Ar plasma treatment, subsequently grafted with copper sulfonated phthalocyanine (CuPc) especially pointing out to the surface and magnetic properties of those composites. Properties of pristine PE and their plasma treated counterparts were studied by different experimental techniques: X-ray photoelectron spectroscopy (XPS), UV-vis spectroscopy, zeta potential and by electron spin resonance (ESR). XPS analysis confirmed the successful grafting of phthalocyanine. The highest absorption was found for the sample grafted with bCuPc for 1 h. Electrokinetic analysis also confirmed the plasma treatment and also subsequent CuPc grafting influence significantly the surface chemistry and charge. These results correspond well with XPS determination. ESR studies confirmed the presence of CuPc grafted on HDPE. It was found, that grafting is mediated by magnetically inactive functional groups, rather than radicals. Magnetic properties of CuPc do not seem to change significantly after grafting CuPc on polyethylene surface.

DISCO Interacting Protein 2 regulates axonal bifurcation and guidance of Drosophila mushroom body neurons.

PubMed

Nitta, Yohei; Yamazaki, Daisuke; Sugie, Atsushi; Hiroi, Makoto; Tabata, Tetsuya

2017-01-15

Axonal branching is one of the key processes within the enormous complexity of the nervous system to enable a single neuron to send information to multiple targets. However, the molecular mechanisms that control branch formation are poorly understood. In particular, previous studies have rarely addressed the mechanisms underlying axonal bifurcation, in which axons form new branches via splitting of the growth cone. We demonstrate that DISCO Interacting Protein 2 (DIP2) is required for precise axonal bifurcation in Drosophila mushroom body (MB) neurons by suppressing ectopic bifurcation and regulating the guidance of sister axons. We also found that DIP2 localize to the plasma membrane. Domain function analysis revealed that the AMP-synthetase domains of DIP2 are essential for its function, which may involve exerting a catalytic activity that modifies fatty acids. Genetic analysis and subsequent biochemical analysis suggested that DIP2 is involved in the fatty acid metabolization of acyl-CoA. Taken together, our results reveal a function of DIP2 in the developing nervous system and provide a potential functional relationship between fatty acid metabolism and axon morphogenesis. Copyright © 2016 Elsevier Inc. All rights reserved.

The increase in medial prefrontal glutamate/glutamine concentration during memory encoding is associated with better memory performance and stronger functional connectivity in the human medial prefrontal-thalamus-hippocampus network.

PubMed

Thielen, Jan-Willem; Hong, Donghyun; Rohani Rankouhi, Seyedmorteza; Wiltfang, Jens; Fernández, Guillén; Norris, David G; Tendolkar, Indira

2018-06-01

The classical model of the declarative memory system describes the hippocampus and its interactions with representational brain areas in posterior neocortex as being essential for the formation of long-term episodic memories. However, new evidence suggests an extension of this classical model by assigning the medial prefrontal cortex (mPFC) a specific, yet not fully defined role in episodic memory. In this study, we utilized 1H magnetic resonance spectroscopy (MRS) and psychophysiological interaction (PPI) analysis to lend further support for the idea of a mnemonic role of the mPFC in humans. By using MRS, we measured mPFC γ-aminobutyric acid (GABA) and glutamate/glutamine (GLx) concentrations before and after volunteers memorized face-name association. We demonstrate that mPFC GLx but not GABA levels increased during the memory task, which appeared to be related to memory performance. Regarding functional connectivity, we used the subsequent memory paradigm and found that the GLx increase was associated with stronger mPFC connectivity to thalamus and hippocampus for associations subsequently recognized with high confidence as opposed to subsequently recognized with low confidence/forgotten. Taken together, we provide new evidence for an mPFC involvement in episodic memory by showing a memory-related increase in mPFC excitatory neurotransmitter levels that was associated with better memory and stronger memory-related functional connectivity in a medial prefrontal-thalamus-hippocampus network. © 2018 The Authors Human Brain Mapping Published by Wiley Periodicals, Inc.

Technical Advance: Live-imaging analysis of human dendritic cell migrating behavior under the influence of immune-stimulating reagents in an organotypic model of lung

PubMed Central

Nguyen Hoang, Anh Thu; Chen, Puran; Björnfot, Sofia; Högstrand, Kari; Lock, John G.; Grandien, Alf; Coles, Mark; Svensson, Mattias

2014-01-01

This manuscript describes technical advances allowing manipulation and quantitative analyses of human DC migratory behavior in lung epithelial tissue. DCs are hematopoietic cells essential for the maintenance of tissue homeostasis and the induction of tissue-specific immune responses. Important functions include cytokine production and migration in response to infection for the induction of proper immune responses. To design appropriate strategies to exploit human DC functional properties in lung tissue for the purpose of clinical evaluation, e.g., candidate vaccination and immunotherapy strategies, we have developed a live-imaging assay based on our previously described organotypic model of the human lung. This assay allows provocations and subsequent quantitative investigations of DC functional properties under conditions mimicking morphological and functional features of the in vivo parental tissue. We present protocols to set up and prepare tissue models for 4D (x, y, z, time) fluorescence-imaging analysis that allow spatial and temporal studies of human DCs in live epithelial tissue, followed by flow cytometry analysis of DCs retrieved from digested tissue models. This model system can be useful for elucidating incompletely defined pathways controlling DC functional responses to infection and inflammation in lung epithelial tissue, as well as the efficacy of locally administered candidate interventions. PMID:24899587

Associations of renal function at 1-year after kidney transplantation with subsequent return to dialysis, mortality, and healthcare costs.

PubMed

Schnitzler, Mark A; Johnston, Karissa; Axelrod, David; Gheorghian, Adrian; Lentine, Krista L

2011-06-27

Improved early kidney transplant outcomes limit the contemporary utility of standard clinical endpoints. Quantifying the relationship of renal function at 1 year after transplant with subsequent clinical outcomes and healthcare costs may facilitate cost-benefit evaluations among transplant recipients. Data for Medicare-insured kidney-only transplant recipients (1995-2003) were drawn from the United States Renal Data System. Associations of estimated glomerular filtration rate (eGFR) level at the first transplant anniversary with subsequent death-censored graft failure and patient death in posttransplant years 1 to 3 and 4 to 7 were examined by parametric survival analysis. Associations of eGFR with total health care costs defined by Medicare payments were assessed with multivariate linear regression. Among 38,015 participants, first anniversary eGFR level demonstrated graded associations with subsequent outcomes. Compared with patients with 12-month eGFR more than or equal to 60 mL/min/1.73 m, the adjusted relative risk of death-censored graft failure in years 1 to 3 was 31% greater for eGFR 45 to 59 mL/min/1.73 m (P<0.0001) and 622% greater for eGFR 15 to 30 mL/min/1.73 m (P<0.0001). Associations of first anniversary eGFR level with graft failure and mortality remained significant in years 4 to 7. The proportions of recipients expected to return to dialysis or die attributable to eGFR less than 60 mL/min/1.73 m over 10 years were 23.1% and 9.4%, respectively, and were significantly higher than proportions attributable to delayed graft function or acute rejection. Reduced eGFR was associated with graded and significant increases in health care spending during years 2 and 3 after transplant (P<0.0001). eGFR is strongly associated with clinical and economic outcomes after kidney transplantation.

The plant leaf movement analyzer (PALMA): a simple tool for the analysis of periodic cotyledon and leaf movement in Arabidopsis thaliana.

PubMed

Wagner, Lucas; Schmal, Christoph; Staiger, Dorothee; Danisman, Selahattin

2017-01-01

The analysis of circadian leaf movement rhythms is a simple yet effective method to study effects of treatments or gene mutations on the circadian clock of plants. Currently, leaf movements are analysed using time lapse photography and subsequent bioinformatics analyses of leaf movements. Programs that are used for this purpose either are able to perform one function (i.e. leaf tip detection or rhythm analysis) or their function is limited to specific computational environments. We developed a leaf movement analysis tool-PALMA-that works in command line and combines image extraction with rhythm analysis using Fast Fourier transformation and non-linear least squares fitting. We validated PALMA in both simulated time series and in experiments using the known short period mutant sensitivity to red light reduced 1 ( srr1 - 1 ). We compared PALMA with two established leaf movement analysis tools and found it to perform equally well. Finally, we tested the effect of reduced iron conditions on the leaf movement rhythms of wild type plants. Here, we found that PALMA successfully detected period lengthening under reduced iron conditions. PALMA correctly estimated the period of both simulated and real-life leaf movement experiments. As a platform-independent console-program that unites both functions needed for the analysis of circadian leaf movements it is a valid alternative to existing leaf movement analysis tools.

A Cost Estimation Analysis of U.S. Navy Ship Fuel-Savings Techniques and Technologies

DTIC Science & Technology

2009-09-01

readings to the boiler operator. The PLC will provide constant automatic trimming of the excess oxygen based upon real time SGA readings. An SCD...the author): The Aegis Combat System is controlled by an advanced, automatic detect-and-track, multi-function three-dimensional passive...subsequently offloaded. An Online Wash System would reduce these maintenance costs and improve fuel efficiency of these engines by keeping the engines

SAS2H Generated Isotopic Concentrations For B&W 15X15 PWR Assembly (SCPB:N/A)

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

J.W. Davis

This analysis is prepared by the Mined Geologic Disposal System (MGDS) Waste Package Development Department (WPDD) to provide pressurized water reactor (PWR) isotopic composition data as a function of time for use in criticality analyses. The objectives of this evaluation are to generate burnup and decay dependant isotopic inventories and to provide these inventories in a form which can easily be utilized in subsequent criticality calculations.

Genome-wide analysis of the Dof transcription factor gene family reveals soybean-specific duplicable and functional characteristics.

PubMed

Guo, Yong; Qiu, Li-Juan

2013-01-01

The Dof domain protein family is a classic plant-specific zinc-finger transcription factor family involved in a variety of biological processes. There is great diversity in the number of Dof genes in different plants. However, there are only very limited reports on the characterization of Dof transcription factors in soybean (Glycine max). In the present study, 78 putative Dof genes were identified from the whole-genome sequence of soybean. The predicted GmDof genes were non-randomly distributed within and across 19 out of 20 chromosomes and 97.4% (38 pairs) were preferentially retained duplicate paralogous genes located in duplicated regions of the genome. Soybean-specific segmental duplications contributed significantly to the expansion of the soybean Dof gene family. These Dof proteins were phylogenetically clustered into nine distinct subgroups among which the gene structure and motif compositions were considerably conserved. Comparative phylogenetic analysis of these Dof proteins revealed four major groups, similar to those reported for Arabidopsis and rice. Most of the GmDofs showed specific expression patterns based on RNA-seq data analyses. The expression patterns of some duplicate genes were partially redundant while others showed functional diversity, suggesting the occurrence of sub-functionalization during subsequent evolution. Comprehensive expression profile analysis also provided insights into the soybean-specific functional divergence among members of the Dof gene family. Cis-regulatory element analysis of these GmDof genes suggested diverse functions associated with different processes. Taken together, our results provide useful information for the functional characterization of soybean Dof genes by combining phylogenetic analysis with global gene-expression profiling.

Geometry program for aerodynamic lifting surface theory

NASA Technical Reports Server (NTRS)

Medan, R. T.

1973-01-01

A computer program that provides the geometry and boundary conditions appropriate for an analysis of a lifting, thin wing with control surfaces in linearized, subsonic, steady flow is presented. The kernel function method lifting surface theory is applied. The data which is generated by the program is stored on disk files or tapes for later use by programs which calculate an influence matrix, plot the wing planform, and evaluate the loads on the wing. In addition to processing data for subsequent use in a lifting surface analysis, the program is useful for computing area and mean geometric chords of the wing and control surfaces.

Divergent Relationships between Fecal Microbiota and Metabolome following Distinct Antibiotic-Induced Disruptions.

PubMed

Choo, Jocelyn M; Kanno, Tokuwa; Zain, Nur Masirah Mohd; Leong, Lex E X; Abell, Guy C J; Keeble, Julie E; Bruce, Kenneth D; Mason, A James; Rogers, Geraint B

2017-01-01

The intestinal microbiome plays an essential role in regulating many aspects of host physiology, and its disruption through antibiotic exposure has been implicated in the development of a range of serious pathologies. The complex metabolic relationships that exist between members of the intestinal microbiota and the potential redundancy in functional pathways mean that an integrative analysis of changes in both structure and function are needed to understand the impact of antibiotic exposure. We used a combination of next-generation sequencing and nuclear magnetic resonance (NMR) metabolomics to characterize the effects of two clinically important antibiotic treatments, ciprofloxacin and vancomycin-imipenem, on the intestinal microbiomes of female C57BL/6 mice. This assessment was performed longitudinally and encompassed both antibiotic challenge and subsequent microbiome reestablishment. Both antibiotic treatments significantly altered the microbiota and metabolite compositions of fecal pellets during challenge and recovery. Spearman's correlation analysis of microbiota and NMR data revealed that, while some metabolites could be correlated with individual operational taxonomic units (OTUs), frequently multiple OTUs were associated with a significant change in a given metabolite. Furthermore, one metabolite, arginine, can be associated with increases/decreases in different sets of OTUs under differing conditions. Taken together, these findings indicate that reliance on shifts in one data set alone will generate an incomplete picture of the functional effect of antibiotic intervention. A full mechanistic understanding will require knowledge of the baseline microbiota composition, combined with both a comparison and an integration of microbiota, metabolomics, and phenotypic data. IMPORTANCE Despite the fundamental importance of antibiotic therapies to human health, their functional impact on the intestinal microbiome and its subsequent ability to recover are poorly understood. Much research in this area has focused on changes in microbiota composition, despite the interdependency and overlapping functions of many members of the microbial community. These relationships make prediction of the functional impact of microbiota-level changes difficult, while analyses based on the metabolome alone provide relatively little insight into the taxon-level changes that underpin changes in metabolite levels. Here, we used combined microbiota and metabolome profiling to characterize changes associated with clinically important antibiotic combinations with distinct effects on the gut. Correlation analysis of changes in the metabolome and microbiota indicate that a combined approach will be essential for a mechanistic understanding of the functional impact of distinct antibiotic classes.

Mapping the Structure-Function Relationship in Glaucoma and Healthy Patients Measured with Spectralis OCT and Humphrey Perimetry

PubMed Central

Muñoz–Negrete, Francisco J.; Oblanca, Noelia; Rebolleda, Gema

2018-01-01

Purpose To study the structure-function relationship in glaucoma and healthy patients assessed with Spectralis OCT and Humphrey perimetry using new statistical approaches. Materials and Methods Eighty-five eyes were prospectively selected and divided into 2 groups: glaucoma (44) and healthy patients (41). Three different statistical approaches were carried out: (1) factor analysis of the threshold sensitivities (dB) (automated perimetry) and the macular thickness (μm) (Spectralis OCT), subsequently applying Pearson's correlation to the obtained regions, (2) nonparametric regression analysis relating the values in each pair of regions that showed significant correlation, and (3) nonparametric spatial regressions using three models designed for the purpose of this study. Results In the glaucoma group, a map that relates structural and functional damage was drawn. The strongest correlation with visual fields was observed in the peripheral nasal region of both superior and inferior hemigrids (r = 0.602 and r = 0.458, resp.). The estimated functions obtained with the nonparametric regressions provided the mean sensitivity that corresponds to each given macular thickness. These functions allowed for accurate characterization of the structure-function relationship. Conclusions Both maps and point-to-point functions obtained linking structure and function damage contribute to a better understanding of this relationship and may help in the future to improve glaucoma diagnosis. PMID:29850196

Transdiagnostic differences in the resting-state functional connectivity of the prefrontal cortex in depression and schizophrenia.

PubMed

Chen, Xi; Liu, Chang; He, Hui; Chang, Xin; Jiang, Yuchao; Li, Yingjia; Duan, Mingjun; Li, Jianfu; Luo, Cheng; Yao, Dezhong

2017-08-01

Depression and schizophrenia are two of the most serious psychiatric disorders. They share similar symptoms but the pathology-specific commonalities and differences remain unknown. This study was conducted to acquire a full picture of the functional alterations in schizophrenia and depression patients. The resting-state fMRI data from 20 patients with schizophrenia, 20 patients with depression and 20 healthy control subjects were collected. A data-driven approach that included local functional connectivity density (FCD) analysis combined with multivariate pattern analysis (MVPA) was used to compare the three groups. Based on the results of the MVPA, the local FCD value in the orbitofrontal cortex (OFC) can differentiate depression patients from schizophrenia patients. The patients with depression had a higher local FCD value in the medial and anterior parts of the OFC than the subjects in the other two groups, which suggested altered abstract and reward reinforces processing in depression patients. Subsequent functional connectivity analysis indicated that the connection in the prefrontal cortex was significantly lower in people with schizophrenia compared to people with depression and healthy controls. The systematically different medications for schizophrenia and depression may have different effects on functional connectivity. These results suggested that the resting-state functional connectivity pattern in the prefrontal cortex may be a transdiagnostic difference between depression and schizophrenia patients. Copyright © 2017 Elsevier B.V. All rights reserved.

Green's function solution to heat transfer of a transparent gas through a tube

NASA Technical Reports Server (NTRS)

Frankel, J. I.

1989-01-01

A heat transfer analysis of a transparent gas flowing through a circular tube of finite thickness is presented. This study includes the effects of wall conduction, internal radiative exchange, and convective heat transfer. The natural mathematical formulation produces a nonlinear, integrodifferential equation governing the wall temperature and an ordinary differential equation describing the gas temperature. This investigation proposes to convert the original system of equations into an equivalent system of integral equations. The Green's function method permits the conversion of an integrodifferential equation into a pure integral equation. The proposed integral formulation and subsequent computational procedure are shown to be stable and accurate.

Evidence against the selfish operon theory.

PubMed

Pál, Csaba; Hurst, Laurence D

2004-06-01

According to the selfish operon hypothesis, the clustering of genes and their subsequent organization into operons is beneficial for the constituent genes because it enables the horizontal gene transfer of weakly selected, functionally coupled genes. The majority of these are expected to be non-essential genes. From our analysis of the Escherichia coli genome, we conclude that the selfish operon hypothesis is unlikely to provide a general explanation for clustering nor can it account for the gene composition of operons. Contrary to expectations, essential genes with related functions have an especially strong tendency to cluster, even if they are not in operons. Moreover, essential genes are particularly abundant in operons.

Dual mechanisms in the perceptual processing of click train temporal regularity.

PubMed

Phillips, Dennis P; Dingle, Rachel N; Hall, Susan E; Jang, Moragh

2012-07-01

Two experiments measured human sensitivity to temporal jitter in 25-click trains with inter-click intervals (ICIs) between 5 and 100 ms. In a naturalistic experiment using wideband clicks, jitter thresholds were a nonmonotonic function of ICI, peaking for ICIs near 40-60 ms. In a subsequent experiment, clicks were high-passed and presented against a low-frequency noise masker. Jitter threshold vs ICI functions lost the positive slope over short ICIs but retained the negative slope at long ICIs. The same behavior was seen in click rate discrimination tasks. Different processes mediate regularity analysis for click trains with ICIs above and below 40-60 ms.

Long-term healthcare costs and functional outcomes associated with lack of remission in schizophrenia: a post-hoc analysis of a prospective observational study

PubMed Central

2012-01-01

Background Little is known about the long-term outcomes for patients with schizophrenia who fail to achieve symptomatic remission. This post-hoc analysis of a 3-year study compared the costs of mental health services and functional outcomes between individuals with schizophrenia who met or did not meet cross-sectional symptom remission at study enrollment. Methods This post-hoc analysis used data from a large, 3-year prospective, non-interventional observational study of individuals treated for schizophrenia in the United States conducted between July 1997 and September 2003. At study enrollment, individuals were classified as non-remitted or remitted using the Schizophrenia Working Group Definition of symptom remission (8 core symptoms rated as mild or less). Mental health service use was measured using medical records. Costs were based on the sites’ medical information systems. Functional outcomes were measured with multiple patient-reported measures and the clinician-rated Quality of Life Scale (QLS). Symptoms were measured using the Positive and Negative Syndrome Scale (PANSS). Outcomes for non-remitted and remitted patients were compared over time using mixed effects models for repeated measures or generalized estimating equations after adjusting for multiple baseline characteristics. Results At enrollment, most of the 2,284 study participants (76.1%) did not meet remission criteria. Non-remitted patients had significantly higher PANSS total scores at baseline, a lower likelihood of being Caucasian, a higher likelihood of hospitalization in the previous year, and a greater likelihood of a substance use diagnosis (all p < 0.05). Total mental health costs were significantly higher for non-remitted patients over the 3-year study (p = 0.008). Non-remitted patients were significantly more likely to be victims of crime, exhibit violent behavior, require emergency services, and lack paid employment during the 3-year study (all p < 0.05). Non-remitted patients also had significantly lower scores on the QLS, SF-12 Mental Component Summary Score, and Global Assessment of Functioning during the 3-year study. Conclusions In this post-hoc analysis of a 3-year prospective observational study, the failure to achieve symptomatic remission at enrollment was associated with higher subsequent healthcare costs and worse functional outcomes. Further examination of outcomes for schizophrenia patients who fail to achieve remission at initial assessment by their subsequent clinical status is warranted. PMID:23216976

Dataset of potential targets for Mycobacterium tuberculosis H37Rv through comparative genome analysis.

PubMed

Asif, Siddiqui M; Asad, Amir; Faizan, Ahmad; Anjali, Malik S; Arvind, Arya; Neelesh, Kapoor; Hirdesh, Kumar; Sanjay, Kumar

2009-12-31

Mycobacterium tuberculosis is the causative agent of the disease, tuberculosis and H37Rv is the most studied clinical strain. We use comparative genome analysis of Mycobacterium tuberculosis H37Rv and human for the identification of potential targets dataset. We used DEG (Database of Essential Genes) to identify essential genes in the H37Rv strain. The analysis shows that 628 of the 3989 genes in Mycobacterium tuberculosis H37Rv were found to be essential of which 324 genes lack similarity to the human genome. Subsequently hypothetical proteins were removed through manual curation. This further resulted in a dataset of 135 proteins with essential function and no homology to human.

Unified functional network and nonlinear time series analysis for complex systems science: The pyunicorn package

NASA Astrophysics Data System (ADS)

Donges, Jonathan; Heitzig, Jobst; Beronov, Boyan; Wiedermann, Marc; Runge, Jakob; Feng, Qing Yi; Tupikina, Liubov; Stolbova, Veronika; Donner, Reik; Marwan, Norbert; Dijkstra, Henk; Kurths, Jürgen

2016-04-01

We introduce the pyunicorn (Pythonic unified complex network and recurrence analysis toolbox) open source software package for applying and combining modern methods of data analysis and modeling from complex network theory and nonlinear time series analysis. pyunicorn is a fully object-oriented and easily parallelizable package written in the language Python. It allows for the construction of functional networks such as climate networks in climatology or functional brain networks in neuroscience representing the structure of statistical interrelationships in large data sets of time series and, subsequently, investigating this structure using advanced methods of complex network theory such as measures and models for spatial networks, networks of interacting networks, node-weighted statistics, or network surrogates. Additionally, pyunicorn provides insights into the nonlinear dynamics of complex systems as recorded in uni- and multivariate time series from a non-traditional perspective by means of recurrence quantification analysis, recurrence networks, visibility graphs, and construction of surrogate time series. The range of possible applications of the library is outlined, drawing on several examples mainly from the field of climatology. pyunicorn is available online at https://github.com/pik-copan/pyunicorn. Reference: J.F. Donges, J. Heitzig, B. Beronov, M. Wiedermann, J. Runge, Q.-Y. Feng, L. Tupikina, V. Stolbova, R.V. Donner, N. Marwan, H.A. Dijkstra, and J. Kurths, Unified functional network and nonlinear time series analysis for complex systems science: The pyunicorn package, Chaos 25, 113101 (2015), DOI: 10.1063/1.4934554, Preprint: arxiv.org:1507.01571 [physics.data-an].

Genes Upregulated in Winter Wheat (Triticum aestivum L.) during Mild Freezing and Subsequent Thawing Suggest Sequential Activation of Multiple Response Mechanisms.

PubMed

Skinner, Daniel Z

2015-01-01

Exposing fully cold-acclimated wheat plants to a mild freeze-thaw cycle of -3 °C for 24h followed by +3 °C for 24 or 48 h results in dramatically improved tolerance of subsequent exposure to sub-freezing temperatures. Gene enrichment analysis of crown tissue from plants collected before or after the -3 °C freeze or after thawing at +3 °C for 24 or 48 h revealed that many biological processes and molecular functions were activated during the freeze-thaw cycle in an increasing cascade of responses such that over 150 processes or functions were significantly enhanced by the end of the 48 h, post-freeze thaw. Nearly 2,000 individual genes were upregulated more than 2-fold over the 72 h course of freezing and thawing, but more than 70% of these genes were upregulated during only one of the time periods examined, suggesting a series of genes and gene functions were involved in activation of the processes that led to enhanced freezing tolerance. This series of functions appeared to include extensive cell signaling, activation of stress response mechanisms and the phenylpropanoid biosynthetic pathway, extensive modification of secondary metabolites, and physical restructuring of cell membranes. By identifying plant lines that are especially able to activate these multiple mechanisms it may be possible to develop lines with enhanced winterhardiness.

Functional biocompatible magnetite-cellulose nanocomposite fibrous networks: Characterization by fourier transformed infrared spectroscopy, X-ray powder diffraction and field emission scanning electron microscopy analysis.

PubMed

Habibi, Neda

2015-02-05

The preparation and characterization of functional biocompatible magnetite-cellulose nano-composite fibrous material is described. Magnetite-cellulose nano-composite was prepared by a combination of the solution-based formation of magnetic nano-particles and subsequent coating with amino celluloses. Characterization was accomplished using X-ray powder diffraction (XRD), fourier transformed infrared (FTIR) and field emission scanning electron microscopy (FESEM) analysis. The peaks of Fe3O4 in the XRD pattern of nanocomposite confirm existence of the nanoparticles in the amino cellulose matrix. Magnetite-cellulose particles exhibit an average diameter of roughly 33nm as demonstrated by field emission scanning electron microscopy. Magnetite nanoparticles were irregular spheres dispersed in the cellulose matrix. The vibration corresponding to the NCH3 functional group about 2850cm(-1) is assigned in the FTIR spectra. Functionalized magnetite-cellulose nano-composite polymers have a potential range of application as targeted drug delivery system in biomedical field. Copyright © 2014 Elsevier B.V. All rights reserved.

Single-Cell Functional Analysis of Stem-Cell Derived Cardiomyocytes on Micropatterned Flexible Substrates.

PubMed

Kijlstra, Jan David; Hu, Dongjian; van der Meer, Peter; Domian, Ibrahim J

2017-11-15

Human pluripotent stem-cell derived cardiomyocytes (hPSC-CMs) hold great promise for applications in human disease modeling, drug discovery, cardiotoxicity screening, and, ultimately, regenerative medicine. The ability to study multiple parameters of hPSC-CM function, such as contractile and electrical activity, calcium cycling, and force generation, is therefore of paramount importance. hPSC-CMs cultured on stiff substrates like glass or polystyrene do not have the ability to shorten during contraction, making them less suitable for the study of hPSC-CM contractile function. Other approaches require highly specialized hardware and are difficult to reproduce. Here we describe a protocol for the preparation of hPSC-CMs on soft substrates that enable shortening, and subsequently the simultaneous quantitative analysis of their contractile and electrical activity, calcium cycling, and force generation at single-cell resolution. This protocol requires only affordable and readily available materials and works with standard imaging hardware. © 2017 by John Wiley & Sons, Inc. Copyright © 2017 John Wiley & Sons, Inc.

Physical activity, self-efficacy, and health-related quality of life in persons with multiple sclerosis: analysis of associations between individual-level changes over one year.

PubMed

Motl, Robert W; McAuley, Edward; Wynn, Daniel; Sandroff, Brian; Suh, Yoojin

2013-03-01

Physical activity and self-efficacy represent behavioral and psychological factors, respectively, that are compromised in persons with multiple sclerosis (MS), but might be modifiable through intervention and result in better health-related quality of life (HRQOL). The present study adopted a panel research design and examined the associations between individual-level changes in physical activity, self-efficacy, and HRQOL over a one-year period in persons with MS. The sample consisted of 269 persons with relapsing-remitting MS who completed the Godin Leisure-Time Questionnaire (GLTEQ), Multiple Sclerosis Self-Efficacy (MSSE) Scale, and Multiple Sclerosis Quality of Life-29 (MSIS-29) Scale on two occasions that were separated by 1 year. The data were analyzed using panel analysis in Mplus 3.0. The initial panel analysis indicated that individual-level change in physical activity was associated with individual-level change in both physical and psychological HRQOL. The subsequent panel analysis indicated that (a) individual-level change in self-efficacy for functioning with MS was associated with individual-level change in physical HRQOL, whereas individual-level change in self-efficacy for control was associated with individual-level change in psychological HRQOL; (b) individual-level change in self-efficacy for functioning with MS, but not self-efficacy for control, mediated the association between individual-level change in physical activity and physical HRQOL; and (c) individual-level change in self-efficacy for controlling MS was the strongest predictor of individual-level change in HRQOL. Physical activity and self-efficacy both might be important targets of subsequent behavioral and self-management interventions for improving the HRQOL of persons with MS, although self-efficacy is seemingly more important than physical activity.

A loss-of-function mutation in the nucleoporin AtNUP160 indicates that normal auxin signalling is required for a proper ethylene response in Arabidopsis

PubMed Central

Robles, Linda M.; Deslauriers, Stephen D.; Alvarez, Ashley A.; Larsen, Paul B.

2012-01-01

As part of a continuing effort to elucidate mechanisms that regulate the magnitude of ethylene signalling, an Arabidopsis mutant with an enhanced ethylene response was identified. Subsequent characterization of this loss-of-function mutant revealed severe hypocotyl shortening in the presence of saturating ethylene along with increased expression in leaves of a subset of ethylene-responsive genes. It was subsequently determined by map-based cloning that the mutant (sar1-7) represents a loss-of-function mutation in the previously described nucleoporin AtNUP160 (At1g33410, SAR1). In support of previously reported results, the sar1-7 mutant partially restored auxin responsiveness to roots of an rce1 loss-of-function mutant, indicating that AtNUP160/SAR1 is required for proper expression of factors responsible for the repression of auxin signalling. Analysis of arf7-1/sar1-7 and arf19-1/sar1-7 double mutants revealed that mutations affecting either ARF7 or ARF19 function almost fully blocked manifestation of the sar1-7-dependent ethylene hypersensitivity phenotype, suggesting that ARF7- and ARF19-mediated auxin signalling is responsible for regulating the magnitude of and/or competence for the ethylene response in Arabidopsis etiolated hypocotyls. Consistent with this, addition of auxin to ethylene-treated seedlings resulted in severe hypocotyl shortening, reminiscent of that seen for other eer (enhanced ethylene response) mutants, suggesting that auxin functions in part synergistically with ethylene to control hypocotyl elongation and other ethylene-dependent phenomena. PMID:22238449

Subpopulations of Ig-secreting cells induced by peroxidase immunization: discrimination according to antibody storage and secretion.

PubMed Central

Bernard, J; Jeannesson, P; Thiernesse, N; Zagury, D; Ternynck, T; Avrameas, S

1979-01-01

Mice were injected in their hind footpads with peroxidase (PO) emulsified in Freund's complete adjuvant. The development of cells secreting anti-peroxidase antibody (Ab) and cells secreting immunoglobulins (Ig) were detected in the draining popliteal lymph nodes in the subsequent 35 days, using local haemolysis plaque assay with sheep red cell blood cells coated with either PO or anti-mouse Ig antibody. Plaque-forming cells (PFC) were isolated from the centre of plaques by micromanipulation and after appropriate treatment, were examined by electron microscopy for their intracellular Ab content and in corporation of [3H]-thymidine. Four subpopulations of Ig secreting cells were distinguished: (1) cells secreting Ig without Ab function and not containing intracellular Ab detectable between days 5 and 20; (2) cells secreting Ig without Ab function but containing Ab appearing on day 6 and present throughout the immune response; (3) cells secreting Ab and containing Ab; (4) cells secreting Ab, but without detectable intracellular Ab. These last subpopulations appeared on day 7 and were found in all subsequent assays. The analysis of the kinetics of these subpopulations suggest that cells secreting Ig without Ab function might be precursors of Ab secreting cells. Images Figure 2a Figure 2b Figure 4 PMID:374259

Impact of liver volume and liver function on posthepatectomy liver failure after portal vein embolization- A multivariable cohort analysis.

PubMed

Alizai, Patrick H; Haelsig, Annabel; Bruners, Philipp; Ulmer, Florian; Klink, Christian D; Dejong, Cornelis H C; Neumann, Ulf P; Schmeding, Maximilian

2018-01-01

Liver failure remains a life-threatening complication after liver resection, and is difficult to predict preoperatively. This retrospective cohort study evaluated different preoperative factors in regard to their impact on posthepatectomy liver failure (PHLF) after extended liver resection and previous portal vein embolization (PVE). Patient characteristics, liver function and liver volumes of patients undergoing PVE and subsequent liver resection were analyzed. Liver function was determined by the LiMAx test (enzymatic capacity of cytochrome P450 1A2). Factors associated with the primary end point PHLF (according to ISGLS definition) were identified through multivariable analysis. Secondary end points were 30-day mortality and morbidity. 95 patients received PVE, of which 64 patients underwent major liver resection. PHLF occurred in 7 patients (11%). Calculated postoperative liver function was significantly lower in patients with PHLF than in patients without PHLF (67 vs. 109 μg/kg/h; p = 0.01). Other factors associated with PHLF by univariable analysis were age, future liver remnant, MELD score, ASA score, renal insufficiency and heart insufficiency. By multivariable analysis, future liver remnant was the only factor significantly associated with PHLF (p = 0.03). Mortality and morbidity rates were 4.7% and 29.7% respectively. Future liver remnant is the only preoperative factor with a significant impact on PHLF. Assessment of preoperative liver function may additionally help identify patients at risk for PHLF.

Cancerouspdomains: comprehensive analysis of cancer type-specific recurrent somatic mutations in proteins and domains.

PubMed

Hashemi, Seirana; Nowzari Dalini, Abbas; Jalali, Adrin; Banaei-Moghaddam, Ali Mohammad; Razaghi-Moghadam, Zahra

2017-08-16

Discriminating driver mutations from the ones that play no role in cancer is a severe bottleneck in elucidating molecular mechanisms underlying cancer development. Since protein domains are representatives of functional regions within proteins, mutations on them may disturb the protein functionality. Therefore, studying mutations at domain level may point researchers to more accurate assessment of the functional impact of the mutations. This article presents a comprehensive study to map mutations from 29 cancer types to both sequence- and structure-based domains. Statistical analysis was performed to identify candidate domains in which mutations occur with high statistical significance. For each cancer type, the corresponding type-specific domains were distinguished among all candidate domains. Subsequently, cancer type-specific domains facilitated the identification of specific proteins for each cancer type. Besides, performing interactome analysis on specific proteins of each cancer type showed high levels of interconnectivity among them, which implies their functional relationship. To evaluate the role of mitochondrial genes, stem cell-specific genes and DNA repair genes in cancer development, their mutation frequency was determined via further analysis. This study has provided researchers with a publicly available data repository for studying both CATH and Pfam domain regions on protein-coding genes. Moreover, the associations between different groups of genes/domains and various cancer types have been clarified. The work is available at http://www.cancerouspdomains.ir .

Study of Staphylococcus aureus N315 Pathogenic Genes by Text Mining and Enrichment Analysis of Pathways and Operons.

PubMed

Yang, Chun-Feng; Gou, Wei-Hui; Dai, Xin-Lun; Li, Yu-Mei

2018-06-01

Staphylococcus aureus (S. aureus) is a versatile pathogen found in many environments and can cause nosocomial infections in the community and hospitals. S. aureus infection is an increasingly serious threat to global public health that requires action across many government bodies, medical and health sectors, and scientific research institutions. In the present study, S. aureus N315 genes that have been shown in the literature to be pathogenic were extracted using a bibliometric method for functional enrichment analysis of pathways and operons to statistically discover novel pathogenic genes associated with S. aureus N315. A total of 383 pathogenic genes were mined from the literature using bibliometrics, and subsequently a few new pathogenic genes of S. aureus N315 were identified by functional enrichment analysis of pathways and operons. The discovery of these novel S. aureus N315 pathogenic genes is of great significance to treat S. aureus induced diseases and identify potential diagnostic markers, thus providing theoretical fundamentals for epidemiological prevention.

Analysis of Protein Kinetics Using Fluorescence Recovery After Photobleaching (FRAP).

PubMed

Giakoumakis, Nickolaos Nikiforos; Rapsomaniki, Maria Anna; Lygerou, Zoi

2017-01-01

Fluorescence recovery after photobleaching (FRAP) is a cutting-edge live-cell functional imaging technique that enables the exploration of protein dynamics in individual cells and thus permits the elucidation of protein mobility, function, and interactions at a single-cell level. During a typical FRAP experiment, fluorescent molecules in a defined region of interest within the cell are bleached by a short and powerful laser pulse, while the recovery of the fluorescence in the region is monitored over time by time-lapse microscopy. FRAP experimental setup and image acquisition involve a number of steps that need to be carefully executed to avoid technical artifacts. Equally important is the subsequent computational analysis of FRAP raw data, to derive quantitative information on protein diffusion and binding parameters. Here we present an integrated in vivo and in silico protocol for the analysis of protein kinetics using FRAP. We focus on the most commonly encountered challenges and technical or computational pitfalls and their troubleshooting so that valid and robust insight into protein dynamics within living cells is gained.

The bioimpedance analysis of a parenchyma of a liver in the conditions of its extensive resection in experiment

NASA Astrophysics Data System (ADS)

Agibalov, D. Y.; Panchenkov, D. N.; Chertyuk, V. B.; Leonov, S. D.; Astakhov, D. A.

2017-01-01

The liver failure which is result of disharmony of functionality of a liver to requirements of an organism is the main reason for unsatisfactory results of an extensive resection of a liver. However, uniform effective criterion of definition of degree of a liver failure it isn’t developed now. One of data acquisition methods about a morfo-functional condition of internals is the bioimpedance analysis (BIA) based on impedance assessment (full electric resistance) of a biological tissue. Measurements of an impedance are used in medicine and biology for the characteristic of physical properties of living tissue, studying of the changes bound to a functional state and its structural features. In experimental conditions we carried out an extensive resection of a liver on 27 white laboratory rats of the Vistar line. The comparative characteristic of data of a bioimpedansometriya in intraoperative and after the operational period with the main existing methods of assessment of a functional condition of a liver was carried out. By results of the work performed by us it is possible to claim that the bioimpedance analysis of a liver on the basis of an invasive bioimpedansometriya allows to estimate morphological features and functional activity of a liver before performance of an extensive resection of a liver. The data obtained during scientific work are experimental justification for use of an impedansometriya during complex assessment of functional reserves of a liver. Preliminary data of clinical approbation at a stage of introduction of a technique speak about rather high informational content of a bioimpedansometriya. The subsequent analysis of efficiency of the invasive bioimpedance analysis of a liver requires further accumulation of clinical data. However even at this stage the method showed the prospect for further use in clinical surgical hepathology.

A Christoffel function weighted least squares algorithm for collocation approximations

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

Narayan, Akil; Jakeman, John D.; Zhou, Tao

Here, we propose, theoretically investigate, and numerically validate an algorithm for the Monte Carlo solution of least-squares polynomial approximation problems in a collocation framework. Our investigation is motivated by applications in the collocation approximation of parametric functions, which frequently entails construction of surrogates via orthogonal polynomials. A standard Monte Carlo approach would draw samples according to the density defining the orthogonal polynomial family. Our proposed algorithm instead samples with respect to the (weighted) pluripotential equilibrium measure of the domain, and subsequently solves a weighted least-squares problem, with weights given by evaluations of the Christoffel function. We present theoretical analysis tomore » motivate the algorithm, and numerical results that show our method is superior to standard Monte Carlo methods in many situations of interest.« less

Genomic Identification and Analysis of Shared Cis-regulator Elements in a Developmentally Critical homeobox Cluster

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

Chris Amemiya

2003-04-01

The goals of this project were to isolate, characterize, and sequence the Dlx3/Dlx7 bigene cluster from twelve different species of mammals. The Dlx3 and Dlx7 genes are known to encode homeobox transcription factors involved in patterning of structures in the vertebrate jaw as well as vertebrate limbs. Genomic sequences from the respective taxa will subsequently be compared in order to identify conserved non-coding sequences that are potential cis-regulatory elements. Based on the comparisons they will fashion transgenic mouse experiments to functionally test the strength of the potential cis-regulatory elements. A goal of the project is to attempt to identify thosemore » elements that may function in coordinately regulating both Dlx3 and Dlx7 functions.« less

A Christoffel function weighted least squares algorithm for collocation approximations

DOE PAGES

Narayan, Akil; Jakeman, John D.; Zhou, Tao

2016-11-28

Here, we propose, theoretically investigate, and numerically validate an algorithm for the Monte Carlo solution of least-squares polynomial approximation problems in a collocation framework. Our investigation is motivated by applications in the collocation approximation of parametric functions, which frequently entails construction of surrogates via orthogonal polynomials. A standard Monte Carlo approach would draw samples according to the density defining the orthogonal polynomial family. Our proposed algorithm instead samples with respect to the (weighted) pluripotential equilibrium measure of the domain, and subsequently solves a weighted least-squares problem, with weights given by evaluations of the Christoffel function. We present theoretical analysis tomore » motivate the algorithm, and numerical results that show our method is superior to standard Monte Carlo methods in many situations of interest.« less

Scientific approaches to science policy.

PubMed

Berg, Jeremy M

2013-11-01

The development of robust science policy depends on use of the best available data, rigorous analysis, and inclusion of a wide range of input. While director of the National Institute of General Medical Sciences (NIGMS), I took advantage of available data and emerging tools to analyze training time distribution by new NIGMS grantees, the distribution of the number of publications as a function of total annual National Institutes of Health support per investigator, and the predictive value of peer-review scores on subsequent scientific productivity. Rigorous data analysis should be used to develop new reforms and initiatives that will help build a more sustainable American biomedical research enterprise.

Model 0A wind turbine generator FMEA

NASA Technical Reports Server (NTRS)

Klein, William E.; Lalli, Vincent R.

1989-01-01

The results of Failure Modes and Effects Analysis (FMEA) conducted for the Wind Turbine Generators are presented. The FMEA was performed for the functional modes of each system, subsystem, or component. The single-point failures were eliminated for most of the systems. The blade system was the only exception. The qualitative probability of a blade separating was estimated at level D-remote. Many changes were made to the hardware as a result of this analysis. The most significant change was the addition of the safety system. Operational experience and need to improve machine availability have resulted in subsequent changes to the various systems which are also reflected in this FMEA.

HRLSim: a high performance spiking neural network simulator for GPGPU clusters.

PubMed

Minkovich, Kirill; Thibeault, Corey M; O'Brien, Michael John; Nogin, Aleksey; Cho, Youngkwan; Srinivasa, Narayan

2014-02-01

Modeling of large-scale spiking neural models is an important tool in the quest to understand brain function and subsequently create real-world applications. This paper describes a spiking neural network simulator environment called HRL Spiking Simulator (HRLSim). This simulator is suitable for implementation on a cluster of general purpose graphical processing units (GPGPUs). Novel aspects of HRLSim are described and an analysis of its performance is provided for various configurations of the cluster. With the advent of inexpensive GPGPU cards and compute power, HRLSim offers an affordable and scalable tool for design, real-time simulation, and analysis of large-scale spiking neural networks.

Technical advance: live-imaging analysis of human dendritic cell migrating behavior under the influence of immune-stimulating reagents in an organotypic model of lung.

PubMed

Nguyen Hoang, Anh Thu; Chen, Puran; Björnfot, Sofia; Högstrand, Kari; Lock, John G; Grandien, Alf; Coles, Mark; Svensson, Mattias

2014-09-01

This manuscript describes technical advances allowing manipulation and quantitative analyses of human DC migratory behavior in lung epithelial tissue. DCs are hematopoietic cells essential for the maintenance of tissue homeostasis and the induction of tissue-specific immune responses. Important functions include cytokine production and migration in response to infection for the induction of proper immune responses. To design appropriate strategies to exploit human DC functional properties in lung tissue for the purpose of clinical evaluation, e.g., candidate vaccination and immunotherapy strategies, we have developed a live-imaging assay based on our previously described organotypic model of the human lung. This assay allows provocations and subsequent quantitative investigations of DC functional properties under conditions mimicking morphological and functional features of the in vivo parental tissue. We present protocols to set up and prepare tissue models for 4D (x, y, z, time) fluorescence-imaging analysis that allow spatial and temporal studies of human DCs in live epithelial tissue, followed by flow cytometry analysis of DCs retrieved from digested tissue models. This model system can be useful for elucidating incompletely defined pathways controlling DC functional responses to infection and inflammation in lung epithelial tissue, as well as the efficacy of locally administered candidate interventions. © 2014 Society for Leukocyte Biology.

Nano-Aptasensing in Mycotoxin Analysis: Recent Updates and Progress.

PubMed

Rhouati, Amina; Bulbul, Gonca; Latif, Usman; Hayat, Akhtar; Li, Zhan-Hong; Marty, Jean Louis

2017-10-28

Recent years have witnessed an overwhelming integration of nanomaterials in the fabrication of biosensors. Nanomaterials have been incorporated with the objective to achieve better analytical figures of merit in terms of limit of detection, linear range, assays stability, low production cost, etc. Nanomaterials can act as immobilization support, signal amplifier, mediator and artificial enzyme label in the construction of aptasensors. We aim in this work to review the recent progress in mycotoxin analysis. This review emphasizes on the function of the different nanomaterials in aptasensors architecture. We subsequently relate their features to the analytical performance of the given aptasensor towards mycotoxins monitoring. In the same context, a critically analysis and level of success for each nano-aptasensing design will be discussed. Finally, current challenges in nano-aptasensing design for mycotoxin analysis will be highlighted.

Developmental Change in the Influence of Domain-General Abilities and Domain-Specific Knowledge on Mathematics Achievement: An Eight-Year Longitudinal Study

PubMed Central

Geary, David C.; Nicholas, Alan; Li, Yaoran; Sun, Jianguo

2016-01-01

The contributions of domain-general abilities and domain-specific knowledge to subsequent mathematics achievement were longitudinally assessed (n = 167) through 8th grade. First grade intelligence and working memory and prior grade reading achievement indexed domain-general effects and domain-specific effects were indexed by prior grade mathematics achievement and mathematical cognition measures of prior grade number knowledge, addition skills, and fraction knowledge. Use of functional data analysis enabled grade-by-grade estimation of overall domain-general and domain-specific effects on subsequent mathematics achievement, the relative importance of individual domain-general and domain-specific variables on this achievement, and linear and non-linear across-grade estimates of these effects. The overall importance of domain-general abilities for subsequent achievement was stable across grades, with working memory emerging as the most important domain-general ability in later grades. The importance of prior mathematical competencies on subsequent mathematics achievement increased across grades, with number knowledge and arithmetic skills critical in all grades and fraction knowledge in later grades. Overall, domain-general abilities were more important than domain-specific knowledge for mathematics learning in early grades but general abilities and domain-specific knowledge were equally important in later grades. PMID:28781382

Electrophoresis gel image processing and analysis using the KODAK 1D software.

PubMed

Pizzonia, J

2001-06-01

The present article reports on the performance of the KODAK 1D Image Analysis Software for the acquisition of information from electrophoresis experiments and highlights the utility of several mathematical functions for subsequent image processing, analysis, and presentation. Digital images of Coomassie-stained polyacrylamide protein gels containing molecular weight standards and ethidium bromide stained agarose gels containing DNA mass standards are acquired using the KODAK Electrophoresis Documentation and Analysis System 290 (EDAS 290). The KODAK 1D software is used to optimize lane and band identification using features such as isomolecular weight lines. Mathematical functions for mass standard representation are presented, and two methods for estimation of unknown band mass are compared. Given the progressive transition of electrophoresis data acquisition and daily reporting in peer-reviewed journals to digital formats ranging from 8-bit systems such as EDAS 290 to more expensive 16-bit systems, the utility of algorithms such as Gaussian modeling, which can correct geometric aberrations such as clipping due to signal saturation common at lower bit depth levels, is discussed. Finally, image-processing tools that can facilitate image preparation for presentation are demonstrated.

Identification of functional candidates amongst hypothetical proteins of Treponema pallidum ssp. pallidum.

PubMed

Naqvi, Ahmad Abu Turab; Shahbaaz, Mohd; Ahmad, Faizan; Hassan, Md Imtaiyaz

2015-01-01

Syphilis is a globally occurring venereal disease, and its infection is propagated through sexual contact. The causative agent of syphilis, Treponema pallidum ssp. pallidum, a Gram-negative sphirochaete, is an obligate human parasite. Genome of T. pallidum ssp. pallidum SS14 strain (RefSeq NC_010741.1) encodes 1,027 proteins, of which 444 proteins are known as hypothetical proteins (HPs), i.e., proteins of unknown functions. Here, we performed functional annotation of HPs of T. pallidum ssp. pallidum using various database, domain architecture predictors, protein function annotators and clustering tools. We have analyzed the sequences of 444 HPs of T. pallidum ssp. pallidum and subsequently predicted the function of 207 HPs with a high level of confidence. However, functions of 237 HPs are predicted with less accuracy. We found various enzymes, transporters, binding proteins in the annotated group of HPs that may be possible molecular targets, facilitating for the survival of pathogen. Our comprehensive analysis helps to understand the mechanism of pathogenesis to provide many novel potential therapeutic interventions.

Audio feature extraction using probability distribution function

NASA Astrophysics Data System (ADS)

Suhaib, A.; Wan, Khairunizam; Aziz, Azri A.; Hazry, D.; Razlan, Zuradzman M.; Shahriman A., B.

2015-05-01

Voice recognition has been one of the popular applications in robotic field. It is also known to be recently used for biometric and multimedia information retrieval system. This technology is attained from successive research on audio feature extraction analysis. Probability Distribution Function (PDF) is a statistical method which is usually used as one of the processes in complex feature extraction methods such as GMM and PCA. In this paper, a new method for audio feature extraction is proposed which is by using only PDF as a feature extraction method itself for speech analysis purpose. Certain pre-processing techniques are performed in prior to the proposed feature extraction method. Subsequently, the PDF result values for each frame of sampled voice signals obtained from certain numbers of individuals are plotted. From the experimental results obtained, it can be seen visually from the plotted data that each individuals' voice has comparable PDF values and shapes.

Investigation of static and dynamic behavior of functionally graded piezoelectric actuated Poly-Si micro cantilever probe

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

Pandey, Vibhuti Bhushan; Parashar, Sandeep Kumar, E-mail: skparashar@rtu.ac.in

In the present paper a novel functionally graded piezoelectric (FGP) actuated Poly-Si micro cantilever probe is proposed for atomic force microscope. The shear piezoelectric coefficient d{sub 15} has much higher value than coupling coefficients d{sub 31} and d{sub 33}, hence in the present work the micro cantilever beam actuated by d{sub 15} effect is utilized. The material properties are graded in the thickness direction of actuator by a simple power law. A three dimensional finite element analysis has been performed using COMSOL Multiphysics® (version 4.2) software. Tip deflection and free vibration analysis for the micro cantilever probe has been done.more » The results presented in the paper shall be useful in the design of micro cantilever probe and their subsequent utilization in atomic force microscopes.« less

A robust anonymous biometric-based authenticated key agreement scheme for multi-server environments

PubMed Central

Huang, Yuanfei; Ma, Fangchao

2017-01-01

In order to improve the security in remote authentication systems, numerous biometric-based authentication schemes using smart cards have been proposed. Recently, Moon et al. presented an authentication scheme to remedy the flaws of Lu et al.’s scheme, and claimed that their improved protocol supports the required security properties. Unfortunately, we found that Moon et al.’s scheme still has weaknesses. In this paper, we show that Moon et al.’s scheme is vulnerable to insider attack, server spoofing attack, user impersonation attack and guessing attack. Furthermore, we propose a robust anonymous multi-server authentication scheme using public key encryption to remove the aforementioned problems. From the subsequent formal and informal security analysis, we demonstrate that our proposed scheme provides strong mutual authentication and satisfies the desirable security requirements. The functional and performance analysis shows that the improved scheme has the best secure functionality and is computational efficient. PMID:29121050

A robust anonymous biometric-based authenticated key agreement scheme for multi-server environments.

PubMed

Guo, Hua; Wang, Pei; Zhang, Xiyong; Huang, Yuanfei; Ma, Fangchao

2017-01-01

In order to improve the security in remote authentication systems, numerous biometric-based authentication schemes using smart cards have been proposed. Recently, Moon et al. presented an authentication scheme to remedy the flaws of Lu et al.'s scheme, and claimed that their improved protocol supports the required security properties. Unfortunately, we found that Moon et al.'s scheme still has weaknesses. In this paper, we show that Moon et al.'s scheme is vulnerable to insider attack, server spoofing attack, user impersonation attack and guessing attack. Furthermore, we propose a robust anonymous multi-server authentication scheme using public key encryption to remove the aforementioned problems. From the subsequent formal and informal security analysis, we demonstrate that our proposed scheme provides strong mutual authentication and satisfies the desirable security requirements. The functional and performance analysis shows that the improved scheme has the best secure functionality and is computational efficient.

Altered functional connectivity of the language network in ASD: Role of classical language areas and cerebellum☆

PubMed Central

Verly, Marjolein; Verhoeven, Judith; Zink, Inge; Mantini, Dante; Peeters, Ronald; Deprez, Sabine; Emsell, Louise; Boets, Bart; Noens, Ilse; Steyaert, Jean; Lagae, Lieven; De Cock, Paul; Rommel, Nathalie; Sunaert, Stefan

2014-01-01

The development of language, social interaction and communicative skills is remarkably different in the child with autism spectrum disorder (ASD). Atypical brain connectivity has frequently been reported in this patient population. However, the neural correlates underlying their disrupted language development and functioning are still poorly understood. Using resting state fMRI, we investigated the functional connectivity properties of the language network in a group of ASD patients with clear comorbid language impairment (ASD-LI; N = 19) and compared them to the language related connectivity properties of 23 age-matched typically developing children. A verb generation task was used to determine language components commonly active in both groups. Eight joint language components were identified and subsequently used as seeds in a resting state analysis. Interestingly, both the interregional and the seed-based whole brain connectivity analysis showed preserved connectivity between the classical intrahemispheric language centers, Wernicke's and Broca's areas. In contrast however, a marked loss of functional connectivity was found between the right cerebellar region and the supratentorial regulatory language areas. Also, the connectivity between the interhemispheric Broca regions and modulatory control dorsolateral prefrontal region was found to be decreased. This disruption of normal modulatory control and automation function by the cerebellum may underlie the abnormal language function in children with ASD-LI. PMID:24567909

Field Analysis and Potential Theory

DTIC Science & Technology

1985-06-01

Levi - Civita , who subsequently wrote 4 "We can find the essentials of Maxwell’s theory even while starting from the classical laws. It is sufficient to...scalar or level with respect to V when V has the same value at all points of the surface. By definition, two level surfaces corresponding to...function having continuous partialBV BV Byhoghug 1ein sae"P n derivatives L-x-iy and L throughout a region of space R, and let P and P be two interior

Exchange of Stuttering From Function Words to Content Words With Age

PubMed Central

Howell, Peter; Au-Yeung, James; Sackin, Stevie

2007-01-01

Dysfluencies on function words in the speech of people who stutter mainly occur when function words precede, rather than follow, content words (Au-Yeung, Howell, & Pilgrim, 1998). It is hypothesized that such function word dysfluencies occur when the plan for the subsequent content word is not ready for execution. Repetition and hesitation on the function words buys time to complete the plan for the content word. Stuttering arises when speakers abandon the use of this delaying strategy and carry on, attempting production of the subsequent, partly prepared content word. To test these hypotheses, the relationship between dysfluency on function and content words was investigated in the spontaneous speech of 51 people who stutter and 68 people who do not stutter. These participants were subdivided into the following age groups: 2–6-year-olds, 7–9-year-olds, 10–12-year-olds, teenagers (13–18 years), and adults (20–40 years). Very few dysfluencies occurred for either fluency group on function words that occupied a position after a content word. For both fluency groups, dysfluency within each phonological word occurred predominantly on either the function word preceding the content word or on the content word itself, but not both. Fluent speakers had a higher percentage of dysfluency on initial function words than content words. Whether dysfluency occurred on initial function words or content words changed over age groups for speakers who stutter. For the 2–6-year-old speakers that stutter, there was a higher percentage of dysfluencies on initial function words than content words. In subsequent age groups, dysfluency decreased on function words and increased on content words. These data are interpreted as suggesting that fluent speakers use repetition of function words to delay production of the subsequent content words, whereas people who stutter carry on and attempt a content word on the basis of an incomplete plan. PMID:10229451

Distinguishing between taskwork and teamwork planning in teams: relations with coordination and interpersonal processes.

PubMed

Fisher, David M

2014-05-01

Planning in teams represents a critical process that lays the groundwork for effective team functioning. The current investigation examined whether emergent team planning can be meaningfully characterized in terms of a distinction between planning that focuses on taskwork and planning that focuses on teamwork. In Study 1, items written to reflect commonly identified indicators of team planning were subjected to an exploratory factor analysis. In Study 2, slightly modified items were provided to a separate sample, and a confirmatory factor analysis was conducted. In Study 3, the relationships between the different forms of planning and other team processes (i.e., coordination, interpersonal processes) were examined in order to determine whether there are unique relationships for task-focused and team-focused planning. Results from the first 2 studies provided support for a 2-factor structure of team planning, whereas Study 3 found independent relationships for taskwork and teamwork planning with subsequent team processes. Both forms of planning also exhibited indirect relationships with team performance via the mediating role of subsequent team processes. (c) 2014 APA, all rights reserved.

ANTONIA perfusion and stroke. A software tool for the multi-purpose analysis of MR perfusion-weighted datasets and quantitative ischemic stroke assessment.

PubMed

Forkert, N D; Cheng, B; Kemmling, A; Thomalla, G; Fiehler, J

2014-01-01

The objective of this work is to present the software tool ANTONIA, which has been developed to facilitate a quantitative analysis of perfusion-weighted MRI (PWI) datasets in general as well as the subsequent multi-parametric analysis of additional datasets for the specific purpose of acute ischemic stroke patient dataset evaluation. Three different methods for the analysis of DSC or DCE PWI datasets are currently implemented in ANTONIA, which can be case-specifically selected based on the study protocol. These methods comprise a curve fitting method as well as a deconvolution-based and deconvolution-free method integrating a previously defined arterial input function. The perfusion analysis is extended for the purpose of acute ischemic stroke analysis by additional methods that enable an automatic atlas-based selection of the arterial input function, an analysis of the perfusion-diffusion and DWI-FLAIR mismatch as well as segmentation-based volumetric analyses. For reliability evaluation, the described software tool was used by two observers for quantitative analysis of 15 datasets from acute ischemic stroke patients to extract the acute lesion core volume, FLAIR ratio, perfusion-diffusion mismatch volume with manually as well as automatically selected arterial input functions, and follow-up lesion volume. The results of this evaluation revealed that the described software tool leads to highly reproducible results for all parameters if the automatic arterial input function selection method is used. Due to the broad selection of processing methods that are available in the software tool, ANTONIA is especially helpful to support image-based perfusion and acute ischemic stroke research projects.

Correlation between hip function and knee kinematics evaluated by three-dimensional motion analysis during lateral and medial side-hopping.

PubMed

Itoh, Hiromitsu; Takiguchi, Kohei; Shibata, Yohei; Okubo, Satoshi; Yoshiya, Shinichi; Kuroda, Ryosuke

2016-09-01

[Purpose] Kinematic and kinetic characteristics of the limb during side-hopping and hip/knee interaction during this motion have not been clarified. The purposes of this study were to examine the biomechanical parameters of the knee during side hop and analyze its relationship with clinical measurements of hip function. [Subjects and Methods] Eleven male college rugby players were included. A three-dimensional motion analysis system was used to assess motion characteristics of the knee during side hop. In addition, hip range of motion and muscle strength were evaluated. Subsequently, the relationship between knee motion and the clinical parameters of the hip was analyzed. [Results] In the lateral touchdown phase, the knee was positioned in an abducted and externally rotated position, and increasing abduction moment was applied to the knee. An analysis of the interaction between knee motion and hip function showed that range of motion for hip internal rotation was significantly correlated with external rotation angle and external rotation/abduction moments of the knee during the lateral touchdown phase. [Conclusion] Range of motion for hip internal rotation should be taken into consideration for identifying the biomechanical characteristics in the side hop test results.

Correlation between hip function and knee kinematics evaluated by three-dimensional motion analysis during lateral and medial side-hopping

PubMed Central

Itoh, Hiromitsu; Takiguchi, Kohei; Shibata, Yohei; Okubo, Satoshi; Yoshiya, Shinichi; Kuroda, Ryosuke

2016-01-01

[Purpose] Kinematic and kinetic characteristics of the limb during side-hopping and hip/knee interaction during this motion have not been clarified. The purposes of this study were to examine the biomechanical parameters of the knee during side hop and analyze its relationship with clinical measurements of hip function. [Subjects and Methods] Eleven male college rugby players were included. A three-dimensional motion analysis system was used to assess motion characteristics of the knee during side hop. In addition, hip range of motion and muscle strength were evaluated. Subsequently, the relationship between knee motion and the clinical parameters of the hip was analyzed. [Results] In the lateral touchdown phase, the knee was positioned in an abducted and externally rotated position, and increasing abduction moment was applied to the knee. An analysis of the interaction between knee motion and hip function showed that range of motion for hip internal rotation was significantly correlated with external rotation angle and external rotation/abduction moments of the knee during the lateral touchdown phase. [Conclusion] Range of motion for hip internal rotation should be taken into consideration for identifying the biomechanical characteristics in the side hop test results. PMID:27799670

Leisure time physical activity and subsequent physical and mental health functioning among midlife Finnish, British and Japanese employees: a follow-up study in three occupational cohorts.

PubMed

Lahti, Jouni; Sabia, Séverine; Singh-Manoux, Archana; Kivimäki, Mika; Tatsuse, Takashi; Yamada, Masaaki; Sekine, Michikazu; Lallukka, Tea

2016-01-06

The aim of this study was to examine whether leisure time physical activity contributes to subsequent physical and mental health functioning among midlife employees. The associations were tested in three occupational cohorts from Finland, Britain and Japan. Cohort study. Finland, Britain and Japan. Prospective employee cohorts from the Finnish Helsinki Health Study (2000-2002 and 2007, n=5958), British Whitehall II study (1997-1999 and 2003-2004, n=4142) and Japanese Civil Servants Study (1998-1999 and 2003, n=1768) were used. Leisure time physical activity was classified into three groups: inactive, moderately active and vigorously active. Mean scores of physical and mental health functioning (SF-36) at follow-up were examined. Physical activity was associated with better subsequent physical health functioning in all three cohorts, however, with varying magnitude and some gender differences. Differences were the clearest among Finnish women (inactive: 46.0, vigorously active: 49.5) and men (inactive: 47.8, active vigorous: 51.1) and British women (inactive: 47.3, active vigorous: 50.4). In mental health functioning, the differences were generally smaller and not that clearly related to the intensity of physical activity. Emerging differences in health functioning were relatively small. Vigorous physical activity was associated with better subsequent physical health functioning in all three cohorts with varying magnitude. For mental health functioning, the intensity of physical activity was less important. Promoting leisure time physical activity may prove useful for the maintenance of health functioning among midlife employees. 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/

Recombinational Cloning Using Gateway and In-Fusion Cloning Schemes

PubMed Central

Throop, Andrea L.; LaBaer, Joshua

2015-01-01

The comprehensive study of protein structure and function, or proteomics, depends on the obtainability of full-length cDNAs in species-specific expression vectors and subsequent functional analysis of the expressed protein. Recombinational cloning is a universal cloning technique based on site-specific recombination that is independent of the insert DNA sequence of interest, which differentiates this method from the classical restriction enzyme-based cloning methods. Recombinational cloning enables rapid and efficient parallel transfer of DNA inserts into multiple expression systems. This unit summarizes strategies for generating expression-ready clones using the most popular recombinational cloning technologies, including the commercially available Gateway® (Life Technologies) and In-Fusion® (Clontech) cloning technologies. PMID:25827088

Laser modification of graphene oxide layers

NASA Astrophysics Data System (ADS)

Malinský, Petr; Macková, Anna; Cutroneo, Mariapompea; Siegel, Jakub; Bohačová, Marie; Klímova, Kateřina; Švorčík, Václav; Sofer, Zdenĕk

2018-01-01

The effect of linearly polarized laser irradiation with various energy densities was successfully used for reduction of graphene oxide (GO). The ion beam analytical methods (RBS, ERDA) were used to follow the elemental composition which is expected as the consequence of GO reduction. The chemical composition analysis was accompanied by structural study showing changed functionalities in the irradiated GO foils using spectroscopy techniques including XPS, FTIR and Raman spectroscopy. The AFM was employed to identify the surface morphology and electric properties evolution were subsequently studied using standard two point method measurement. The used analytical methods report on reduction of irradiated graphene oxide on the surface and the decrease of surface resistivity as a growing function of the laser beam energy density.

Improving reliability of aggregation, numerical simulation and analysis of complex systems by empirical data

NASA Astrophysics Data System (ADS)

Dobronets, Boris S.; Popova, Olga A.

2018-05-01

The paper considers a new approach of regression modeling that uses aggregated data presented in the form of density functions. Approaches to Improving the reliability of aggregation of empirical data are considered: improving accuracy and estimating errors. We discuss the procedures of data aggregation as a preprocessing stage for subsequent to regression modeling. An important feature of study is demonstration of the way how represent the aggregated data. It is proposed to use piecewise polynomial models, including spline aggregate functions. We show that the proposed approach to data aggregation can be interpreted as the frequency distribution. To study its properties density function concept is used. Various types of mathematical models of data aggregation are discussed. For the construction of regression models, it is proposed to use data representation procedures based on piecewise polynomial models. New approaches to modeling functional dependencies based on spline aggregations are proposed.

Going outdoors daily predicts long-term functional and health benefits among ambulatory older people.

PubMed

Jacobs, Jeremy M; Cohen, Aaron; Hammerman-Rozenberg, Robert; Azoulay, Daniel; Maaravi, Yoram; Stessman, Jochanan

2008-04-01

This article examines the association between frequency of going out of the house and health and functional status among older people. A randomly chosen cohort of ambulatory participants born in 1920 or 1921 from the Jerusalem Longitudinal Study underwent assessments for health, functional, and psychosocial variables at ages 70 and 77. Twelve-year mortality data were collected. Women went out daily less than did men. Participants going out daily at age 70 reported significantly fewer new complaints at age 77 of musculoskeletal pain, sleep problems, urinary incontinence, and decline in activities of daily living (ADLs). Logistic regression analysis indicated that not going out daily at age 70 was predictive of subsequent dependence in ADL, poor self-rated health, and urinary incontinence at age 77. Going out daily is beneficial among independent older people, correlating with reduced functional decline and improved health measures.

A study of material damping in large space structures

NASA Technical Reports Server (NTRS)

Highsmith, A. L.; Allen, D. H.

1989-01-01

A constitutive model was developed for predicting damping as a function of damage in continuous fiber reinforced laminated composites. The damage model is a continuum formulation, and uses internal state variables to quantify damage and its subsequent effect on material response. The model is sensitive to the stacking sequence of the laminate. Given appropriate baseline data from unidirectional material, and damping as a function of damage in one crossply laminate, damage can be predicted as a function of damage in other crossply laminates. Agreement between theory and experiment was quite good. A micromechanics model was also developed for examining the influence of damage on damping. This model explicitly includes crack surfaces. The model provides reasonable predictions of bending stiffness as a function of damage. Damping predictions are not in agreement with the experiment. This is thought to be a result of dissipation mechanisms such as friction, which are not presently included in the analysis.

Preparation and surface functionalization of MWCNTs: study of the composite materials produced by the interaction with an iron phthalocyanine complex

PubMed Central

2011-01-01

Carbon nanotubes [CNTs] were synthesized by the catalytic vapor decomposition method. Thereafter, they were functionalized in order to incorporate the oxygen groups (OCNT) and subsequently the amine groups (ACNT). All three CNTs (the as-synthesized and functionalized) underwent reaction with an iron organometallic complex (FePcS), iron(III) phthalocyanine-4,4",4",4""-tetrasulfonic acid, in order to study the nature of the interaction between this complex and the CNTs and the potential formation of nanocomposite materials. Transmission electronic microscopy, N2 adsorption at 77 K, thermogravimetric analysis, temperature-programmed desorption, and X-ray photoelectron spectroscopy were the characterization techniques employed to confirm the successful functionalization of CNTs as well as the type of interaction existing with the FePcS. All results obtained led to the same conclusion: There were no specific chemical interactions between CNTs and the fixed FePcS. PMID:21711881

Preparation and surface functionalization of MWCNTs: study of the composite materials produced by the interaction with an iron phthalocyanine complex

NASA Astrophysics Data System (ADS)

Asedegbega-Nieto, Esther; Pérez-Cadenas, María; Carter, Jonathan; Anderson, James A.; Guerrero-Ruiz, Antonio

2011-04-01

Carbon nanotubes [CNTs] were synthesized by the catalytic vapor decomposition method. Thereafter, they were functionalized in order to incorporate the oxygen groups (OCNT) and subsequently the amine groups (ACNT). All three CNTs (the as-synthesized and functionalized) underwent reaction with an iron organometallic complex (FePcS), iron(III) phthalocyanine-4,4",4",4""-tetrasulfonic acid, in order to study the nature of the interaction between this complex and the CNTs and the potential formation of nanocomposite materials. Transmission electronic microscopy, N2 adsorption at 77 K, thermogravimetric analysis, temperature-programmed desorption, and X-ray photoelectron spectroscopy were the characterization techniques employed to confirm the successful functionalization of CNTs as well as the type of interaction existing with the FePcS. All results obtained led to the same conclusion: There were no specific chemical interactions between CNTs and the fixed FePcS.

The Relationship between Symptom Relief and Psychosocial Functional Improvement during Acute Electroconvulsive Therapy for Patients with Major Depressive Disorder.

PubMed

Lin, Ching-Hua; Yang, Wei-Cheng

2017-07-01

We aimed to compare the degree of symptom relief to psychosocial functional (abbreviated as "functional") improvement and explore the relationships between symptom relief and functional improvement during acute electroconvulsive therapy for patients with major depressive disorder. Major depressive disorder inpatients (n=130) requiring electroconvulsive therapy were recruited. Electroconvulsive therapy was generally performed for a maximum of 12 treatments. Symptom severity, using the 17-item Hamilton Depression Rating Scale, and psychosocial functioning (abbreviated as "functioning"), using the Modified Work and Social Adjustment Scale, were assessed before electroconvulsive therapy, after every 3 electroconvulsive therapy treatments, and after the final electroconvulsive therapy. Both 17-item Hamilton Depression Rating Scale and Modified Work and Social Adjustment Scale scores were converted to T-score units to compare the degrees of changes between depressive symptoms and functioning after electroconvulsive therapy. Structural equation modeling was used to test the relationships between 17-item Hamilton Depression Rating Scale and Modified Work and Social Adjustment Scale during acute electroconvulsive therapy. One hundred sixteen patients who completed at least the first 3 electroconvulsive therapy treatments entered the analysis. Reduction of 17-item Hamilton Depression Rating Scale T-scores was significantly greater than that of Modified Work and Social Adjustment Scale T-scores at assessments 2, 3, 4, and 5. The model analyzed by structural equation modeling satisfied all indices of goodness-of-fit (chi-square = 32.882, P =.107, TLI = 0.92, CFI = 0.984, RMSEA = 0.057). The 17-item Hamilton Depression Rating Scale change did not predict subsequent Modified Work and Social Adjustment Scale change. Functioning improved less than depressive symptoms during acute electroconvulsive therapy. Symptom reduction did not predict subsequent functional improvement. Depressive symptoms and functional impairment are distinct domains and should be assessed independently to accurately reflect the effectiveness of electroconvulsive therapy. © The Author 2017. Published by Oxford University Press on behalf of CINP.

Characterizing the role of the hippocampus during episodic simulation and encoding.

PubMed

Thakral, Preston P; Benoit, Roland G; Schacter, Daniel L

2017-12-01

The hippocampus has been consistently associated with episodic simulation (i.e., the mental construction of a possible future episode). In a recent study, we identified an anterior-posterior temporal dissociation within the hippocampus during simulation. Specifically, transient simulation-related activity occurred in relatively posterior portions of the hippocampus and sustained activity occurred in anterior portions. In line with previous theoretical proposals of hippocampal function during simulation, the posterior hippocampal activity was interpreted as reflecting a transient retrieval process for the episodic details necessary to construct an episode. In contrast, the sustained anterior hippocampal activity was interpreted as reflecting the continual recruitment of encoding and/or relational processing associated with a simulation. In the present study, we provide a direct test of these interpretations by conducting a subsequent memory analysis of our previously published data to assess whether successful encoding during episodic simulation is associated with the anterior hippocampus. Analyses revealed a subsequent memory effect (i.e., later remembered > later forgotten simulations) in the anterior hippocampus. The subsequent memory effect was transient and not sustained. Taken together, the current findings provide further support for a component process model of hippocampal function during simulation. That is, unique regions of the hippocampus support dissociable processes during simulation, which include the transient retrieval of episodic information, the sustained binding of such information into a coherent episode, and the transient encoding of that episode for later retrieval. © 2017 Wiley Periodicals, Inc.

Processing communications events in parallel active messaging interface by awakening thread from wait state

DOEpatents

Archer, Charles J; Blocksome, Michael A; Ratterman, Joseph D; Smith, Brian E

2013-10-22

Processing data communications events in a parallel active messaging interface (`PAMI`) of a parallel computer that includes compute nodes that execute a parallel application, with the PAMI including data communications endpoints, and the endpoints are coupled for data communications through the PAMI and through other data communications resources, including determining by an advance function that there are no actionable data communications events pending for its context, placing by the advance function its thread of execution into a wait state, waiting for a subsequent data communications event for the context; responsive to occurrence of a subsequent data communications event for the context, awakening by the thread from the wait state; and processing by the advance function the subsequent data communications event now pending for the context.

Impact of angiotensin II on skeletal muscle metabolism and function in mice: contribution of IGF-1, Sirtuin-1 and PGC-1α.

PubMed

Kackstein, Katharina; Teren, Andrej; Matsumoto, Yasuharu; Mangner, Norman; Möbius-Winkler, Sven; Linke, Axel; Schuler, Gerhard; Punkt, Karla; Adams, Volker

2013-05-01

Activation of the renin-angiotensin-aldosterone system and increased levels of angiotensin II (Ang-II) occurs in numerous cardiovascular diseases such as chronic heart failure (CHF). Another hallmark in CHF is a reduced exercise tolerance with impaired skeletal muscle function. The aim of this study was to investigate in an animal model the impact of Ang-II on skeletal muscle function and concomitant molecular alterations. Mice were infused with Ang-II for 4 weeks. Subsequently, skeletal muscle function of the soleus muscle was assessed. Expression of selected proteins was quantified by qRT-PCR and Western blot. Infusion of Ang-II resulted in a 33% reduction of contractile force, despite a lack of changes in muscle weight. At the molecular level an increased expression of NAD(P)H oxidase and a reduced expression of Sirt1, PGC-1α and IGF-1 were noticed. No change was evident for the ubiquitin E3-ligases MuRF1 and MafBx and α-sarcomeric actin expression. Cytophotometrical analysis of the soleus muscle revealed a metabolic shift toward a glycolytic profile. This study provides direct evidence of Ang-II-mediated, metabolic deterioration of skeletal muscle function despite preserved muscle mass. One may speculate that the Ang-II-mediated loss of muscle force is due to an activation of NAD(P)H oxidase expression and a subsequent ROS-induced down regulation of IGF-1, PGC-1α and Sirt1. Copyright © 2012 Elsevier GmbH. All rights reserved.

Pivotal roles of Fezf2 in differentiation of cone OFF bipolar cells and functional maturation of cone ON bipolar cells in retina.

PubMed

Suzuki-Kerr, Haruna; Iwagawa, Toshiro; Sagara, Hiroshi; Mizota, Atsushi; Suzuki, Yutaka; Watanabe, Sumiko

2018-06-01

During development of the retina, common retinal progenitor cells give rise to six classes of neurons that subsequently further diversify into more than 55 subtypes of neuronal subtypes. Here, we have investigated the expression and function of Fezf2, Fez zinc finger family of protein, in the developing mouse retina. Expression of Fezf2 transcripts was strongly observed in the embryonic retinal progenitors at E14.5 and declined quickly in subsequent development of retina. Then, in postnatal stage at around day 8, Fezf2 was transiently expressed then declined again. Loss-of-function analysis using retinas from mice in which Fezf2 coding region was substituted with β-galactosidase showed that Fezf2 is expressed in a subset of cone OFF bipolar cells and required for their differentiation. Using electroretinogram, we found that Fezf2 knockout retina exhibited significantly reduced photopic b-wave, suggesting functional abnormality of cone ON bipolar cells. Furthermore, reduced expression of synaptic protein Trpm1 and structural alteration of ON bipolar cell invagination, both of which affected cone photoreceptor terminal synaptic activity, was identified by transmission electron microscopy and immunohistochemistry, respectively. Taken together, our results show that Fezf2 is indispensable in differentiation of bipolar precursors into cone OFF bipolar cells and in functional maturation of cone ON bipolar cells during development of mouse retina. These results contribute to our understanding of how diversity of neuronal subtypes and hence specificity of neuronal connections are established in the retina by intrinsic cues. Copyright © 2018 Elsevier Ltd. All rights reserved.

Efficient production and purification of functional bacteriorhodopsin with a wheat-germ cell-free system and a combination of Fos-choline and CHAPS detergents.

PubMed

Genji, Takahisa; Nozawa, Akira; Tozawa, Yuzuru

2010-10-01

Cell-free translation is one potential approach to the production of functional transmembrane proteins. We have now examined various detergents as supplements to a wheat-germ cell-free system in order to optimize the production and subsequent purification of a functional model transmembrane protein, bacteriorhodopsin. We found that Fos-choline and CHAPS detergents counteracted each other's inhibitory effects on cell-free translation activity and thereby allowed the efficient production and subsequent purification of functional bacteriorhodopsin in high yield. Copyright © 2010 Elsevier Inc. All rights reserved.

Loneliness and Cognitive Function in Older Adults: Findings From the Chinese Longitudinal Healthy Longevity Survey.

PubMed

Zhong, Bao-Liang; Chen, Shu-Lin; Tu, Xin; Conwell, Yeates

2017-01-01

To examine the relationship between loneliness and cognitive function and to explore the mediating role of physical health on the loneliness-cognition relationship in Chinese older adults (OAs). Data came from a nationally representative sample of 14,199 Chinese OAs (aged 65+) from 2002, 2005, 2008, and 2011 waves of the Chinese Longitudinal Healthy Longevity Survey. A latent variable cross-lagged panel model combined with mediation analysis was used to determine the relationship between loneliness and cognitive function and the mediating effect of increase in the number of chronic conditions (ΔNCCs) on the ascertained loneliness-cognition relationship. Severe loneliness at prior assessment points was significantly associated with poorer cognitive function at subsequent assessments, and vice versa. The ΔNCCs partially mediated this prospective reciprocal relationships, accounting for 2.58% of the total effect of loneliness on cognition and 4.44% of the total effect of cognition on loneliness, respectively. Loneliness may predict subsequent cognitive decline, and vice versa. This loneliness-cognition relationship is partially explained by their impact on physical health. Multidisciplinary interventions aimed at reducing loneliness and cognitive decline per se and their associated risk factors as well as improving chronic illness management would be beneficial for emotional well-being and cognitive health in OAs. © The Author 2016. Published by Oxford University Press on behalf of The Gerontological Society of America. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Relationships between Circulating Urea Concentrations and Endometrial Function in Postpartum Dairy Cows.

PubMed

Cheng, Zhangrui; Oguejiofor, Chike F; Swangchan-Uthai, Theerawat; Carr, Susan; Wathes, D Claire

2015-08-14

Both high and low circulating urea concentrations, a product of protein metabolism, are associated with decreased fertility in dairy cows through poorly defined mechanisms. The rate of involution and the endometrial ability to mount an adequate innate immune response after calving are both critical for subsequent fertility. Study 1 used microarray analysis to identify genes whose endometrial expression 2 weeks postpartum correlated significantly with the mean plasma urea per cow, ranging from 3.2 to 6.6 mmol/L. The biological functions of 781 mapped genes were analysed using Ingenuity Pathway Analysis. These were predominantly associated with tissue turnover (e.g., BRINP1, FOXG1), immune function (e.g., IL17RB, CRISPLD2), inflammation (e.g., C3, SERPINF1, SERPINF2) and lipid metabolism (e.g., SCAP, ACBD5, SLC10A). Study 2 investigated the relationship between urea concentration and expression of 6 candidate genes (S100A8, HSP5A, IGF1R, IL17RB, BRINP1, CRISPLD2) in bovine endometrial cell culture. These were treated with 0, 2.5, 5.0 or 7.5 mmol/L urea, equivalent to low, medium and high circulating values with or without challenge by bacterial lipopolysaccharide (LPS). LPS increased S100A8 expression as expected but urea treatment had no effect on expression of any tested gene. Examination of the genes/pathways involved suggests that plasma urea levels may reflect variations in lipid metabolism. Our results suggest that it is the effects of lipid metabolism rather than the urea concentration which probably alter the rate of involution and innate immune response, in turn influencing subsequent fertility.

γδT cells but not αβT cells contribute to sepsis-induced white matter injury and motor abnormalities in mice.

PubMed

Zhang, Xiaoli; Rocha-Ferreira, Eridan; Li, Tao; Vontell, Regina; Jabin, Darakhshan; Hua, Sha; Zhou, Kai; Nazmi, Arshed; Albertsson, Anna-Maj; Sobotka, Kristina; Ek, Joakim; Thornton, Claire; Hagberg, Henrik; Mallard, Carina; Leavenworth, Jianmei W; Zhu, Changlian; Wang, Xiaoyang

2017-12-20

Infection and sepsis are associated with brain white matter injury in preterm infants and the subsequent development of cerebral palsy. In the present study, we used a neonatal mouse sepsis-induced white matter injury model to determine the contribution of different T cell subsets (αβT cells and γδT cells) to white matter injury and consequent behavioral changes. C57BL/6J wild-type (WT), T cell receptor (TCR) δ-deficient (Tcrd -/- , lacking γδT cells), and TCRα-deficient (Tcra -/- , lacking αβT cells) mice were administered with lipopolysaccharide (LPS) at postnatal day (PND) 2. Brain myelination was examined at PNDs 12, 26, and 60. Motor function and anxiety-like behavior were evaluated at PND 26 or 30 using DigiGait analysis and an elevated plus maze. White matter development was normal in Tcrd -/- and Tcrα -/- compared to WT mice. LPS exposure induced reductions in white matter tissue volume in WT and Tcrα -/- mice, but not in the Tcrd -/- mice, compared with the saline-treated groups. Neither LPS administration nor the T cell deficiency affected anxiety behavior in these mice as determined with the elevated plus maze. DigiGait analysis revealed motor function deficiency after LPS-induced sepsis in both WT and Tcrα -/- mice, but no such effect was observed in Tcrd -/- mice. Our results suggest that γδT cells but not αβT cells contribute to sepsis-induced white matter injury and subsequent motor function abnormalities in early life. Modulating the activity of γδT cells in the early stages of preterm white matter injury might represent a novel therapeutic strategy for the treatment of perinatal brain injury.

Cross-sectional and longitudinal associations of functional and health status with institutional care use: results from the Survey of Health and Living Status of the Elderly in Taiwan.

PubMed

Tsai, Hsin-Jen

2013-07-01

This study evaluated the cross-sectional and longitudinal associations of functional and health status with institutional care, and examined determinants of institutional care use over time. Data of this study were obtained from the Survey of Health and Living Status of the Elderly in Taiwan (SHLSET), which was launched in 1989 and involved a nationally representative sample of nearly-old and old Taiwanese. The baseline data in this present study were collected in 1999, and followed in 2003 and 2007. Participants with institutional care use had a higher activities of daily living (ADL) score, more self-reported diseases and poorer self-reported health status than participants without institutional care use (all P<0.05). Cross-sectional analysis showed that a higher ADL score, having heart diseases and having a stroke were positively associated with institutional care use (P<0.05); whereas the number of self-reported diseases and poor self-reported health status were not associated with institutional care use. Longitudinal analysis showed that increased ADL scores and the number of self-reported diseases over 4- and 8 years were associated with an increased likelihood of subsequent institutional care use (all P<0.05). Worsening health status over 4 years was associated with an increased likelihood of subsequent institutional care use, but this association did not exist over 8 years. Only ADL and ADL deterioration over time are cross-sectionally and longitudinally associated with increased institutional care use. Declining functional status is a major determinant of institutional care use for Taiwanese aged over 53 years. © 2012 Japan Geriatrics Society.

Transient Infiltration Analysis for Infinite Slopes using the Modified Function of Unsaturated Hydraulic Conductivity

NASA Astrophysics Data System (ADS)

Oh, Seboong; Achmad Zaky, Fauzi; Mog Park, Young

2016-04-01

The hydraulic behaviors in the soil layer are crucial to the transient infiltration analysis into natural slopes, in which unsaturated hydraulic conductivity (HC) can be evaluated theoretically from soil water retention curves (SWRC) by Mualem's equation. In the nonlinear infiltration analysis, the solution by some of smooth SWRCs is not converge for heavy rainfall condition, since the gradient of HCs is extremely steep near saturation. The van Genuchten's SWRC model has been modified near saturation and subsequently an analytical HC function was proposed to improve the van Genuchten-Mualem HC. Using the examples on 1-D infiltration analysis by the modified HC model, it is validated that any solutions can be converged for various rainfall conditions to keep numerical stability. Stability analysis based on unsaturated effective stress could simulate the infinite slope failure by the proposed HC model. The pore water pressure and the ratio of saturation increased from the surface to shallow depth (˜1m) and the factor of safety decreased gradually due to infiltration. Acknowledgements This research is supported by grants from Korean NRF (2012M3A2A1050974 and 2015R1A2A2A01), which are greatly appreciated.

Advanced correlation grid: Analysis and visualisation of functional connectivity among multiple spike trains.

PubMed

Masud, Mohammad Shahed; Borisyuk, Roman; Stuart, Liz

2017-07-15

This study analyses multiple spike trains (MST) data, defines its functional connectivity and subsequently visualises an accurate diagram of connections. This is a challenging problem. For example, it is difficult to distinguish the common input and the direct functional connection of two spike trains. The new method presented in this paper is based on the traditional pairwise cross-correlation function (CCF) and a new combination of statistical techniques. First, the CCF is used to create the Advanced Correlation Grid (ACG) correlation where both the significant peak of the CCF and the corresponding time delay are used for detailed analysis of connectivity. Second, these two features of functional connectivity are used to classify connections. Finally, the visualization technique is used to represent the topology of functional connections. Examples are presented in the paper to demonstrate the new Advanced Correlation Grid method and to show how it enables discrimination between (i) influence from one spike train to another through an intermediate spike train and (ii) influence from one common spike train to another pair of analysed spike trains. The ACG method enables scientists to automatically distinguish between direct connections from spurious connections such as common source connection and indirect connection whereas existing methods require in-depth analysis to identify such connections. The ACG is a new and effective method for studying functional connectivity of multiple spike trains. This method can identify accurately all the direct connections and can distinguish common source and indirect connections automatically. Copyright © 2017 Elsevier B.V. All rights reserved.

Ability to walk 1/4 mile predicts subsequent disability, mortality, and health care costs.

PubMed

Hardy, Susan E; Kang, Yihuang; Studenski, Stephanie A; Degenholtz, Howard B

2011-02-01

Mobility, such as walking 1/4 mile, is a valuable but underutilized health indicator among older adults. For mobility to be successfully integrated into clinical practice and health policy, an easily assessed marker that predicts subsequent health outcomes is required. To determine the association between mobility, defined as self-reported ability to walk 1/4 mile, and mortality, functional decline, and health care utilization and costs during the subsequent year. Analysis of longitudinal data from the 2003-2004 Medicare Current Beneficiary Survey, a nationally representative sample of Medicare beneficiaries. Participants comprised 5895 community-dwelling adults aged 65 years or older enrolled in Medicare. Mobility (self-reported ability to walk 1/4 mile), mortality, incident difficulty with activities of daily living (ADLs), total annual health care costs, and hospitalization rates. Among older adults, 28% reported difficulty and 17% inability to walk 1/4 mile at baseline. Compared to those without difficulty and adjusting for demographics, socioeconomic status, chronic conditions, and health behaviors, mortality was greater in those with difficulty [AOR (95% CI): 1.57 (1.10-2.24)] and inability [AOR (CI): 2.73 (1.79-4.15)]. New functional disability also occurred more frequently as self-reported ability to walk 1/4 mile declined (subsequent incident disability among those with no difficulty, difficulty, or inability to walk 1/4 mile at baseline was 11%, 29%, and 47% for instrumental ADLs, and 4%, 14%, and 23% for basic ADLs). Total annual health care costs were $2773 higher (95% CI $1443-4102) in persons with difficulty and $3919 higher (CI $1948-5890) in those who were unable. For each 100 persons, older adults reporting difficulty walking 1/4 mile at baseline experienced an additional 14 hospitalizations (95% CI 8-20), and those who were unable experienced an additional 22 hospitalizations (CI 14-30) during the follow-up period, compared to persons without walking difficulty. Mobility disability, a simple self-report measure, is a powerful predictor of future health, function, and utilization independent of usual health and demographic indicators. Mobility disability may be used to target high-risk patients for care management and preventive interventions.

Sliding-window analysis tracks fluctuations in amygdala functional connectivity associated with physiological arousal and vigilance during fear conditioning.

PubMed

Baczkowski, Blazej M; Johnstone, Tom; Walter, Henrik; Erk, Susanne; Veer, Ilya M

2017-06-01

We evaluated whether sliding-window analysis can reveal functionally relevant brain network dynamics during a well-established fear conditioning paradigm. To this end, we tested if fMRI fluctuations in amygdala functional connectivity (FC) can be related to task-induced changes in physiological arousal and vigilance, as reflected in the skin conductance level (SCL). Thirty-two healthy individuals participated in the study. For the sliding-window analysis we used windows that were shifted by one volume at a time. Amygdala FC was calculated for each of these windows. Simultaneously acquired SCL time series were averaged over time frames that corresponded to the sliding-window FC analysis, which were subsequently regressed against the whole-brain seed-based amygdala sliding-window FC using the GLM. Surrogate time series were generated to test whether connectivity dynamics could have occurred by chance. In addition, results were contrasted against static amygdala FC and sliding-window FC of the primary visual cortex, which was chosen as a control seed, while a physio-physiological interaction (PPI) was performed as cross-validation. During periods of increased SCL, the left amygdala became more strongly coupled with the bilateral insula and anterior cingulate cortex, core areas of the salience network. The sliding-window analysis yielded a connectivity pattern that was unlikely to have occurred by chance, was spatially distinct from static amygdala FC and from sliding-window FC of the primary visual cortex, but was highly comparable to that of the PPI analysis. We conclude that sliding-window analysis can reveal functionally relevant fluctuations in connectivity in the context of an externally cued task. Copyright © 2017 Elsevier Inc. All rights reserved.

The complex genetics of gait speed: genome-wide meta-analysis approach

PubMed Central

Lunetta, Kathryn L.; Smith, Jennifer A.; Eicher, John D.; Vered, Rotem; Deelen, Joris; Arnold, Alice M.; Buchman, Aron S.; Tanaka, Toshiko; Faul, Jessica D.; Nethander, Maria; Fornage, Myriam; Adams, Hieab H.; Matteini, Amy M.; Callisaya, Michele L.; Smith, Albert V.; Yu, Lei; De Jager, Philip L.; Evans, Denis A.; Gudnason, Vilmundur; Hofman, Albert; Pattie, Alison; Corley, Janie; Launer, Lenore J.; Knopman, Davis S.; Parimi, Neeta; Turner, Stephen T.; Bandinelli, Stefania; Beekman, Marian; Gutman, Danielle; Sharvit, Lital; Mooijaart, Simon P.; Liewald, David C.; Houwing-Duistermaat, Jeanine J.; Ohlsson, Claes; Moed, Matthijs; Verlinden, Vincent J.; Mellström, Dan; van der Geest, Jos N.; Karlsson, Magnus; Hernandez, Dena; McWhirter, Rebekah; Liu, Yongmei; Thomson, Russell; Tranah, Gregory J.; Uitterlinden, Andre G.; Weir, David R.; Zhao, Wei; Starr, John M.; Johnson, Andrew D.; Ikram, M. Arfan; Bennett, David A.; Cummings, Steven R.; Deary, Ian J.; Harris, Tamara B.; Kardia, Sharon L. R.; Mosley, Thomas H.; Srikanth, Velandai K.; Windham, Beverly G.; Newman, Ann B.; Walston, Jeremy D.; Davies, Gail; Evans, Daniel S.; Slagboom, Eline P.; Ferrucci, Luigi; Kiel, Douglas P.; Murabito, Joanne M.; Atzmon, Gil

2017-01-01

Emerging evidence suggests that the basis for variation in late-life mobility is attributable, in part, to genetic factors, which may become increasingly important with age. Our objective was to systematically assess the contribution of genetic variation to gait speed in older individuals. We conducted a meta-analysis of gait speed GWASs in 31,478 older adults from 17 cohorts of the CHARGE consortium, and validated our results in 2,588 older adults from 4 independent studies. We followed our initial discoveries with network and eQTL analysis of candidate signals in tissues. The meta-analysis resulted in a list of 536 suggestive genome wide significant SNPs in or near 69 genes. Further interrogation with Pathway Analysis placed gait speed as a polygenic complex trait in five major networks. Subsequent eQTL analysis revealed several SNPs significantly associated with the expression of PRSS16, WDSUB1 and PTPRT, which in addition to the meta-analysis and pathway suggested that genetic effects on gait speed may occur through synaptic function and neuronal development pathways. No genome-wide significant signals for gait speed were identified from this moderately large sample of older adults, suggesting that more refined physical function phenotypes will be needed to identify the genetic basis of gait speed in aging. PMID:28077804

Influence of a cyclic combination chemotherapeutic protocol on primary haemostasis in dogs suffering from malignant lymphoma.

PubMed

Eberle, N; Mischke, R

2010-03-01

The purpose of this study was to examine the influence of cyclic combination chemotherapy on primary haemostasis in dogs with malignant lymphoma. Seventeen dogs receiving cytostatic treatment for high-grade lymphoma were included in the study. The dogs were treated with a Madison-Wisconsin derived protocol, which included asparaginase, vincristine, doxorubicin and prednisolone. At different time points during the first 4 weeks of induction, platelet count, capillary bleeding time, analysis of the platelet function using the platelet function analyser PFA-100, and platelet aggregation by the Born-method were measured. The most obvious changes were found for median values of the platelet count, which increased significantly from 210,000/microL before induction to 349,000/microL during the second week of induction (P=0.0010). Median platelet count subsequently decreased by the fourth week of treatment (Friedman-test: P<0.0001). None of the parameters of platelet function (capillary bleeding time, automatic platelet function analysis, aggregation maximum) showed significant changes with time (P>0.05, Friedman-test). The results did not suggest that significant platelet dysfunction was induced by the chemotherapeutic protocol used in the study. 2009 Elsevier Ltd. All rights reserved.

Surface functionalization of solid state ultra-high molecular weight polyethylene through chemical grafting

NASA Astrophysics Data System (ADS)

Sherazi, Tauqir A.; Rehman, Tayyiba; Naqvi, Syed Ali Raza; Shaikh, Ahson Jabbar; Shahzad, Sohail Anjum; Abbas, Ghazanfar; Raza, Rizwan; Waseem, Amir

2015-12-01

The surface of ultra-high molecular weight polyethylene (UHMWPE) powder was functionalized with styrene using chemical grafting technique. The grafting process was initiated through radical generation on base polymer matrix in the solid state by sodium thiosulfate, while peroxides formed at radical sites during this process were dissociated by ceric ammonium nitrate. Various factors were optimized and reasonably high level of monomer grafting was achieved, i.e., 15.6%. The effect of different acids as additive and divinyl benzene (DVB) as a cross-linking agent was also studied. Post-grafting sulfonation was conducted to introduce the ionic moieties to the grafted polymer. Ion-exchange capacity (IEC) was measured experimentally and is found to be 1.04 meq g-1, which is in close agreement with the theoretical IEC values. The chemical structure of grafted and functionalized polymer was characterized by attenuated total reflection infrared spectroscopy (ATR-FTIR) and thermal properties were investigated by thermo gravimetric analysis (TGA) and differential scanning calorimetry (DSC). Thermal analysis depicts that the presence of radicals on the polymer chain accelerates the thermal decomposition process. The results signify that the chemical grafting is an effective tool for substantial surface modification and subsequent functionalization of polyethylene.

Systematic analyses of the ultraviolet radiation resistance-associated gene product (UVRAG) protein interactome by tandem affinity purification.

PubMed

Son, Ji-Hye; Hwang, Eurim C; Kim, Joungmok

2016-03-01

Ultraviolet radiation resistance-associated gene product (UVRAG) was originally identified as a protein involved in cellular responses to UV irradiation. Subsequent studies have demonstrated that UVRAG plays as an important role in autophagy, a lysosome-dependent catabolic program, as a part of a pro-autophagy PIK3C3/VPS34 lipid kinase complex. Several recent studies have shown that UVRAG is also involved in autophagy-independent cellular functions, such as DNA repair/stability and vesicular trafficking/fusion. Here, we examined the UVRAG protein interactome to obtain information about its functional network. To this end, we screened UVRAG-interacting proteins using a tandem affinity purification method coupled with MALDI-TOF/MS analysis. Our results demonstrate that UVRAG interacts with various proteins involved in a wide spectrum of cellular functions, including genome stability, protein translational elongation, protein localization (trafficking), vacuole organization, transmembrane transport as well as autophagy. Notably, the interactome list of high-confidence UVRAG-interacting proteins is enriched for proteins involved in the regulation of genome stability. Our systematic UVRAG interactome analysis should provide important clues for understanding a variety of UVRAG functions.

Superposed epoch analysis of O+ auroral outflow during sawtooth events and substorms

NASA Astrophysics Data System (ADS)

Nowrouzi, N.; Kistler, L. M.; Lund, E. J.; Cai, X.

2017-12-01

Sawtooth events are repeated injection of energetic particles at geosynchronous orbit. Studies have shown that 94% of sawtooth events occurred during magnetic storm times. The main factor that causes a sawtooth event is still an open question. Simulations have suggested that heavy ions like O+ may play a role in triggering the injections. One of the sources of the O+ in the Earth's magnetosphere is the nightside aurora. O+ ions coming from the nightside auroral region have direct access to the near-earth magnetotail. A model (Brambles et al. 2013) for interplanetary coronal mass ejection driven sawtooth events found that nightside O+ outflow caused the subsequent teeth of the sawtooth event through a feedback mechanism. This work is a superposed epoch analysis to test whether the observed auroral outflow supports this model. Using FAST spacecraft data from 1997-2007, we examine the auroral O+ outflow as a function of time relative to an injection onset. Then we determine whether the profile of outflow flux of O+ during sawtooth events is different from the outflow observed during isolated substorms. The auroral region boundaries are estimated using the method of (Andersson et al. 2004). Subsequently the O+ outflow flux inside these boundaries are calculated and binned as a function of superposed epoch time for substorms and sawtooth "teeth". In this way, we will determine if sawtooth events do in fact have greater O+ outflow, and if that outflow is predominantly from the nightside, as suggested by the model results.

Attenuation analysis of real GPR wavelets: The equivalent amplitude spectrum (EAS)

NASA Astrophysics Data System (ADS)

Economou, Nikos; Kritikakis, George

2016-03-01

Absorption of a Ground Penetrating Radar (GPR) pulse is a frequency dependent attenuation mechanism which causes a spectral shift on the dominant frequency of GPR data. Both energy variation of GPR amplitude spectrum and spectral shift were used for the estimation of Quality Factor (Q*) and subsequently the characterization of the subsurface material properties. The variation of the amplitude spectrum energy has been studied by Spectral Ratio (SR) method and the frequency shift by the estimation of the Frequency Centroid Shift (FCS) or the Frequency Peak Shift (FPS) methods. The FPS method is more automatic, less robust. This work aims to increase the robustness of the FPS method by fitting a part of the amplitude spectrum of GPR data with Ricker, Gaussian, Sigmoid-Gaussian or Ricker-Gaussian functions. These functions fit different parts of the spectrum of a GPR reference wavelet and the Equivalent Amplitude Spectrum (EAS) is selected, reproducing Q* values used in forward Q* modeling analysis. Then, only the peak frequencies and the time differences between the reference wavelet and the subsequent reflected wavelets are used to estimate Q*. As long as the EAS is estimated, it is used for Q* evaluation in all the GPR section, under the assumption that the selected reference wavelet is representative. De-phasing and constant phase shift, for obtaining symmetrical wavelets, proved useful in the sufficiency of the horizons picking. Synthetic, experimental and real GPR data were examined in order to demonstrate the effectiveness of the proposed methodology.

To what extent do joint attention, imitation, and object play behaviors in infancy predict later communication and intellectual functioning in ASD?

PubMed

Poon, Kenneth K; Watson, Linda R; Baranek, Grace T; Poe, Michele D

2012-06-01

The extent to which early social communication behaviors predict later communication and intellectual outcomes was investigated via retrospective video analysis. Joint attention, imitation, and complex object play behaviors were coded from edited home videos featuring scenes of 29 children with ASD at 9-12 and/or 15-18 months. A quantitative interval recording of behavior and a qualitative rating of the developmental level were applied. Social communication behaviors increased between 9-12 and 15-18 months. Their mean level during infancy, but not the rate of change, predicted both Vineland Communication scores and intellectual functioning at 3-7 years. The two methods of measurement yielded similar results. Thus, early social communicative behaviors may play pivotal roles in the development of subsequent communication and intellectual functioning.

Functional Response of NiTi Elements for Smart Micro-actuation Applications

NASA Astrophysics Data System (ADS)

Biffi, C. A.; Nespoli, A.; Previtali, B.; Villa, E.; Tuissi, A.

2014-07-01

Shape memory alloys (SMAs) can be considered a good candidate for actuation applications in the current micro-technology field. In the micro-scale, the temporal response of the SMA actuators can be improved, because of faster cooling during the austenite-martensite transformation. One of the most investigated geometries for this purpose has been the snake-like arrangement, which allows high strokes with considerable forces to be obtained. In this work, SMA elements for micro-actuators were patterned by laser machining in a snake-like shape. Subsequent surface chemical etching was adopted to improve the functional properties of the micro-elements. Calorimetric analysis and thermo-mechanical response of 90 μm thick SMA elements were reported for the evaluation of their functional performances. Moreover, the effect of post-thermal treatment and grain orientation were also evaluated on the final performances.

Concordance Between Patient and Family Reports of Family Functioning in Bipolar I Disorder and Major Depressive Disorder

PubMed Central

Weinstock, Lauren M.; Wenze, Susan J.; Munroe, Mary K.; Miller, Ivan W.

2013-01-01

Despite the extensive literature on family functioning and mood disorders, less is known about concordance between patient- and family-reported family functioning. To address this question, adults with bipolar I disorder (BD; n = 92), major depressive disorder (MDD; n = 121), and their family members (ns = 135 and 201, respectively) were recruited from hospital sources. All patients and their family members completed the Family Assessment Device (Epstein et al., 1983). Intraclass correlation coefficients revealed that, in contrast to the moderate degree of concordance in the MDD sample, degree of concordance between patient- and family-reported family functioning was significantly weaker in BD. Subsequent analysis revealed that this discordance was driven by the reports of the child and young adolescent family members of the patients with BD. Results highlight the importance of collateral reports in the assessment of family functioning, especially among families of patients with BD, in research and treatment. PMID:23588224

Concordance between patient and family reports of family functioning in bipolar I disorder and major depressive disorder.

PubMed

Weinstock, Lauren M; Wenze, Susan J; Munroe, Mary K; Miller, Ivan W

2013-05-01

Despite the extensive literature on family functioning and mood disorders, less is known about concordance between patient- and family-reported family functioning. To address this question, adults with bipolar I disorder (BD; n = 92) or major depressive disorder (MDD; n = 121) and their family members (n = 135 and 201, respectively) were recruited from hospital sources. All patients and their family members completed the Family Assessment Device (Epstein, Baldwin, Bishop. J Marital Fam Ther. 9:171-180, 1983). Intraclass correlation coefficients revealed that, in contrast to the moderate degree of concordance in the MDD sample, degree of concordance between patient- and family-reported family functioning was significantly weaker in BD. Subsequent analysis revealed that this discordance was driven by the reports of the child and young adolescent family members of the patients with BD. Results highlight the importance of collateral reports in the assessment of family functioning, especially among families of patients with BD, in research and treatment.

Common and Rare EGFR and KRAS Mutations in a Dutch Non-Small-Cell Lung Cancer Population and Their Clinical Outcome

PubMed Central

Kerner, Gerald S. M. A.; Schuuring, Ed; Sietsma, Johanna; Hiltermann, Thijo J. N.; Pieterman, Remge M.; de Leede, Gerard P. J.; van Putten, John W. G.; Liesker, Jeroen; Renkema, Tineke E. J.; van Hengel, Peter; Platteel, Inge; Timens, Wim; Groen, Harry J. M.

2013-01-01

Introduction In randomly assigned studies with EGFR TKI only a minor proportion of patients with NSCLC have genetically profiled biopsies. Guidelines provide evidence to perform EGFR and KRAS mutation analysis in non-squamous NSCLC. We explored tumor biopsy quality offered for mutation testing, different mutations distribution, and outcome with EGFR TKI. Patient and Methods Clinical data from 8 regional hospitals were studied for patient and tumor characteristics, treatment and overall survival. Biopsies sent to the central laboratory were evaluated for DNA quality and subsequently analyzed for mutations in exons 18–21 of EGFR and exon 2 of KRAS by bidirectional sequence analysis. Results Tumors from 442 subsequent patients were analyzed. For 74 patients (17%) tumors were unsuitable for mutation analysis. Thirty-eight patients (10.9%) had EGFR mutations with 79% known activating mutations. One hundred eight patients (30%) had functional KRAS mutations. The mutation spectrum was comparable to the Cosmic database. Following treatment in the first or second line with EGFR TKI median overall survival for patients with EGFR (n = 14), KRAS (n = 14) mutations and wild type EGFR/KRAS (n = 31) was not reached, 20 and 9 months, respectively. Conclusion One out of every 6 tumor samples was inadequate for mutation analysis. Patients with EGFR activating mutations treated with EGFR-TKI have the longest survival. PMID:23922984

Network Analysis of Sequence-Function Relationships and Exploration of Sequence Space of TEM β-Lactamases.

PubMed

Zeil, Catharina; Widmann, Michael; Fademrecht, Silvia; Vogel, Constantin; Pleiss, Jürgen

2016-05-01

The Lactamase Engineering Database (www.LacED.uni-stuttgart.de) was developed to facilitate the classification and analysis of TEM β-lactamases. The current version contains 474 TEM variants. Two hundred fifty-nine variants form a large scale-free network of highly connected point mutants. The network was divided into three subnetworks which were enriched by single phenotypes: one network with predominantly 2be and two networks with 2br phenotypes. Fifteen positions were found to be highly variable, contributing to the majority of the observed variants. Since it is expected that a considerable fraction of the theoretical sequence space is functional, the currently sequenced 474 variants represent only the tip of the iceberg of functional TEM β-lactamase variants which form a huge natural reservoir of highly interconnected variants. Almost 50% of the variants are part of a quartet. Thus, two single mutations that result in functional enzymes can be combined into a functional protein. Most of these quartets consist of the same phenotype, or the mutations are additive with respect to the phenotype. By predicting quartets from triplets, 3,916 unknown variants were constructed. Eighty-seven variants complement multiple quartets and therefore have a high probability of being functional. The construction of a TEM β-lactamase network and subsequent analyses by clustering and quartet prediction are valuable tools to gain new insights into the viable sequence space of TEM β-lactamases and to predict their phenotype. The highly connected sequence space of TEM β-lactamases is ideally suited to network analysis and demonstrates the strengths of network analysis over tree reconstruction methods. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

Nano-Aptasensing in Mycotoxin Analysis: Recent Updates and Progress

PubMed Central

Rhouati, Amina; Bulbul, Gonca; Hayat, Akhtar; Marty, Jean Louis

2017-01-01

Recent years have witnessed an overwhelming integration of nanomaterials in the fabrication of biosensors. Nanomaterials have been incorporated with the objective to achieve better analytical figures of merit in terms of limit of detection, linear range, assays stability, low production cost, etc. Nanomaterials can act as immobilization support, signal amplifier, mediator and artificial enzyme label in the construction of aptasensors. We aim in this work to review the recent progress in mycotoxin analysis. This review emphasizes on the function of the different nanomaterials in aptasensors architecture. We subsequently relate their features to the analytical performance of the given aptasensor towards mycotoxins monitoring. In the same context, a critically analysis and level of success for each nano-aptasensing design will be discussed. Finally, current challenges in nano-aptasensing design for mycotoxin analysis will be highlighted. PMID:29143760

Processing data communications events by awakening threads in parallel active messaging interface of a parallel computer

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

Archer, Charles J.; Blocksome, Michael A.; Ratterman, Joseph D.

Processing data communications events in a parallel active messaging interface (`PAMI`) of a parallel computer that includes compute nodes that execute a parallel application, with the PAMI including data communications endpoints, and the endpoints are coupled for data communications through the PAMI and through other data communications resources, including determining by an advance function that there are no actionable data communications events pending for its context, placing by the advance function its thread of execution into a wait state, waiting for a subsequent data communications event for the context; responsive to occurrence of a subsequent data communications event for themore » context, awakening by the thread from the wait state; and processing by the advance function the subsequent data communications event now pending for the context.« less

Sociotechnical systems as a framework for regulatory system design and evaluation: Using Work Domain Analysis to examine a new regulatory system.

PubMed

Carden, Tony; Goode, Natassia; Read, Gemma J M; Salmon, Paul M

2017-03-15

Like most work systems, the domain of adventure activities has seen a series of serious incidents and subsequent calls to improve regulation. Safety regulation systems aim to promote safety and reduce accidents. However, there is scant evidence they have led to improved safety outcomes. In fact there is some evidence that the poor integration of regulatory system components has led to adverse safety outcomes in some contexts. Despite this, there is an absence of methods for evaluating regulatory and compliance systems. This article argues that sociotechnical systems theory and methods provide a suitable framework for evaluating regulatory systems. This is demonstrated through an analysis of a recently introduced set of adventure activity regulations. Work Domain Analysis (WDA) was used to describe the regulatory system in terms of its functional purposes, values and priority measures, purpose-related functions, object-related processes and cognitive objects. This allowed judgement to be made on the nature of the new regulatory system and on the constraints that may impact its efficacy following implementation. Importantly, the analysis suggests that the new system's functional purpose of ensuring safe activities is not fully supported in terms of the functions and objects available to fulfil them. Potential improvements to the design of the system are discussed along with the implications for regulatory system design and evaluation across the safety critical domains generally. Copyright © 2017 Elsevier Ltd. All rights reserved.

Loss-of-Function FANCL Mutations Associate with Severe Fanconi Anemia Overlapping the VACTERL Association.

PubMed

Vetro, Annalisa; Iascone, Maria; Limongelli, Ivan; Ameziane, Najim; Gana, Simone; Della Mina, Erika; Giussani, Ursula; Ciccone, Roberto; Forlino, Antonella; Pezzoli, Laura; Rooimans, Martin A; van Essen, Antoni J; Messa, Jole; Rizzuti, Tommaso; Bianchi, Paolo; Dorsman, Josephine; de Winter, Johan P; Lalatta, Faustina; Zuffardi, Orsetta

2015-05-01

The diagnosis of VACTERL syndrome can be elusive, especially in the prenatal life, due to the presence of malformations that overlap those present in other genetic conditions, including the Fanconi anemia (FA). We report on three VACTERL cases within two families, where the two who arrived to be born died shortly after birth due to severe organs' malformations. The suspicion of VACTERL association was based on prenatal ultrasound assessment and postnatal features. Subsequent chromosome breakage analysis suggested the diagnosis of FA. Finally, by next-generation sequencing based on the analysis of the exome in one family and of a panel of Fanconi genes in the second one, we identified novel FANCL truncating mutations in both families. We used ectopic expression of wild-type FANCL to functionally correct the cellular FA phenotype for both mutations. Our study emphasizes that the diagnosis of FA should be considered when VACTERL association is suspected. Furthermore, we show that loss-of-function mutations in FANCL result in a severe clinical phenotype characterized by early postnatal death. © 2015 WILEY PERIODICALS, INC.

Idiopathic restrictive cardiomyopathy is part of the clinical expression of cardiac troponin I mutations

PubMed Central

Mogensen, Jens; Kubo, Toru; Duque, Mauricio; Uribe, William; Shaw, Anthony; Murphy, Ross; Gimeno, Juan R.; Elliott, Perry; McKenna, William J.

2003-01-01

Restrictive cardiomyopathy (RCM) is an uncommon heart muscle disorder characterized by impaired filling of the ventricles with reduced volume in the presence of normal or near normal wall thickness and systolic function. The disease may be associated with systemic disease but is most often idiopathic. We recognized a large family in which individuals were affected by either idiopathic RCM or hypertrophic cardiomyopathy (HCM). Linkage analysis to selected sarcomeric contractile protein genes identified cardiac troponin I (TNNI3) as the likely disease gene. Subsequent mutation analysis revealed a novel missense mutation, which cosegregated with the disease in the family (lod score: 4.8). To determine if idiopathic RCM is part of the clinical expression of TNNI3 mutations, genetic investigations of the gene were performed in an additional nine unrelated RCM patients with restrictive filling patterns, bi-atrial dilatation, normal systolic function, and normal wall thickness. TNNI3 mutations were identified in six of these nine RCM patients. Two of the mutations identified in young individuals were de novo mutations. All mutations appeared in conserved and functionally important domains of the gene. PMID:12531876

More with less: A comparative kinematical analysis of Django Reinhardt's adaptations to hand injury.

PubMed

Wininger, Michael; Williams, David J

2015-06-01

At the age of 18 years, jazz guitarist Django Reinhardt (1910-1953) sustained significant burns to his left-hand ring and little fingers; yet, subsequently, he relearned to play and achieved international fame, despite his injuries. Archive film footage and novel motion analysis software were used to compare movements of Django's fretting hand with that of six other guitarists of the same genre. Django employed greater abduction of index and middle fingers (-9.11 ± 6.52° vs -5.78 ± 2.41°; p < 0.001) and more parallel alignment of fingers to the guitar neck (157.7 ± 3.37° vs 150.59 ± 2.67°; p < 0.001) compared to controls. In response to debilitating hand injury, Django developed quantifiable compensatory adaptation of function of his remaining functional fingers by developing an original playing technique. Hand function following injury may be optimized by maximizing latent degrees of freedom in remaining digits, rather than through extensive surgical reconstruction or complex prostheses. Further study of adaptation strategies may inform prosthesis design. © The International Society for Prosthetics and Orthotics 2014.

In vivo optical microscopy of peripheral nerve myelination with polarization sensitive-optical coherence tomography

PubMed Central

Henry, Francis P.; Wang, Yan; Rodriguez, Carissa L. R.; Randolph, Mark A.; Rust, Esther A. Z.; Winograd, Jonathan M.; de Boer, Johannes F.; Park, B. Hyle

2015-01-01

Abstract. Assessing nerve integrity and myelination after injury is necessary to provide insight for treatment strategies aimed at restoring neuromuscular function. Currently, this is largely done with electrical analysis, which lacks direct quantitative information. In vivo optical imaging with sufficient imaging depth and resolution could be used to assess the nerve microarchitecture. In this study, we examine the use of polarization sensitive-optical coherence tomography (PS-OCT) to quantitatively assess the sciatic nerve microenvironment through measurements of birefringence after applying a nerve crush injury in a rat model. Initial loss of function and subsequent recovery were demonstrated by calculating the sciatic function index (SFI). We found that the PS-OCT phase retardation slope, which is proportional to birefringence, increased monotonically with the SFI. Additionally, histomorphometric analysis of the myelin thickness and g-ratio shows that the PS-OCT slope is a good indicator of myelin health and recovery after injury. These results demonstrate that PS-OCT is capable of providing nondestructive and quantitative assessment of nerve health after injury and shows promise for continued use both clinically and experimentally in neuroscience. PMID:25858593

In vivo optical microscopy of peripheral nerve myelination with polarization sensitive-optical coherence tomography.

PubMed

Henry, Francis P; Wang, Yan; Rodriguez, Carissa L R; Randolph, Mark A; Rust, Esther A Z; Winograd, Jonathan M; de Boer, Johannes F; Park, B Hyle

2015-04-01

Assessing nerve integrity and myelination after injury is necessary to provide insight for treatment strategies aimed at restoring neuromuscular function. Currently, this is largely done with electrical analysis, which lacks direct quantitative information. In vivo optical imaging with sufficient imaging depth and resolution could be used to assess the nerve microarchitecture. In this study, we examine the use of polarization sensitive-optical coherence tomography (PS-OCT) to quantitatively assess the sciatic nerve microenvironment through measurements of birefringence after applying a nerve crush injury in a rat model. Initial loss of function and subsequent recovery were demonstrated by calculating the sciatic function index (SFI). We found that the PS-OCT phase retardation slope, which is proportional to birefringence, increased monotonically with the SFI. Additionally, histomorphometric analysis of the myelin thickness and g-ratio shows that the PS-OCT slope is a good indicator of myelin health and recovery after injury. These results demonstrate that PS-OCT is capable of providing nondestructive and quantitative assessment of nerve health after injury and shows promise for continued use both clinically and experimentally in neuroscience.

A computer-controlled scintiscanning system and associated computer graphic techniques for study of regional distribution of blood flow.

NASA Technical Reports Server (NTRS)

Coulam, C. M.; Dunnette, W. H.; Wood, E. H.

1970-01-01

Two methods whereby a digital computer may be used to regulate a scintiscanning process are discussed from the viewpoint of computer input-output software. The computer's function, in this case, is to govern the data acquisition and storage, and to display the results to the investigator in a meaningful manner, both during and subsequent to the scanning process. Several methods (such as three-dimensional maps, contour plots, and wall-reflection maps) have been developed by means of which the computer can graphically display the data on-line, for real-time monitoring purposes, during the scanning procedure and subsequently for detailed analysis of the data obtained. A computer-governed method for converting scintiscan data recorded over the dorsal or ventral surfaces of the thorax into fractions of pulmonary blood flow traversing the right and left lungs is presented.

DNA stable-isotope probing (DNA-SIP).

PubMed

Dunford, Eric A; Neufeld, Josh D

2010-08-02

DNA stable-isotope probing (DNA-SIP) is a powerful technique for identifying active microorganisms that assimilate particular carbon substrates and nutrients into cellular biomass. As such, this cultivation-independent technique has been an important methodology for assigning metabolic function to the diverse communities inhabiting a wide range of terrestrial and aquatic environments. Following the incubation of an environmental sample with stable-isotope labelled compounds, extracted nucleic acid is subjected to density gradient ultracentrifugation and subsequent gradient fractionation to separate nucleic acids of differing densities. Purification of DNA from cesium chloride retrieves labelled and unlabelled DNA for subsequent molecular characterization (e.g. fingerprinting, microarrays, clone libraries, metagenomics). This JoVE video protocol provides visual step-by-step explanations of the protocol for density gradient ultracentrifugation, gradient fractionation and recovery of labelled DNA. The protocol also includes sample SIP data and highlights important tips and cautions that must be considered to ensure a successful DNA-SIP analysis.

An Atlas of Peroxiredoxins Created Using an Active Site Profile-Based Approach to Functionally Relevant Clustering of Proteins.

PubMed

Harper, Angela F; Leuthaeuser, Janelle B; Babbitt, Patricia C; Morris, John H; Ferrin, Thomas E; Poole, Leslie B; Fetrow, Jacquelyn S

2017-02-01

Peroxiredoxins (Prxs or Prdxs) are a large protein superfamily of antioxidant enzymes that rapidly detoxify damaging peroxides and/or affect signal transduction and, thus, have roles in proliferation, differentiation, and apoptosis. Prx superfamily members are widespread across phylogeny and multiple methods have been developed to classify them. Here we present an updated atlas of the Prx superfamily identified using a novel method called MISST (Multi-level Iterative Sequence Searching Technique). MISST is an iterative search process developed to be both agglomerative, to add sequences containing similar functional site features, and divisive, to split groups when functional site features suggest distinct functionally-relevant clusters. Superfamily members need not be identified initially-MISST begins with a minimal representative set of known structures and searches GenBank iteratively. Further, the method's novelty lies in the manner in which isofunctional groups are selected; rather than use a single or shifting threshold to identify clusters, the groups are deemed isofunctional when they pass a self-identification criterion, such that the group identifies itself and nothing else in a search of GenBank. The method was preliminarily validated on the Prxs, as the Prxs presented challenges of both agglomeration and division. For example, previous sequence analysis clustered the Prx functional families Prx1 and Prx6 into one group. Subsequent expert analysis clearly identified Prx6 as a distinct functionally relevant group. The MISST process distinguishes these two closely related, though functionally distinct, families. Through MISST search iterations, over 38,000 Prx sequences were identified, which the method divided into six isofunctional clusters, consistent with previous expert analysis. The results represent the most complete computational functional analysis of proteins comprising the Prx superfamily. The feasibility of this novel method is demonstrated by the Prx superfamily results, laying the foundation for potential functionally relevant clustering of the universe of protein sequences.

An Atlas of Peroxiredoxins Created Using an Active Site Profile-Based Approach to Functionally Relevant Clustering of Proteins

PubMed Central

Babbitt, Patricia C.; Ferrin, Thomas E.

2017-01-01

Peroxiredoxins (Prxs or Prdxs) are a large protein superfamily of antioxidant enzymes that rapidly detoxify damaging peroxides and/or affect signal transduction and, thus, have roles in proliferation, differentiation, and apoptosis. Prx superfamily members are widespread across phylogeny and multiple methods have been developed to classify them. Here we present an updated atlas of the Prx superfamily identified using a novel method called MISST (Multi-level Iterative Sequence Searching Technique). MISST is an iterative search process developed to be both agglomerative, to add sequences containing similar functional site features, and divisive, to split groups when functional site features suggest distinct functionally-relevant clusters. Superfamily members need not be identified initially—MISST begins with a minimal representative set of known structures and searches GenBank iteratively. Further, the method’s novelty lies in the manner in which isofunctional groups are selected; rather than use a single or shifting threshold to identify clusters, the groups are deemed isofunctional when they pass a self-identification criterion, such that the group identifies itself and nothing else in a search of GenBank. The method was preliminarily validated on the Prxs, as the Prxs presented challenges of both agglomeration and division. For example, previous sequence analysis clustered the Prx functional families Prx1 and Prx6 into one group. Subsequent expert analysis clearly identified Prx6 as a distinct functionally relevant group. The MISST process distinguishes these two closely related, though functionally distinct, families. Through MISST search iterations, over 38,000 Prx sequences were identified, which the method divided into six isofunctional clusters, consistent with previous expert analysis. The results represent the most complete computational functional analysis of proteins comprising the Prx superfamily. The feasibility of this novel method is demonstrated by the Prx superfamily results, laying the foundation for potential functionally relevant clustering of the universe of protein sequences. PMID:28187133

Gene Network Construction from Microarray Data Identifies a Key Network Module and Several Candidate Hub Genes in Age-Associated Spatial Learning Impairment

PubMed Central

Uddin, Raihan; Singh, Shiva M.

2017-01-01

As humans age many suffer from a decrease in normal brain functions including spatial learning impairments. This study aimed to better understand the molecular mechanisms in age-associated spatial learning impairment (ASLI). We used a mathematical modeling approach implemented in Weighted Gene Co-expression Network Analysis (WGCNA) to create and compare gene network models of young (learning unimpaired) and aged (predominantly learning impaired) brains from a set of exploratory datasets in rats in the context of ASLI. The major goal was to overcome some of the limitations previously observed in the traditional meta- and pathway analysis using these data, and identify novel ASLI related genes and their networks based on co-expression relationship of genes. This analysis identified a set of network modules in the young, each of which is highly enriched with genes functioning in broad but distinct GO functional categories or biological pathways. Interestingly, the analysis pointed to a single module that was highly enriched with genes functioning in “learning and memory” related functions and pathways. Subsequent differential network analysis of this “learning and memory” module in the aged (predominantly learning impaired) rats compared to the young learning unimpaired rats allowed us to identify a set of novel ASLI candidate hub genes. Some of these genes show significant repeatability in networks generated from independent young and aged validation datasets. These hub genes are highly co-expressed with other genes in the network, which not only show differential expression but also differential co-expression and differential connectivity across age and learning impairment. The known function of these hub genes indicate that they play key roles in critical pathways, including kinase and phosphatase signaling, in functions related to various ion channels, and in maintaining neuronal integrity relating to synaptic plasticity and memory formation. Taken together, they provide a new insight and generate new hypotheses into the molecular mechanisms responsible for age associated learning impairment, including spatial learning. PMID:29066959

Gene Network Construction from Microarray Data Identifies a Key Network Module and Several Candidate Hub Genes in Age-Associated Spatial Learning Impairment.

PubMed

Uddin, Raihan; Singh, Shiva M

2017-01-01

As humans age many suffer from a decrease in normal brain functions including spatial learning impairments. This study aimed to better understand the molecular mechanisms in age-associated spatial learning impairment (ASLI). We used a mathematical modeling approach implemented in Weighted Gene Co-expression Network Analysis (WGCNA) to create and compare gene network models of young (learning unimpaired) and aged (predominantly learning impaired) brains from a set of exploratory datasets in rats in the context of ASLI. The major goal was to overcome some of the limitations previously observed in the traditional meta- and pathway analysis using these data, and identify novel ASLI related genes and their networks based on co-expression relationship of genes. This analysis identified a set of network modules in the young, each of which is highly enriched with genes functioning in broad but distinct GO functional categories or biological pathways. Interestingly, the analysis pointed to a single module that was highly enriched with genes functioning in "learning and memory" related functions and pathways. Subsequent differential network analysis of this "learning and memory" module in the aged (predominantly learning impaired) rats compared to the young learning unimpaired rats allowed us to identify a set of novel ASLI candidate hub genes. Some of these genes show significant repeatability in networks generated from independent young and aged validation datasets. These hub genes are highly co-expressed with other genes in the network, which not only show differential expression but also differential co-expression and differential connectivity across age and learning impairment. The known function of these hub genes indicate that they play key roles in critical pathways, including kinase and phosphatase signaling, in functions related to various ion channels, and in maintaining neuronal integrity relating to synaptic plasticity and memory formation. Taken together, they provide a new insight and generate new hypotheses into the molecular mechanisms responsible for age associated learning impairment, including spatial learning.

A "footprint" of plant carbon fixation cycle functions during the development of a heterotrophic fungus.

PubMed

Lyu, Xueliang; Shen, Cuicui; Xie, Jiatao; Fu, Yanping; Jiang, Daohong; Hu, Zijin; Tang, Lihua; Tang, Liguang; Ding, Feng; Li, Kunfei; Wu, Song; Hu, Yanping; Luo, Lilian; Li, Yuanhao; Wang, Qihua; Li, Guoqing; Cheng, Jiasen

2015-08-11

Carbon fixation pathway of plants (CFPP) in photosynthesis converts solar energy to biomass, bio-products and biofuel. Intriguingly, a large number of heterotrophic fungi also possess enzymes functionally associated with CFPP, raising the questions about their roles in fungal development and in evolution. Here, we report on the presence of 17 CFPP associated enzymes (ten in Calvin-Benson-Basham reductive pentose phosphate pathway and seven in C4-dicarboxylic acid cycle) in the genome of Sclerotinia sclerotiorum, a heterotrophic phytopathogenic fungus, and only two unique enzymes: ribulose-1, 5-bisphosphate carboxylase-oxygenase (Rubisco) and phosphoribulokinase (PRK) were absent. This data suggested an incomplete CFPP-like pathway (CLP) in fungi. Functional profile analysis demonstrated that the activity of the incomplete CLP was dramatically regulated during different developmental stages of S. sclerotiorum. Subsequent experiments confirmed that many of them were essential to the virulence and/or sclerotial formation. Most of the CLP associated genes are conserved in fungi. Phylogenetic analysis showed that many of them have undergone gene duplication, gene acquisition or loss and functional diversification in evolutionary history. These findings showed an evolutionary links in the carbon fixation processes of autotrophs and heterotrophs and implicated the functions of related genes were in course of continuous change in different organisms in evolution.

Comprehensive reliability allocation method for CNC lathes based on cubic transformed functions of failure mode and effects analysis

NASA Astrophysics Data System (ADS)

Yang, Zhou; Zhu, Yunpeng; Ren, Hongrui; Zhang, Yimin

2015-03-01

Reliability allocation of computerized numerical controlled(CNC) lathes is very important in industry. Traditional allocation methods only focus on high-failure rate components rather than moderate failure rate components, which is not applicable in some conditions. Aiming at solving the problem of CNC lathes reliability allocating, a comprehensive reliability allocation method based on cubic transformed functions of failure modes and effects analysis(FMEA) is presented. Firstly, conventional reliability allocation methods are introduced. Then the limitations of direct combination of comprehensive allocation method with the exponential transformed FMEA method are investigated. Subsequently, a cubic transformed function is established in order to overcome these limitations. Properties of the new transformed functions are discussed by considering the failure severity and the failure occurrence. Designers can choose appropriate transform amplitudes according to their requirements. Finally, a CNC lathe and a spindle system are used as an example to verify the new allocation method. Seven criteria are considered to compare the results of the new method with traditional methods. The allocation results indicate that the new method is more flexible than traditional methods. By employing the new cubic transformed function, the method covers a wider range of problems in CNC reliability allocation without losing the advantages of traditional methods.

MRI correlates of interaction between gender and expressive suppression among the Chinese population.

PubMed

Wang, Kangcheng; Huang, Hui; Chen, Li; Hou, Xin; Zhang, Yong; Yang, Junyi; Hao, Xin; Qiu, Jiang

2017-04-07

Expressive suppression is a kind of emotion regulation strategies by suppressing behaviors related to emotional responding. Despite the amount of behavioral research on expressive suppression, the structural and functional mechanisms underlying the interaction between gender and expressive suppression in Chinese healthy subjects have remained unknown. In the current study, we assessed the levels of expressive suppression and acquired the structural and functional imaging data from 273 Chinese individuals. A nearly automatic cortical processing technique was used to calculate cortical thickness for each subject. The results from cortical thickness analyses revealed a significant interaction between gender and expressive suppression in the superior frontal gyrus. Then, we conducted the whole-brain functional connectivity analysis with the seed of the superior frontal gyrus to explore the functionally related regions of brain. Subsequent analysis of the interaction between gender and expressive suppression indicated a significant functional connectivity between the superior frontal gyrus and default mode network (DMN) core regions, including the medial prefrontal cortex, precuneus and parahippocampal gyrus. Our results provided the robust empirical evidence illustrating the role of the superior frontal gyrus and DMN in gender difference of expressive suppression among the Chinese population. These findings might have implications for understanding gender difference in emotion processing and regulation. Copyright © 2017 IBRO. Published by Elsevier Ltd. All rights reserved.

Executive functioning complaints and escitalopram treatment response in late-life depression.

PubMed

Manning, Kevin J; Alexopoulos, George S; Banerjee, Samprit; Morimoto, Sarah Shizuko; Seirup, Joanna K; Klimstra, Sibel A; Yuen, Genevieve; Kanellopoulos, Theodora; Gunning-Dixon, Faith

2015-05-01

Executive dysfunction may play a key role in the pathophysiology of late-life depression. Executive dysfunction can be assessed with cognitive tests and subjective report of difficulties with executive skills. The present study investigated the association between subjective report of executive functioning complaints and time to escitalopram treatment response in older adults with major depressive disorder (MDD). 100 older adults with MDD (58 with executive functioning complaints and 42 without executive functioning complaints) completed a 12-week trial of escitalopram. Treatment response over 12 weeks, as measured by repeated Hamilton Depression Rating Scale scores, was compared for adults with and without executive complaints using mixed-effects modeling. Mixed effects analysis revealed a significant group × time interaction, F(1, 523.34) = 6.00, p = 0.01. Depressed older adults who reported executive functioning complaints at baseline demonstrated a slower response to escitalopram treatment than those without executive functioning complaints. Self-report of executive functioning difficulties may be a useful prognostic indicator for subsequent speed of response to antidepressant medication. Copyright © 2015 American Association for Geriatric Psychiatry. Published by Elsevier Inc. All rights reserved.

An electroglottographical analysis-based discriminant function model differentiating multiple sclerosis patients from healthy controls.

PubMed

Vavougios, George D; Doskas, Triantafyllos; Konstantopoulos, Kostas

2018-05-01

Dysarthrophonia is a predominant symptom in many neurological diseases, affecting the quality of life of the patients. In this study, we produced a discriminant function equation that can differentiate MS patients from healthy controls, using electroglottographic variables not analyzed in a previous study. We applied stepwise linear discriminant function analysis in order to produce a function and score derived from electroglottographic variables extracted from a previous study. The derived discriminant function's statistical significance was determined via Wilk's λ test (and the associated p value). Finally, a 2 × 2 confusion matrix was used to determine the function's predictive accuracy, whereas the cross-validated predictive accuracy is estimated via the "leave-one-out" classification process. Discriminant function analysis (DFA) was used to create a linear function of continuous predictors. DFA produced the following model (Wilk's λ = 0.043, χ2 = 388.588, p < 0.0001, Tables 3 and 4): D (MS vs controls) = 0.728*DQx1 mean monologue + 0.325*CQx monologue + 0.298*DFx1 90% range monologue + 0.443*DQx1 90% range reading - 1.490*DQx1 90% range monologue. The derived discriminant score (S1) was used subsequently in order to form the coordinates of a ROC curve. Thus, a cutoff score of - 0.788 for S1 corresponded to a perfect classification (100% sensitivity and 100% specificity, p = 1.67e -22 ). Consistent with previous findings, electroglottographic evaluation represents an easy to implement and potentially important assessment in MS patients, achieving adequate classification accuracy. Further evaluation is needed to determine its use as a biomarker.

Changes in social functioning and circulating oxytocin and vasopressin following the migration to a new country.

PubMed

Gouin, Jean-Philippe; Pournajafi-Nazarloo, Hossein; Carter, C Sue

2015-02-01

Prior studies have reported associations between plasma oxytocin and vasopressin and markers of social functioning. However, because most human studies have used cross-sectional designs, it is unclear whether plasma oxytocin and vasopressin influences social functioning or whether social functioning modulates the production and peripheral release of these peptides. In order to address this question, we followed individuals who experienced major changes in social functioning subsequent to the migration to a new country. In this study, 59 new international students were recruited shortly after arrival in the host country and reassessed 2 and 5 months later. At each assessment participants provided information on their current social functioning and blood samples for oxytocin and vasopressin analysis. Results indicated that changes in social functioning were not related to changes in plasma oxytocin. Instead, baseline oxytocin predicted changes in social relationship satisfaction, social support, and loneliness over time. In contrast, plasma vasopressin changed as a function of social integration. Baseline vasopressin was not related to changes in social functioning over time. These results emphasize the different roles of plasma oxytocin and vasopressin in responses to changes in social functioning in humans. Copyright © 2014 Elsevier Inc. All rights reserved.

An interactive web-based application for Comprehensive Analysis of RNAi-screen Data.

PubMed

Dutta, Bhaskar; Azhir, Alaleh; Merino, Louis-Henri; Guo, Yongjian; Revanur, Swetha; Madhamshettiwar, Piyush B; Germain, Ronald N; Smith, Jennifer A; Simpson, Kaylene J; Martin, Scott E; Buehler, Eugen; Beuhler, Eugen; Fraser, Iain D C

2016-02-23

RNAi screens are widely used in functional genomics. Although the screen data can be susceptible to a number of experimental biases, many of these can be corrected by computational analysis. For this purpose, here we have developed a web-based platform for integrated analysis and visualization of RNAi screen data named CARD (for Comprehensive Analysis of RNAi Data; available at https://card.niaid.nih.gov). CARD allows the user to seamlessly carry out sequential steps in a rigorous data analysis workflow, including normalization, off-target analysis, integration of gene expression data, optimal thresholds for hit selection and network/pathway analysis. To evaluate the utility of CARD, we describe analysis of three genome-scale siRNA screens and demonstrate: (i) a significant increase both in selection of subsequently validated hits and in rejection of false positives, (ii) an increased overlap of hits from independent screens of the same biology and (iii) insight to microRNA (miRNA) activity based on siRNA seed enrichment.

An interactive web-based application for Comprehensive Analysis of RNAi-screen Data

PubMed Central

Dutta, Bhaskar; Azhir, Alaleh; Merino, Louis-Henri; Guo, Yongjian; Revanur, Swetha; Madhamshettiwar, Piyush B.; Germain, Ronald N.; Smith, Jennifer A.; Simpson, Kaylene J.; Martin, Scott E.; Beuhler, Eugen; Fraser, Iain D. C.

2016-01-01

RNAi screens are widely used in functional genomics. Although the screen data can be susceptible to a number of experimental biases, many of these can be corrected by computational analysis. For this purpose, here we have developed a web-based platform for integrated analysis and visualization of RNAi screen data named CARD (for Comprehensive Analysis of RNAi Data; available at https://card.niaid.nih.gov). CARD allows the user to seamlessly carry out sequential steps in a rigorous data analysis workflow, including normalization, off-target analysis, integration of gene expression data, optimal thresholds for hit selection and network/pathway analysis. To evaluate the utility of CARD, we describe analysis of three genome-scale siRNA screens and demonstrate: (i) a significant increase both in selection of subsequently validated hits and in rejection of false positives, (ii) an increased overlap of hits from independent screens of the same biology and (iii) insight to microRNA (miRNA) activity based on siRNA seed enrichment. PMID:26902267

The moisture outgassing kinetics of a silica reinforced polydimethylsiloxane

NASA Astrophysics Data System (ADS)

Sharma, H. N.; McLean, W.; Maxwell, R. S.; Dinh, L. N.

2016-09-01

A silica-filled polydimethylsiloxane (PDMS) composite M9787 was investigated for potential outgassing in a vacuum/dry environment with the temperature programmed desorption/reaction method. The outgassing kinetics of 463 K vacuum heat-treated samples, vacuum heat-treated samples which were subsequently re-exposed to moisture, and untreated samples were extracted using the isoconversional and constrained iterative regression methods in a complementary fashion. Density functional theory (DFT) calculations of water interactions with a silica surface were also performed to provide insight into the structural motifs leading to the obtained kinetic parameters. Kinetic analysis/model revealed that no outgassing occurs from the vacuum heat-treated samples in subsequent vacuum/dry environment applications at room temperature (˜300 K). The main effect of re-exposure of the vacuum heat-treated samples to a glove box condition (˜30 ppm by volume of H2O) for even a couple of days was the formation, on the silica surface fillers, of ˜60 ppm by weight of physisorbed and loosely bonded moisture, which subsequently outgasses at room temperature in a vacuum/dry environment in a time span of 10 yr. However, without any vacuum heat treatment and even after 1 h of vacuum pump down, about 300 ppm by weight of H2O would be released from the PDMS in the next few hours. Thereafter the outgassing rate slows down substantially. The presented methodology of using the isoconversional kinetic analysis results and some appropriate nature of the reaction as the constraints for more accurate iterative regression analysis/deconvolution of complex kinetic spectra, and of checking the so-obtained results with first principle calculations such as DFT can serve as a template for treating other complex physical/chemical processes as well.

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

Sharma, H. N.; McLean, W.; Maxwell, R. S.

We investigated a silica-filled polydimethylsiloxane (PDMS) composite M9787 for potential outgassing in a vacuum/dry environment with the temperature programmed desorption/reaction method. The outgassing kinetics of 463 K vacuum heat-treated samples, vacuum heat-treated samples which were subsequently re-exposed to moisture, and untreated samples were extracted using the isoconversional and constrained iterative regression methods in a complementary fashion. Density functional theory (DFT) calculations of water interactions with a silica surface were also performed to provide insight into the structural motifs leading to the obtained kinetic parameters. Kinetic analysis/model revealed that no outgassing occurs from the vacuum heat-treated samples in subsequent vacuum/dry environmentmore » applications at room temperature (~300 K). Moreover, the main effect of re-exposure of the vacuum heat-treated samples to a glove box condition (~30 ppm by volume of H 2O) for even a couple of days was the formation, on the silica surface fillers, of ~60 ppm by weight of physisorbed and loosely bonded moisture, which subsequently outgasses at room temperature in a vacuum/dry environment in a time span of 10 yr. However, without any vacuum heat treatment and even after 1 h of vacuum pump down, about 300 ppm by weight of H 2O would be released from the PDMS in the next few hours. Thereafter the outgassing rate slows down substantially. Our presented methodology of using the isoconversional kinetic analysis results and some appropriate nature of the reaction as the constraints for more accurate iterative regression analysis/deconvolution of complex kinetic spectra, and of checking the so-obtained results with first principle calculations such as DFT can serve as a template for treating other complex physical/chemical processes as well.« less

The moisture outgassing kinetics of a silica reinforced polydimethylsiloxane

DOE PAGES

Sharma, H. N.; McLean, W.; Maxwell, R. S.; ...

2016-09-21

We investigated a silica-filled polydimethylsiloxane (PDMS) composite M9787 for potential outgassing in a vacuum/dry environment with the temperature programmed desorption/reaction method. The outgassing kinetics of 463 K vacuum heat-treated samples, vacuum heat-treated samples which were subsequently re-exposed to moisture, and untreated samples were extracted using the isoconversional and constrained iterative regression methods in a complementary fashion. Density functional theory (DFT) calculations of water interactions with a silica surface were also performed to provide insight into the structural motifs leading to the obtained kinetic parameters. Kinetic analysis/model revealed that no outgassing occurs from the vacuum heat-treated samples in subsequent vacuum/dry environmentmore » applications at room temperature (~300 K). Moreover, the main effect of re-exposure of the vacuum heat-treated samples to a glove box condition (~30 ppm by volume of H 2O) for even a couple of days was the formation, on the silica surface fillers, of ~60 ppm by weight of physisorbed and loosely bonded moisture, which subsequently outgasses at room temperature in a vacuum/dry environment in a time span of 10 yr. However, without any vacuum heat treatment and even after 1 h of vacuum pump down, about 300 ppm by weight of H 2O would be released from the PDMS in the next few hours. Thereafter the outgassing rate slows down substantially. Our presented methodology of using the isoconversional kinetic analysis results and some appropriate nature of the reaction as the constraints for more accurate iterative regression analysis/deconvolution of complex kinetic spectra, and of checking the so-obtained results with first principle calculations such as DFT can serve as a template for treating other complex physical/chemical processes as well.« less

EEG-tomographic studies with LORETA on vigilance differences between narcolepsy patients and controls and subsequent double-blind, placebo-controlled studies with modafinil.

PubMed

Saletu, M; Anderer, P; Saletu-Zyhlarz, G M; Mandl, M; Arnold, O; Zeitlhofer, J; Saletu, B

2004-11-01

The aim of the present study was to identify brain regions associated with vigilance in untreated and modafinil-treated narcoleptic patients by means of low-resolution brain electromagnetic tomography (LORETA). 16 drug-free narcoleptics and 16 normal controls were included in the baseline investigation. Subsequently patients participated in a double-blind, placebo-controlled crossover study receiving a three-week fixed titration of modafinil (200, 300, 400 mg) and placebo. Measurements comprised LORETA, the Multiple Sleep Latency Test (MSLT) and the Epworth Sleepiness Scale (ESS) obtained before and after three weeks' therapy. Statistical overall analysis by means of the omnibus significance test demonstrated significant inter-group differences in the resting (R-EEG), but not in the vigilance-controlled recordings (V-EEG). Subsequent univariate analysis revealed a decrease in alpha-2 and beta 1-3 power in prefrontal, temporal and parietal cortices, with the right hemisphere slightly more involved in this vigilance decrement. Modafinil 400 mg/d as compared with placebo induced changes opposite to the aforementioned baseline differences (key-lock principle) with a preponderance in the left hemisphere. This increase in vigilance resulted in an improvement in the MSLT and the ESS. LORETA provided evidence of a functional deterioration of the fronto-temporo-parietal network of the right-hemispheric vigilance system in narcolepsy and a therapeutic effect of modafinil on the left hemisphere, which is less affected by the disease.

Social support and subsequent disability: it is not the size of your network that counts.

PubMed

McLaughlin, Deirdre; Leung, Janni; Pachana, Nancy; Flicker, Leon; Hankey, Graeme; Dobson, Annette

2012-09-01

high levels of social support and engagement may help sustain good health and functional ability. However, the definition of social support in previous research has been inconsistent and findings are mixed. The aim of this analysis was to explore the effect of two aspects of social support on subsequent disability in a group of community dwelling older women and men. data were drawn from two concurrent prospective observational cohort studies of community-based older Australian women (N = 2,013) and men (N = 680). Baseline and follow-up data were drawn from the second (1999) and fifth (2008) surveys of the women and the second (2001) and third (2008) surveys of the men. At baseline, social support was measured by the two subscales (social network and subjective support) of the Duke Social Support Index (DSSI). The outcome measure was Activities of Daily Living (ADLs) and Instrumental Activities of Daily Living (IADLs). overall, social network size was not associated with subsequent disability in either women or men. After adjusting for health status at baseline, lack of satisfaction with social support was associated with greater difficulties in ADLs and IADLs for both women and men. our results suggest that the provision of social support is insufficient to limit subsequent disability: support provided must be subjectively perceived to be relevant and adequate.

Another procedure for the preliminary ordering of loci based on two point lod scores.

PubMed

Curtis, D

1994-01-01

Because of the difficulty of performing full likelihood analysis over multiple loci and the large numbers of possible orders, a number of methods have been proposed for quickly evaluating orders and, to a lesser extent, for generating good orders. A new method is proposed which uses a function which is moderately laborious to compute, the sum of lod scores between all pairs of loci. This function can be smoothly minimized by initially allowing the loci to be placed anywhere in space, and only subsequently constraining them to lie along a one-dimensional map. Application of this approach to sample data suggests that it has promise and might usefully be combined with other methods when loci need to be ordered.

Resolving TYK2 locus genotype-to-phenotype differences in autoimmunity

PubMed Central

Dendrou, Calliope A.; Cortes, Adrian; Shipman, Lydia; Evans, Hayley G.; Attfield, Kathrine E.; Jostins, Luke; Barber, Thomas; Kaur, Gurman; Kuttikkatte, Subita Balaram; Leach, Oliver A.; Desel, Christiane; Faergeman, Soren L.; Cheeseman, Jane; Neville, Matt J.; Sawcer, Stephen; Compston, Alastair; Johnson, Adam R.; Everett, Christine; Bell, John I.; Karpe, Fredrik; Ultsch, Mark; Eigenbrot, Charles; McVean, Gil; Fugger, Lars

2017-01-01

Thousands of genetic variants have been identified that contribute to the development of complex diseases, but determining how to fully elucidate their biological consequences for translation into clinical benefit is challenging. Conflicting evidence regarding the functional impact of genetic variants in the tyrosine kinase 2 (TYK2) gene, which is differentially associated with common autoimmune diseases, currently obscures the potential of TYK2 as a therapeutic target. We aimed to resolve this conflict by performing genetic meta-analysis across disorders, subsequent molecular, cellular, in vivo and structural functional follow-up and epidemiological studies. Our data revealed a protective homozygous effect that defined a signaling optimum between autoimmunity and immunodeficiency and identified TYK2 as a potential drug target for multiple autoimmune disorders. PMID:27807284

Analysis of effect of the solubility on gas exchange in nonhomogeneous lungs

NASA Technical Reports Server (NTRS)

Colburn, W. E., Jr.; Evans, J. W.; West, J. B.

1974-01-01

A comparison is made of the gas exchange in nonhomogeneous lung models and in homogeneous lung models with the same total blood flow and ventilation. It is shown that the ratio of the rate of gas transfer of the inhomogeneous lung model over the rate of gas transfer of the homogeneous lung model as a function of gas solubility always has the qualitative features for gases with linear dissociation curves. This ratio is 1 for a gas with zero solubility and decreases to a single minimum. It subsequently rises to approach 1 as the solubility tends to infinity. The early portion of the graph of this function is convex, then after a single inflection point it is concave.

Quantifying cadherin mechanotransduction machinery assembly/disassembly dynamics using fluorescence covariance analysis.

PubMed

Vedula, Pavan; Cruz, Lissette A; Gutierrez, Natasha; Davis, Justin; Ayee, Brian; Abramczyk, Rachel; Rodriguez, Alexis J

2016-06-30

Quantifying multi-molecular complex assembly in specific cytoplasmic compartments is crucial to understand how cells use assembly/disassembly of these complexes to control function. Currently, biophysical methods like Fluorescence Resonance Energy Transfer and Fluorescence Correlation Spectroscopy provide quantitative measurements of direct protein-protein interactions, while traditional biochemical approaches such as sub-cellular fractionation and immunoprecipitation remain the main approaches used to study multi-protein complex assembly/disassembly dynamics. In this article, we validate and quantify multi-protein adherens junction complex assembly in situ using light microscopy and Fluorescence Covariance Analysis. Utilizing specific fluorescently-labeled protein pairs, we quantified various stages of adherens junction complex assembly, the multiprotein complex regulating epithelial tissue structure and function following de novo cell-cell contact. We demonstrate: minimal cadherin-catenin complex assembly in the perinuclear cytoplasm and subsequent localization to the cell-cell contact zone, assembly of adherens junction complexes, acto-myosin tension-mediated anchoring, and adherens junction maturation following de novo cell-cell contact. Finally applying Fluorescence Covariance Analysis in live cells expressing fluorescently tagged adherens junction complex proteins, we also quantified adherens junction complex assembly dynamics during epithelial monolayer formation.

Network representation of protein interactions: Theory of graph description and analysis.

PubMed

Kurzbach, Dennis

2016-09-01

A methodological framework is presented for the graph theoretical interpretation of NMR data of protein interactions. The proposed analysis generalizes the idea of network representations of protein structures by expanding it to protein interactions. This approach is based on regularization of residue-resolved NMR relaxation times and chemical shift data and subsequent construction of an adjacency matrix that represents the underlying protein interaction as a graph or network. The network nodes represent protein residues. Two nodes are connected if two residues are functionally correlated during the protein interaction event. The analysis of the resulting network enables the quantification of the importance of each amino acid of a protein for its interactions. Furthermore, the determination of the pattern of correlations between residues yields insights into the functional architecture of an interaction. This is of special interest for intrinsically disordered proteins, since the structural (three-dimensional) architecture of these proteins and their complexes is difficult to determine. The power of the proposed methodology is demonstrated at the example of the interaction between the intrinsically disordered protein osteopontin and its natural ligand heparin. © 2016 The Protein Society.

Decomposition of metabolic network into functional modules based on the global connectivity structure of reaction graph.

PubMed

Ma, Hong-Wu; Zhao, Xue-Ming; Yuan, Ying-Jin; Zeng, An-Ping

2004-08-12

Metabolic networks are organized in a modular, hierarchical manner. Methods for a rational decomposition of the metabolic network into relatively independent functional subsets are essential to better understand the modularity and organization principle of a large-scale, genome-wide network. Network decomposition is also necessary for functional analysis of metabolism by pathway analysis methods that are often hampered by the problem of combinatorial explosion due to the complexity of metabolic network. Decomposition methods proposed in literature are mainly based on the connection degree of metabolites. To obtain a more reasonable decomposition, the global connectivity structure of metabolic networks should be taken into account. In this work, we use a reaction graph representation of a metabolic network for the identification of its global connectivity structure and for decomposition. A bow-tie connectivity structure similar to that previously discovered for metabolite graph is found also to exist in the reaction graph. Based on this bow-tie structure, a new decomposition method is proposed, which uses a distance definition derived from the path length between two reactions. An hierarchical classification tree is first constructed from the distance matrix among the reactions in the giant strong component of the bow-tie structure. These reactions are then grouped into different subsets based on the hierarchical tree. Reactions in the IN and OUT subsets of the bow-tie structure are subsequently placed in the corresponding subsets according to a 'majority rule'. Compared with the decomposition methods proposed in literature, ours is based on combined properties of the global network structure and local reaction connectivity rather than, primarily, on the connection degree of metabolites. The method is applied to decompose the metabolic network of Escherichia coli. Eleven subsets are obtained. More detailed investigations of the subsets show that reactions in the same subset are really functionally related. The rational decomposition of metabolic networks, and subsequent studies of the subsets, make it more amenable to understand the inherent organization and functionality of metabolic networks at the modular level. http://genome.gbf.de/bioinformatics/

Idea density measured in late life predicts subsequent cognitive trajectories: implications for the measurement of cognitive reserve.

PubMed

Farias, Sarah Tomaszewski; Chand, Vineeta; Bonnici, Lisa; Baynes, Kathleen; Harvey, Danielle; Mungas, Dan; Simon, Christa; Reed, Bruce

2012-11-01

The Nun Study showed that lower linguistic ability in young adulthood, measured by idea density (ID), increased the risk of dementia in late life. The present study examined whether ID measured in late life continues to predict the trajectory of cognitive change. ID was measured in 81 older adults who were followed longitudinally for an average of 4.3 years. Changes in global cognition and 4 specific neuropsychological domains (episodic memory, semantic memory, spatial abilities, and executive function) were examined as outcomes. Separate random effects models tested the effect of ID on longitudinal change in outcomes, adjusted for age and education. Lower ID was associated with greater subsequent decline in global cognition, semantic memory, episodic memory, and spatial abilities. When analysis was restricted to only participants without dementia at the time ID was collected, results were similar. Linguistic ability in young adulthood, as measured by ID, has been previously proposed as an index of neurocognitive development and/or cognitive reserve. The present study provides evidence that even when ID is measured in old age, it continues to be associated with subsequent cognitive decline and as such may continue to provide a marker of cognitive reserve.

Corrosion consequences of microfouling in water reclamation systems

NASA Technical Reports Server (NTRS)

Ford, Tim; Mitchell, Ralph

1991-01-01

This paper examines the potential fouling and corrosion problems associated with microbial film formation throughout the water reclamation system (WRS) designed for the Space Station Freedom. It is shown that the use of advanced metal sputtering techiques combined with image analysis and FTIR spectroscopy will present realistic solutions for investigating the formation and function of biofilm on different alloys, the subsequent corrosion, and the efficiency of different treatments. These techniques, used in combination with electrochemical measurements of corrosion, will provide a powerful approach to examinations of materials considered for use in the WRS.

New atmospheric sensor analysis study

NASA Technical Reports Server (NTRS)

Parker, K. G.

1989-01-01

The functional capabilities of the ESAD Research Computing Facility are discussed. The system is used in processing atmospheric measurements which are used in the evaluation of sensor performance, conducting design-concept simulation studies, and also in modeling the physical and dynamical nature of atmospheric processes. The results may then be evaluated to furnish inputs into the final design specifications for new space sensors intended for future Spacelab, Space Station, and free-flying missions. In addition, data gathered from these missions may subsequently be analyzed to provide better understanding of requirements for numerical modeling of atmospheric phenomena.

Meta-analyses of cognitive and motor function in youth aged 16 years and younger who subsequently develop schizophrenia.

PubMed

Dickson, H; Laurens, K R; Cullen, A E; Hodgins, S

2012-04-01

Previous reviews have reported cognitive and motor deficits in childhood and adolescence among individuals who later develop schizophrenia. However, these reviews focused exclusively on studies of individuals with affected relatives or on population/birth cohorts, incorporated studies with estimated measures of pre-morbid intelligence, or included investigations that examined symptomatic at-risk participants or participants 18 years or older. Thus, it remains unclear whether cognitive and motor deficits constitute robust antecedents of schizophrenia. Meta-analyses were conducted on published studies that examined cognitive or motor function in youth aged 16 years or younger who later developed schizophrenia or a schizophrenia spectrum disorder (SSD) and those who did not. Twenty-three studies fulfilled the following inclusion criteria: (1) written in English; (2) prospective investigations of birth or genetic high-risk cohorts, or follow-back investigations of population samples; (3) objective measures of cognitive or motor performance at age 16 or younger; (4) results provided for individuals who did and who did not develop schizophrenia/SSD later in life; and (5) sufficient data to calculate effect sizes. Four domains of function were examined: IQ; Motor Function; General Academic Achievement; and Mathematics Achievement. Meta-analyses showed that, by age 16, individuals who subsequently developed schizophrenia/SSD displayed significant deficits in IQ (d=0.51) and motor function (d=0.56), but not in general academic achievement (d=0.25) or mathematics achievement (d=0.21). Subsidiary analysis indicated that the IQ deficit was present by age 13. These results demonstrate that deficits in IQ and motor performance precede the prodrome and the onset of illness.

Functional Outcome of Neurologic-Controlled HAL-Exoskeletal Neurorehabilitation in Chronic Spinal Cord Injury: A Pilot With One Year Treatment and Variable Treatment Frequency.

PubMed

Jansen, Oliver; Schildhauer, Thomas A; Meindl, Renate C; Tegenthoff, Martin; Schwenkreis, Peter; Sczesny-Kaiser, Matthias; Grasmücke, Dennis; Fisahn, Christian; Aach, Mirko

2017-12-01

Longitudinal prospective study. Whether 1-year HAL-BWSTT of chronic spinal cord injured patients can improve independent ambulated mobility further as a function of training frequency, after an initial 3-month training period. Eight patients with chronic SCI were enrolled. They initially received full standard physical therapy and neurorehabilitation in the acute/subacute posttrauma phase. During this trial, all patients first underwent a daily (5 per week) HAL-BWSTT for 12 weeks. Subsequently, these patients performed a 40-week HAL-BWSTT with a training session frequency of either 1 or 3 to 5 sessions per week. The patients' functional status including HAL-associated treadmill-walking time, -distance, and -speed with additional analysis of gait pattern, and their independent (without wearing the robot suit) functional mobility improvements, were assessed using the 10-Meter-Walk Test (10MWT), Timed-Up-and-Go Test (TUG) and 6-Minute-Walk Test (6MinWT) on admission, at 6 weeks, 12 weeks, and 1 year after enrollment. The data were analyzed separately for the 2 training frequency subgroups after the initial 12-week training period, which was identical in both groups. During the 1-year follow-up, HAL-associated walking parameters and independent functional improvements were maintained in all the patients. This result held irrespective of the training frequency. Long-term 1-year maintenance of HAL-associated treadmill walking parameters and of improved independent walking abilities after initial 12 weeks of daily HAL-BWSTT is possible and depends mainly on the patients' ambulatory status accomplished after initial training period. Subsequent regular weekly training, but not higher frequency training, seems to be sufficient to preserve the improvements accomplished.

Functional Outcome of Neurologic-Controlled HAL-Exoskeletal Neurorehabilitation in Chronic Spinal Cord Injury: A Pilot With One Year Treatment and Variable Treatment Frequency

PubMed Central

Schildhauer, Thomas A.; Meindl, Renate C.; Tegenthoff, Martin; Schwenkreis, Peter; Sczesny-Kaiser, Matthias; Grasmücke, Dennis; Fisahn, Christian; Aach, Mirko

2017-01-01

Study Design: Longitudinal prospective study. Objectives: Whether 1-year HAL-BWSTT of chronic spinal cord injured patients can improve independent ambulated mobility further as a function of training frequency, after an initial 3-month training period. Methods: Eight patients with chronic SCI were enrolled. They initially received full standard physical therapy and neurorehabilitation in the acute/subacute posttrauma phase. During this trial, all patients first underwent a daily (5 per week) HAL-BWSTT for 12 weeks. Subsequently, these patients performed a 40-week HAL-BWSTT with a training session frequency of either 1 or 3 to 5 sessions per week. The patients’ functional status including HAL-associated treadmill-walking time, -distance, and -speed with additional analysis of gait pattern, and their independent (without wearing the robot suit) functional mobility improvements, were assessed using the 10-Meter-Walk Test (10MWT), Timed-Up-and-Go Test (TUG) and 6-Minute-Walk Test (6MinWT) on admission, at 6 weeks, 12 weeks, and 1 year after enrollment. The data were analyzed separately for the 2 training frequency subgroups after the initial 12-week training period, which was identical in both groups. Results: During the 1-year follow-up, HAL-associated walking parameters and independent functional improvements were maintained in all the patients. This result held irrespective of the training frequency. Conclusions: Long-term 1-year maintenance of HAL-associated treadmill walking parameters and of improved independent walking abilities after initial 12 weeks of daily HAL-BWSTT is possible and depends mainly on the patients’ ambulatory status accomplished after initial training period. Subsequent regular weekly training, but not higher frequency training, seems to be sufficient to preserve the improvements accomplished. PMID:29238636

Gene Editing Vectors for Studying Nicotinic Acetylcholine Receptors in Cholinergic Transmission.

PubMed

Peng, Can; Yan, Yijin; Kim, Veronica J; Engle, Staci E; Berry, Jennifer N; McIntosh, J Michael; Neve, Rachael L; Drenan, Ryan M

2018-05-19

Nicotinic acetylcholine receptors (nAChRs), prototype members of the cys-loop ligand gated ion channel family, are key mediators of cholinergic transmission in the central nervous system. Despite their importance, technical gaps exist in our ability to dissect the function of individual subunits in the brain. To overcome these barriers, we designed CRISPR/Cas9 small guide RNA sequences (sgRNAs) for production of loss-of-function alleles in mouse nAChR genes. These sgRNAs were validated in vitro via deep sequencing. We subsequently targeted candidate nAChR genes in vivo by creating herpes simplex virus (HSV) vectors delivering sgRNAs and Cas9 expression to mouse brain. Production of loss-of-function insertions or deletions (indels) by these "all-in-one" HSV vectors was confirmed using brain slice patch clamp electrophysiology coupled with pharmacological analysis. Next, we developed a scheme for cell type-specific gene editing in mouse brain. Knockin mice expressing Cas9 in a Cre-dependent manner were validated using viral microinjections and genetic crosses to common Cre-driver mouse lines. We subsequently confirmed functional Cas9 activity by targeting the ubiquitous neuronal protein, NeuN, using adeno associated virus (AAV) delivery of sgRNAs. Finally, the mouse β2 nAChR gene was successfully targeted in dopamine transporter (DAT) positive neurons via CRISPR/Cas9. The sgRNA sequences and viral vectors, including our scheme for Cre-dependent gene editing, should be generally useful to the scientific research community. These tools could lead to new discoveries related to the function of nAChRs in neurotransmission and behavioral processes. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

Neural mechanisms of reactivation-induced updating that enhance and distort memory

PubMed Central

St. Jacques, Peggy L.; Olm, Christopher; Schacter, Daniel L.

2013-01-01

We remember a considerable number of personal experiences because we are frequently reminded of them, a process known as memory reactivation. Although memory reactivation helps to stabilize and update memories, reactivation may also introduce distortions if novel information becomes incorporated with memory. Here we used functional magnetic resonance imaging (fMRI) to investigate the neural mechanisms mediating reactivation-induced updating in memory for events experienced during a museum tour. During scanning, participants were shown target photographs to reactivate memories from the museum tour followed by a novel lure photograph from an alternate tour. Later, participants were presented with target and lure photographs and asked to determine whether the photographs showed a stop they visited during the tour. We used a subsequent memory analysis to examine neural recruitment during reactivation that was associated with later true and false memories. We predicted that the quality of reactivation, as determined by online ratings of subjective recollection, would increase subsequent true memories but also facilitate incorporation of the lure photograph, thereby increasing subsequent false memories. The fMRI results revealed that the quality of reactivation modulated subsequent true and false memories via recruitment of left posterior parahippocampal, bilateral retrosplenial, and bilateral posterior inferior parietal cortices. However, the timing of neural recruitment and the way in which memories were reactivated contributed to differences in whether memory reactivation led to distortions or not. These data reveal the neural mechanisms recruited during memory reactivation that modify how memories will be subsequently retrieved, supporting the flexible and dynamic aspects of memory. PMID:24191059

Neural mechanisms of reactivation-induced updating that enhance and distort memory.

PubMed

St Jacques, Peggy L; Olm, Christopher; Schacter, Daniel L

2013-12-03

We remember a considerable number of personal experiences because we are frequently reminded of them, a process known as memory reactivation. Although memory reactivation helps to stabilize and update memories, reactivation may also introduce distortions if novel information becomes incorporated with memory. Here we used functional magnetic resonance imaging (fMRI) to investigate the neural mechanisms mediating reactivation-induced updating in memory for events experienced during a museum tour. During scanning, participants were shown target photographs to reactivate memories from the museum tour followed by a novel lure photograph from an alternate tour. Later, participants were presented with target and lure photographs and asked to determine whether the photographs showed a stop they visited during the tour. We used a subsequent memory analysis to examine neural recruitment during reactivation that was associated with later true and false memories. We predicted that the quality of reactivation, as determined by online ratings of subjective recollection, would increase subsequent true memories but also facilitate incorporation of the lure photograph, thereby increasing subsequent false memories. The fMRI results revealed that the quality of reactivation modulated subsequent true and false memories via recruitment of left posterior parahippocampal, bilateral retrosplenial, and bilateral posterior inferior parietal cortices. However, the timing of neural recruitment and the way in which memories were reactivated contributed to differences in whether memory reactivation led to distortions or not. These data reveal the neural mechanisms recruited during memory reactivation that modify how memories will be subsequently retrieved, supporting the flexible and dynamic aspects of memory.

Computational techniques for design optimization of thermal protection systems for the space shuttle vehicle. Volume 1: Final report

NASA Technical Reports Server (NTRS)

1971-01-01

Computational techniques were developed and assimilated for the design optimization. The resulting computer program was then used to perform initial optimization and sensitivity studies on a typical thermal protection system (TPS) to demonstrate its application to the space shuttle TPS design. The program was developed in Fortran IV for the CDC 6400 but was subsequently converted to the Fortran V language to be used on the Univac 1108. The program allows for improvement and update of the performance prediction techniques. The program logic involves subroutines which handle the following basic functions: (1) a driver which calls for input, output, and communication between program and user and between the subroutines themselves; (2) thermodynamic analysis; (3) thermal stress analysis; (4) acoustic fatigue analysis; and (5) weights/cost analysis. In addition, a system total cost is predicted based on system weight and historical cost data of similar systems. Two basic types of input are provided, both of which are based on trajectory data. These are vehicle attitude (altitude, velocity, and angles of attack and sideslip), for external heat and pressure loads calculation, and heating rates and pressure loads as a function of time.

Function library programming to support B89 evaluation of Sheffield Apollo RS50 DCC (Direct Computer Control) CMM (Coordinate Measuring Machine)

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

Frank, R.N.

1990-02-28

The Inspection Shop at Lawrence Livermore Lab recently purchased a Sheffield Apollo RS50 Direct Computer Control Coordinate Measuring Machine. The performance of the machine was specified to conform to B89 standard which relies heavily upon using the measuring machine in its intended manner to verify its accuracy (rather than parametric tests). Although it would be possible to use the interactive measurement system to perform these tasks, a more thorough and efficient job can be done by creating Function Library programs for certain tasks which integrate Hewlett-Packard Basic 5.0 language and calls to proprietary analysis and machine control routines. This combinationmore » provides efficient use of the measuring machine with a minimum of keyboard input plus an analysis of the data with respect to the B89 Standard rather than a CMM analysis which would require subsequent interpretation. This paper discusses some characteristics of the Sheffield machine control and analysis software and my use of H-P Basic language to create automated measurement programs to support the B89 performance evaluation of the CMM. 1 ref.« less

In situ and in-transit analysis of cosmological simulations

DOE PAGES

Friesen, Brian; Almgren, Ann; Lukic, Zarija; ...

2016-08-24

Modern cosmological simulations have reached the trillion-element scale, rendering data storage and subsequent analysis formidable tasks. To address this circumstance, we present a new MPI-parallel approach for analysis of simulation data while the simulation runs, as an alternative to the traditional workflow consisting of periodically saving large data sets to disk for subsequent ‘offline’ analysis. We demonstrate this approach in the compressible gasdynamics/N-body code Nyx, a hybrid MPI+OpenMP code based on the BoxLib framework, used for large-scale cosmological simulations. We have enabled on-the-fly workflows in two different ways: one is a straightforward approach consisting of all MPI processes periodically haltingmore » the main simulation and analyzing each component of data that they own (‘ in situ’). The other consists of partitioning processes into disjoint MPI groups, with one performing the simulation and periodically sending data to the other ‘sidecar’ group, which post-processes it while the simulation continues (‘in-transit’). The two groups execute their tasks asynchronously, stopping only to synchronize when a new set of simulation data needs to be analyzed. For both the in situ and in-transit approaches, we experiment with two different analysis suites with distinct performance behavior: one which finds dark matter halos in the simulation using merge trees to calculate the mass contained within iso-density contours, and another which calculates probability distribution functions and power spectra of various fields in the simulation. Both are common analysis tasks for cosmology, and both result in summary statistics significantly smaller than the original data set. We study the behavior of each type of analysis in each workflow in order to determine the optimal configuration for the different data analysis algorithms.« less

Early prediction of cerebral palsy by computer-based video analysis of general movements: a feasibility study.

PubMed

Adde, Lars; Helbostad, Jorunn L; Jensenius, Alexander R; Taraldsen, Gunnar; Grunewaldt, Kristine H; Støen, Ragnhild

2010-08-01

The aim of this study was to investigate the predictive value of a computer-based video analysis of the development of cerebral palsy (CP) in young infants. A prospective study of general movements used recordings from 30 high-risk infants (13 males, 17 females; mean gestational age 31wks, SD 6wks; range 23-42wks) between 10 and 15 weeks post term when fidgety movements should be present. Recordings were analysed using computer vision software. Movement variables, derived from differences between subsequent video frames, were used for quantitative analyses. CP status was reported at 5 years. Thirteen infants developed CP (eight hemiparetic, four quadriparetic, one dyskinetic; seven ambulatory, three non-ambulatory, and three unknown function), of whom one had fidgety movements. Variability of the centroid of motion had a sensitivity of 85% and a specificity of 71% in identifying CP. By combining this with variables reflecting the amount of motion, specificity increased to 88%. Nine out of 10 children with CP, and for whom information about functional level was available, were correctly predicted with regard to ambulatory and non-ambulatory function. Prediction of CP can be provided by computer-based video analysis in young infants. The method may serve as an objective and feasible tool for early prediction of CP in high-risk infants.

Transcriptome profile and unique genetic evolution of positively selected genes in yak lungs.

PubMed

Lan, DaoLiang; Xiong, XianRong; Ji, WenHui; Li, Jian; Mipam, Tserang-Donko; Ai, Yi; Chai, ZhiXin

2018-04-01

The yak (Bos grunniens), which is a unique bovine breed that is distributed mainly in the Qinghai-Tibetan Plateau, is considered a good model for studying plateau adaptability in mammals. The lungs are important functional organs that enable animals to adapt to their external environment. However, the genetic mechanism underlying the adaptability of yak lungs to harsh plateau environments remains unknown. To explore the unique evolutionary process and genetic mechanism of yak adaptation to plateau environments, we performed transcriptome sequencing of yak and cattle (Bos taurus) lungs using RNA-Seq technology and a subsequent comparison analysis to identify the positively selected genes in the yak. After deep sequencing, a normal transcriptome profile of yak lung that containing a total of 16,815 expressed genes was obtained, and the characteristics of yak lungs transcriptome was described by functional analysis. Furthermore, Ka/Ks comparison statistics result showed that 39 strong positively selected genes are identified from yak lungs. Further GO and KEGG analysis was conducted for the functional annotation of these genes. The results of this study provide valuable data for further explorations of the unique evolutionary process of high-altitude hypoxia adaptation in yaks in the Tibetan Plateau and the genetic mechanism at the molecular level.

Identification of Functional Candidates amongst Hypothetical Proteins of Treponema pallidum ssp. pallidum

PubMed Central

Naqvi, Ahmad Abu Turab; Shahbaaz, Mohd; Ahmad, Faizan; Hassan, Md. Imtaiyaz

2015-01-01

Syphilis is a globally occurring venereal disease, and its infection is propagated through sexual contact. The causative agent of syphilis, Treponema pallidum ssp. pallidum, a Gram-negative sphirochaete, is an obligate human parasite. Genome of T. pallidum ssp. pallidum SS14 strain (RefSeq NC_010741.1) encodes 1,027 proteins, of which 444 proteins are known as hypothetical proteins (HPs), i.e., proteins of unknown functions. Here, we performed functional annotation of HPs of T. pallidum ssp. pallidum using various database, domain architecture predictors, protein function annotators and clustering tools. We have analyzed the sequences of 444 HPs of T. pallidum ssp. pallidum and subsequently predicted the function of 207 HPs with a high level of confidence. However, functions of 237 HPs are predicted with less accuracy. We found various enzymes, transporters, binding proteins in the annotated group of HPs that may be possible molecular targets, facilitating for the survival of pathogen. Our comprehensive analysis helps to understand the mechanism of pathogenesis to provide many novel potential therapeutic interventions. PMID:25894582

The natural history of children with joint hypermobility syndrome and Ehlers-Danlos hypermobility type: a longitudinal cohort study.

PubMed

Scheper, Mark C; Nicholson, Lesley L; Adams, Roger D; Tofts, Louise; Pacey, Verity

2017-12-01

The objective of the manuscript was to describe the natural history of complaints and disability in children diagnosed with joint hypermobility syndrome (JHS)/Ehlers-Danlos-hypermobility type (EDS-HT) and to identify the constructs that underlie functional decline. One hundred and one JHS/EDS-HT children were observed over 3 years and assessed at three time points on the following: functional impairments, quality of life, connective tissue laxity, muscle function, postural control and musculoskeletal and multi-systemic complaints. Cluster analysis was performed to identify subgroups in severity. Clinical profiles were determined for these subgroups, and differences were assessed by multivariate analysis of covariance. Mixed linear regression models were used to determine the subsequent trajectories. Finally, an exploratory factor analysis was used to uncover the underlying constructs of functional impairment. Three clusters of children were identified in terms of functional impairment: mild, moderately and severely affected. Functional impairment at baseline was predictive of worsening trajectories in terms of reduced walking distance and decreased quality of life (P ⩽ 0.05) over 3 years. Multiple interactions between the secondary outcomes were observed, with four underlying constructs identified. All four constructs (multi-systemic effects, pain, fatigue and loss of postural control) contributed significantly to disability (P ⩽ 0.046). Children diagnosed with JHS/EDS-HT who have a high incidence of multi-systemic complaints (particularly, orthostatic intolerance, urinary incontinence and diarrhoea) and poor postural control in addition to high levels of pain and fatigue at baseline are most likely to have a deteriorating trajectory of functional impairment and, accordingly, warrant clinical prioritization. © The Author 2017. Published by Oxford University Press on behalf of the British Society for Rheumatology. All rights reserved. For Permissions, please email: journals.permissions@oup.com

Large-Scale Network Analysis of Whole-Brain Resting-State Functional Connectivity in Spinal Cord Injury: A Comparative Study.

PubMed

Kaushal, Mayank; Oni-Orisan, Akinwunmi; Chen, Gang; Li, Wenjun; Leschke, Jack; Ward, Doug; Kalinosky, Benjamin; Budde, Matthew; Schmit, Brian; Li, Shi-Jiang; Muqeet, Vaishnavi; Kurpad, Shekar

2017-09-01

Network analysis based on graph theory depicts the brain as a complex network that allows inspection of overall brain connectivity pattern and calculation of quantifiable network metrics. To date, large-scale network analysis has not been applied to resting-state functional networks in complete spinal cord injury (SCI) patients. To characterize modular reorganization of whole brain into constituent nodes and compare network metrics between SCI and control subjects, fifteen subjects with chronic complete cervical SCI and 15 neurologically intact controls were scanned. The data were preprocessed followed by parcellation of the brain into 116 regions of interest (ROI). Correlation analysis was performed between every ROI pair to construct connectivity matrices and ROIs were categorized into distinct modules. Subsequently, local efficiency (LE) and global efficiency (GE) network metrics were calculated at incremental cost thresholds. The application of a modularity algorithm organized the whole-brain resting-state functional network of the SCI and the control subjects into nine and seven modules, respectively. The individual modules differed across groups in terms of the number and the composition of constituent nodes. LE demonstrated statistically significant decrease at multiple cost levels in SCI subjects. GE did not differ significantly between the two groups. The demonstration of modular architecture in both groups highlights the applicability of large-scale network analysis in studying complex brain networks. Comparing modules across groups revealed differences in number and membership of constituent nodes, indicating modular reorganization due to neural plasticity.

Functional magnetic resonance imaging (fMRI) response to alcohol pictures predicts subsequent transition to heavy drinking in college students.

PubMed

Dager, Alecia D; Anderson, Beth M; Rosen, Rivkah; Khadka, Sabin; Sawyer, Broderick; Jiantonio-Kelly, Rachel E; Austad, Carol S; Raskin, Sarah A; Tennen, Howard; Wood, Rebecca M; Fallahi, Carolyn R; Pearlson, Godfrey D

2014-04-01

Young adults show the highest rates of escalating drinking, yet the neural risk mechanisms remain unclear. Heavy drinkers show variant functional magnetic resonance imaging (fMRI) blood oxygen level-dependent (BOLD) response to alcohol cues, which may presage increasing drinking. In this longitudinal study, we ascertained whether BOLD response to alcohol pictures predicted subsequent heavy drinking among college students. Participants were 43 18-21-year-olds in the United States who underwent BOLD scanning and completed monthly substance use surveys over the following year. Participants were categorized according to baseline and follow-up drinking into 13 continuously moderate drinkers, 16 continuously heavy drinkers and 14 transitioners who drank moderately at baseline but heavily by follow-up. During fMRI scanning at baseline, participants viewed alcohol and matched non-alcohol beverage images. We observed group differences in alcohol cue-elicited BOLD response in bilateral caudate, orbitofrontal cortex, medial frontal cortex/anterior cingulate and left insula (clusters > 2619 ml, voxelwise F(2,40)  > 3.23, P < 0.05, whole-brain corrected P < 0.05), where transitioners hyperactivated compared with moderate and heavy drinkers (all Tukey P < 0.05). Exploratory factor analysis revealed a single brain network differentiating those who subsequently increased drinking. Exploratory regressions showed that, compared with other risk factors (e.g., alcoholism family history, impulsivity), BOLD response best predicted escalating drinking amount and alcohol-related problems. Neural response to pictures of alcohol is substantially enhanced among United States college students who subsequently escalate drinking. Greater cue-reactivity is associated with larger increases in drinking and alcohol-related problems, regardless of other baseline factors. Thus, neural cue-reactivity could uniquely facilitate identifying individuals at greatest risk for future problematic drinking. © 2013 Society for the Study of Addiction.

Synaptic scaffold evolution generated components of vertebrate cognitive complexity

PubMed Central

Nithianantharajah, J.; Komiyama, N.H.; McKechanie, A.; Johnstone, M.; Blackwood, D. H.; St Clair, D.; Emes, R.D.; van de Lagemaat, L. N.; Saksida, L.M.; Bussey, T.J.; Grant, S.G.N.

2014-01-01

The origins and evolution of higher cognitive functions including complex forms of learning, attention and executive functions are unknown. A potential mechanism driving the evolution of vertebrate cognition early in the vertebrate lineage (550 My ago) was genome duplication and subsequent diversification of postsynaptic genes. Here we report the first genetic analysis of a vertebrate gene family in cognitive functions measured using computerized touchscreens. Comparison of mice carrying mutations in all four Dlg paralogs show simple associative learning required Dlg4, while Dlg2 and Dlg3 diversified to play opposing roles in complex cognitive processes. Exploiting the translational utility of touchscreens in humans and mice, testing Dlg2 mutations in both species showed Dlg2’s role in complex learning, cognitive flexibility and attention has been highly conserved over 100 My. Dlg family mutations underlie psychiatric disorders suggesting genome evolution expanded the complexity of vertebrate cognition at the cost of susceptibility to mental illness. PMID:23201973

A new BP Fourier algorithm and its application in English teaching evaluation

NASA Astrophysics Data System (ADS)

Pei, Xuehui; Pei, Guixin

2017-08-01

BP neural network algorithm has wide adaptability and accuracy when used in complicated system evaluation, but its calculation defects such as slow convergence have limited its practical application. The paper tries to speed up the calculation convergence of BP neural network algorithm with Fourier basis functions and presents a new BP Fourier algorithm for complicated system evaluation. First, shortages and working principle of BP algorithm are analyzed for subsequent targeted improvement; Second, the presented BP Fourier algorithm adopts Fourier basis functions to simplify calculation structure, designs new calculation transfer function between input and output layers, and conducts theoretical analysis to prove the efficiency of the presented algorithm; Finally, the presented algorithm is used in evaluating university English teaching and the application results shows that the presented BP Fourier algorithm has better performance in calculation efficiency and evaluation accuracy and can be used in evaluating complicated system practically.

Prediction of enzymatic pathways by integrative pathway mapping

PubMed Central

Wichelecki, Daniel J; San Francisco, Brian; Zhao, Suwen; Rodionov, Dmitry A; Vetting, Matthew W; Al-Obaidi, Nawar F; Lin, Henry; O'Meara, Matthew J; Scott, David A; Morris, John H; Russel, Daniel; Almo, Steven C; Osterman, Andrei L

2018-01-01

The functions of most proteins are yet to be determined. The function of an enzyme is often defined by its interacting partners, including its substrate and product, and its role in larger metabolic networks. Here, we describe a computational method that predicts the functions of orphan enzymes by organizing them into a linear metabolic pathway. Given candidate enzyme and metabolite pathway members, this aim is achieved by finding those pathways that satisfy structural and network restraints implied by varied input information, including that from virtual screening, chemoinformatics, genomic context analysis, and ligand -binding experiments. We demonstrate this integrative pathway mapping method by predicting the L-gulonate catabolic pathway in Haemophilus influenzae Rd KW20. The prediction was subsequently validated experimentally by enzymology, crystallography, and metabolomics. Integrative pathway mapping by satisfaction of structural and network restraints is extensible to molecular networks in general and thus formally bridges the gap between structural biology and systems biology. PMID:29377793

Enhancer scanning to locate regulatory regions in genomic loci

PubMed Central

Buckley, Melissa; Gjyshi, Anxhela; Mendoza-Fandiño, Gustavo; Baskin, Rebekah; Carvalho, Renato S.; Carvalho, Marcelo A.; Woods, Nicholas T.; Monteiro, Alvaro N.A.

2016-01-01

The present protocol provides a rapid, streamlined and scalable strategy to systematically scan genomic regions for the presence of transcriptional regulatory regions active in a specific cell type. It creates genomic tiles spanning a region of interest that are subsequently cloned by recombination into a luciferase reporter vector containing the Simian Virus 40 promoter. Tiling clones are transfected into specific cell types to test for the presence of transcriptional regulatory regions. The protocol includes testing of different SNP (single nucleotide polymorphism) alleles to determine their effect on regulatory activity. This procedure provides a systematic framework to identify candidate functional SNPs within a locus during functional analysis of genome-wide association studies. This protocol adapts and combines previous well-established molecular biology methods to provide a streamlined strategy, based on automated primer design and recombinational cloning to rapidly go from a genomic locus to a set of candidate functional SNPs in eight weeks. PMID:26658467

Mussel inspired polymerized P(TA-TETA) for facile functionalization of carbon nanotube

NASA Astrophysics Data System (ADS)

Si, Shuxian; Gao, Tingting; Wang, Junhao; Liu, Qinze; Zhou, Guowei

2018-03-01

This article describes a novel and effective approach for non-covalent modification of carbon nanotube (CNT) via the mussel inspired polymerization of tannic acid (TA) and triethylenetetramine (TETA) and subsequent surface initiated atom transfer radical polymerization (SI-ATRP). Fourier transform infrared spectroscopy (FT-IR), thermo-gravimetric analysis (TGA), transmission electron microscope (TEM), X-ray photoelectron spectroscopy (XPS) and photograph were used to study the successful preparation of polymer brush grafted CNT (CNT-P(TA-TETA)-PDMAEMA) composite as well as the pH-responsive behavior of the composite. Furthermore, by amine protonation and in situ reduction, gold nanoparticles were successfully uploaded and the catalytic property of CNT-P(TA-TETA)-PDMAEMA/Au was investigated. We believe that the surface functionalization strategy can be extended to graphene and other substrates, and the surface properties can be regulated by grafting polymer brushes with different functionalities.

Automatic control system for uniformly paving iron ore pellets

NASA Astrophysics Data System (ADS)

Wang, Bowen; Qian, Xiaolong

2014-05-01

In iron and steelmaking industry, iron ore pellet qualities are crucial to end-product properties, manufacturing costs and waste emissions. Uniform pellet pavements on the grate machine are a fundamental prerequisite to ensure even heat-transfer and pellet induration successively influences performance of the following metallurgical processes. This article presents an automatic control system for uniformly paving green pellets on the grate, via a mechanism mainly constituted of a mechanical linkage, a swinging belt, a conveyance belt and a grate. Mechanism analysis illustrates that uniform pellet pavements demand the frontend of the swinging belt oscillate at a constant angular velocity. Subsequently, kinetic models are formulated to relate oscillatory movements of the swinging belt's frontend to rotations of a crank link driven by a motor. On basis of kinetic analysis of the pellet feeding mechanism, a cubic B-spline model is built for numerically computing discrete frequencies to be modulated during a motor rotation. Subsequently, the pellet feeding control system is presented in terms of compositional hardware and software components, and their functional relationships. Finally, pellet feeding experiments are carried out to demonstrate that the control system is effective, reliable and superior to conventional methods.

Age-related differences in brain activity in the subsequent memory paradigm: a meta-analysis.

PubMed

Maillet, David; Rajah, M Natasha

2014-09-01

Healthy aging is associated with declines in episodic memory. This reduction is thought to be due in part to age-related differences in encoding-related processes. In the current study, we performed an activation likelihood estimation meta-analysis of functional magnetic resonance imaging (fMRI) studies assessing age-related differences in the neural correlates of episodic encoding. Only studies using the subsequent memory paradigm were included. We found age-related under-recruitment of occipital and fusiform cortex, but over-recruitment in a set of regions including bilateral middle/superior frontal gyri, anterior medial frontal gyrus, precuneus and left inferior parietal lobe. We demonstrate that all of the regions consistently over-recruited by older adults during successful encoding exhibit either direct overlap, or occur in close vicinity to regions consistently involved in unsuccessful encoding in young adults. We discuss the possibility that this overall pattern of age-related differences represents an age-related shift in focus: away from perceptual details, and toward evaluative and personal thoughts and feelings during memory tasks. We discuss whether these age-related differences in brain activation benefit performance in older adults, and additional considerations. Copyright © 2014 Elsevier Ltd. All rights reserved.

Comprehensive Analysis of the Gas- and Particle-Phase Products of VOC Oxidation

NASA Astrophysics Data System (ADS)

Bakker-Arkema, J.; Ziemann, P. J.

2017-12-01

Controlled environmental chamber studies are important for determining atmospheric reaction mechanisms and gas and aerosol products formed in the oxidation of volatile organic compounds (VOCs). Such information is necessary for developing detailed chemical models for use in predicting the atmospheric fate of VOCs and also secondary organic aerosol (SOA) formation. However, complete characterization of atmospheric oxidation reactions, including gas- and particle-phase product yields, and reaction branching ratios, are difficult to achieve. In this work, we investigated the reactions of terminal and internal alkenes with OH radicals in the presence of NOx in an attempt to fully characterize the chemistry of these systems while minimizing and accounting for the inherent uncertainties associated with environmental chamber experiments. Gas-phase products (aldehydes formed by alkoxy radical decomposition) and particle-phase products (alkyl nitrates, β-hydroxynitrates, dihydroxynitrates, 1,4-hydroxynitrates, 1,4-hydroxycarbonyls, and dihydroxycarbonyls) formed through pathways involving addition of OH to the C=C double bond as well as H-atom abstraction were identified and quantified using a suite of analytical techniques. Particle-phase products were analyzed in real time with a thermal desorption particle beam mass spectrometer; and off-line by collection onto filters, extraction, and subsequent analysis of functional groups by derivatization-spectrophotometric methods developed in our lab. Derivatized products were also separated by liquid chromatography for molecular quantitation by UV absorbance and identification using chemical ionization-ion trap mass spectrometry. Gas phase aldehydes were analyzed off-line by collection onto Tenax and a 5-channel denuder with subsequent analysis by gas chromatography, or by collection onto DNPH-coated cartridges and subsequent analysis by liquid chromatography. The full product identification and quantitation, with careful minimization of uncertainties for the various components of the experiment and analyses, demonstrates our capability to comprehensively and accurately analyze the complex chemical composition of products formed in the oxidation of organic compounds in laboratory chamber studies.

Cost drivers and resource allocation in military health care systems.

PubMed

Fulton, Larry; Lasdon, Leon S; McDaniel, Reuben R

2007-03-01

This study illustrates the feasibility of incorporating technical efficiency considerations in the funding of military hospitals and identifies the primary drivers for hospital costs. Secondary data collected for 24 U.S.-based Army hospitals and medical centers for the years 2001 to 2003 are the basis for this analysis. Technical efficiency was measured by using data envelopment analysis; subsequently, efficiency estimates were included in logarithmic-linear cost models that specified cost as a function of volume, complexity, efficiency, time, and facility type. These logarithmic-linear models were compared against stochastic frontier analysis models. A parsimonious, three-variable, logarithmic-linear model composed of volume, complexity, and efficiency variables exhibited a strong linear relationship with observed costs (R(2) = 0.98). This model also proved reliable in forecasting (R(2) = 0.96). Based on our analysis, as much as $120 million might be reallocated to improve the United States-based Army hospital performance evaluated in this study.

Automatic network coupling analysis for dynamical systems based on detailed kinetic models.

PubMed

Lebiedz, Dirk; Kammerer, Julia; Brandt-Pollmann, Ulrich

2005-10-01

We introduce a numerical complexity reduction method for the automatic identification and analysis of dynamic network decompositions in (bio)chemical kinetics based on error-controlled computation of a minimal model dimension represented by the number of (locally) active dynamical modes. Our algorithm exploits a generalized sensitivity analysis along state trajectories and subsequent singular value decomposition of sensitivity matrices for the identification of these dominant dynamical modes. It allows for a dynamic coupling analysis of (bio)chemical species in kinetic models that can be exploited for the piecewise computation of a minimal model on small time intervals and offers valuable functional insight into highly nonlinear reaction mechanisms and network dynamics. We present results for the identification of network decompositions in a simple oscillatory chemical reaction, time scale separation based model reduction in a Michaelis-Menten enzyme system and network decomposition of a detailed model for the oscillatory peroxidase-oxidase enzyme system.

Confirmatory Factor Analysis and Differential Relationships of the Two Subdomains of Negative Symptoms in Chronically Ill Psychotic Patients

PubMed Central

Stiekema, Annemarie P. M.; Liemburg, Edith J.; van der Meer, Lisette; Castelein, Stynke; Stewart, Roy; van Weeghel, Jaap; Aleman, André; Bruggeman, Richard

2016-01-01

Research suggests a two factor structure for negative symptoms in patients with psychotic disorders: social amotivation (SA) and expressive deficits (ED). Applying this two-factor structure in clinical settings may provide valuable information with regard to outcomes and to target treatments. We aimed to investigate 1) whether the factor structure is also supported in chronically ill patients with a psychotic disorder and 2) what the relationship is between these factors and functioning (overall functioning and living situation), depressive symptoms and quality of life. 1157 Patients with a psychotic disorder and a duration of illness of 5 years or more were included in the analysis (data selected from the Pharmacotherapy Monitoring Outcome Survey; PHAMOUS). A confirmatory factor analysis was performed using items of the Positive and Negative Syndrome Scale that were previously identified to reflect negative symptoms (N1-4, N6, G5, G7, G13, G16). Subsequently, regression analysis was performed on outcomes. The results confirmed the distinction between SA (N2, N4, G16) and ED (N1, N3, N6, G5, G7, G13) in chronically ill patients. Both factors were related to worse overall functioning as measured with the Health of the Nation Outcome Scales, ED was uniquely associated with residential living status. Higher scores for SA were associated with more depressive symptoms and worse quality of life. Thus, SA is most strongly related to level of social-emotional functioning, while ED are more related to living situation and thereby are indicative of level of everyday functioning. This subdivision may be useful for research purposes and be a valuable additional tool in clinical practice and treatment development. PMID:26895203

Identification and Functional Analysis of Healing Regulators in Drosophila

PubMed Central

Álvarez-Fernández, Carmen; Tamirisa, Srividya; Prada, Federico; Chernomoretz, Ariel; Podhajcer, Osvaldo; Blanco, Enrique; Martín-Blanco, Enrique

2015-01-01

Wound healing is an essential homeostatic mechanism that maintains the epithelial barrier integrity after tissue damage. Although we know the overall steps in wound healing, many of the underlying molecular mechanisms remain unclear. Genetically amenable systems, such as wound healing in Drosophila imaginal discs, do not model all aspects of the repair process. However, they do allow the less understood aspects of the healing response to be explored, e.g., which signal(s) are responsible for initiating tissue remodeling? How is sealing of the epithelia achieved? Or, what inhibitory cues cancel the healing machinery upon completion? Answering these and other questions first requires the identification and functional analysis of wound specific genes. A variety of different microarray analyses of murine and humans have identified characteristic profiles of gene expression at the wound site, however, very few functional studies in healing regulation have been carried out. We developed an experimentally controlled method that is healing-permissive and that allows live imaging and biochemical analysis of cultured imaginal discs. We performed comparative genome-wide profiling between Drosophila imaginal cells actively involved in healing versus their non-engaged siblings. Sets of potential wound-specific genes were subsequently identified. Importantly, besides identifying and categorizing new genes, we functionally tested many of their gene products by genetic interference and overexpression in healing assays. This non-saturated analysis defines a relevant set of genes whose changes in expression level are functionally significant for proper tissue repair. Amongst these we identified the TCP1 chaperonin complex as a key regulator of the actin cytoskeleton essential for the wound healing response. There is promise that our newly identified wound-healing genes will guide future work in the more complex mammalian wound healing response. PMID:25647511

Glycan Remodeling with Processing Inhibitors and Lectin-Resistant Eukaryotic Cells.

PubMed

Chang, Veronica T; Spooner, Robert A; Crispin, Max; Davis, Simon J

2015-01-01

Some of the most important and interesting molecules in metazoan biology are glycoproteins. The importance of the carbohydrate component of these structures is often revealed by the disease phenotypes that manifest when the biosynthesis of particular glycoforms is disrupted. On the other hand, the presence of large amounts of carbohydrate can often hinder the structural and functional analysis of glycoproteins. There are often good reasons, therefore, for wanting to engineer and predefine the N-glycans present on glycoproteins, e.g., in order to characterize the functions of the glycans or facilitate their subsequent removal. Here, we describe in detail two distinct ways in which to usefully interfere with oligosaccharide processing, one involving the use of specific processing inhibitors, and the other the selection of cell lines mutated at gene loci that control oligosaccharide processing, using cytotoxic lectins. Both approaches have the capacity for controlled, radical alteration of oligosaccharide processing in eukaryotic cells used for heterologous protein expression, and have great utility in the structural analysis of glycoproteins.

Upside/Downside statistical mechanics of nonequilibrium Brownian motion. I. Distributions, moments, and correlation functions of a free particle.

PubMed

Craven, Galen T; Nitzan, Abraham

2018-01-28

Statistical properties of Brownian motion that arise by analyzing, separately, trajectories over which the system energy increases (upside) or decreases (downside) with respect to a threshold energy level are derived. This selective analysis is applied to examine transport properties of a nonequilibrium Brownian process that is coupled to multiple thermal sources characterized by different temperatures. Distributions, moments, and correlation functions of a free particle that occur during upside and downside events are investigated for energy activation and energy relaxation processes and also for positive and negative energy fluctuations from the average energy. The presented results are sufficiently general and can be applied without modification to the standard Brownian motion. This article focuses on the mathematical basis of this selective analysis. In subsequent articles in this series, we apply this general formalism to processes in which heat transfer between thermal reservoirs is mediated by activated rate processes that take place in a system bridging them.

Upside/Downside statistical mechanics of nonequilibrium Brownian motion. I. Distributions, moments, and correlation functions of a free particle

NASA Astrophysics Data System (ADS)

Craven, Galen T.; Nitzan, Abraham

2018-01-01

Statistical properties of Brownian motion that arise by analyzing, separately, trajectories over which the system energy increases (upside) or decreases (downside) with respect to a threshold energy level are derived. This selective analysis is applied to examine transport properties of a nonequilibrium Brownian process that is coupled to multiple thermal sources characterized by different temperatures. Distributions, moments, and correlation functions of a free particle that occur during upside and downside events are investigated for energy activation and energy relaxation processes and also for positive and negative energy fluctuations from the average energy. The presented results are sufficiently general and can be applied without modification to the standard Brownian motion. This article focuses on the mathematical basis of this selective analysis. In subsequent articles in this series, we apply this general formalism to processes in which heat transfer between thermal reservoirs is mediated by activated rate processes that take place in a system bridging them.

Negotiating safer sex: a detailed analysis of attitude functions, anticipated emotions, relationship status and gender.

PubMed

Wang, Xiao

2013-01-01

Because interpersonal discussion about condom use can encourage subsequent condom use, this project aims to examine the psychological antecedents of intentions to discuss or request the use of condoms with a sexual partner. The data were collected from 849 heterosexual college students in the U.S.A. through an online survey. The survey contained several measures related to attitude functions (i.e., motivations), efficacy, norms and intentions to discuss condom use with a sexual partner. Participants' attitude functions weakly predicted intentions to discuss condom use. Communication efficacy was a more important predictor of intentions for females (vs. males) and for those in other relationships or not in a relationship (vs. long-term monogamous relationships). Anticipated negative emotions were a stronger predictor of intentions for those in long-term monogamous relationships (vs. other relationships or not in a relationship). Future research needs to consider more detailed attitude functions and anticipated emotions. Furthermore, background variables (e.g., gender and relationship status) can be moderators in addition to being distal predictors.

Droplet activation, separation, and compositional analysis: laboratory studies and atmospheric measurements

NASA Astrophysics Data System (ADS)

Hiranuma, N.; Kohn, M.; Pekour, M. S.; Nelson, D. A.; Shilling, J. E.; Cziczo, D. J.

2011-10-01

Droplets produced in a cloud condensation nuclei chamber (CCNC) as a function of supersaturation have been separated from unactivated aerosol particles using counterflow virtual impaction. Residual material after droplets were evaporated was chemically analyzed with an Aerodyne Aerosol Mass Spectrometer (AMS) and the Particle Analysis by Laser Mass Spectrometry (PALMS) instrument. Experiments were initially conducted to verify activation conditions for monodisperse ammonium sulfate particles and to determine the resulting droplet size distribution as a function of supersaturation. Based on the observed droplet size, the counterflow virtual impactor cut-size was set to differentiate droplets from unactivated interstitial particles. Validation experiments were then performed to verify that only droplets with sufficient size passed through the counterflow virtual impactor for subsequent analysis. A two-component external mixture of monodisperse particles was also exposed to a supersaturation which would activate one of the types (hygroscopic salts) but not the other (polystyrene latex spheres or adipic acid). The mass spectrum observed after separation indicated only the former, validating separation of droplets from unactivated particles. Results from ambient measurements using this technique and AMS analysis were inconclusive, showing little chemical differentiation between ambient aerosol and activated droplet residuals, largely due to low signal levels. When employing as single particle mass spectrometer for compositional analysis, however, we observed enhancement of sulfate in droplet residuals.

Remembering beauty: roles of orbitofrontal and hippocampal regions in successful memory encoding of attractive faces.

PubMed

Tsukiura, Takashi; Cabeza, Roberto

2011-01-01

Behavioral data have shown that attractive faces are better remembered but the neural mechanisms of this effect are largely unknown. To investigate this issue, female participants were scanned with event-related functional MRI (fMRI) while rating the attractiveness of male faces. Memory for the faces was tested after fMRI scanning and was used to identify successful encoding activity (subsequent memory paradigm). As expected, attractive faces were remembered better than other faces. The study yielded three main fMRI findings. First, activity in the right orbitofrontal cortex increased linearly as a function of attractiveness ratings. Second, activity in the left hippocampus increased as a function of subsequent memory (subsequent misses

Remembering beauty: Roles of orbitofrontal and hippocampal regions in successful memory encoding of attractive faces

PubMed Central

Tsukiura, Takashi; Cabeza, Roberto

2010-01-01

Behavioral data have shown that attractive faces are better remembered but the neural mechanisms of this effect are largely unknown. To investigate this issue, female participants were scanned with event-related functional MRI (fMRI) while rating the attractiveness of male faces. Memory for the faces was tested after fMRI scanning and was used to identify successful encoding activity (subsequent memory paradigm). As expected, attractive faces were remembered better than other faces. The study yielded three main fMRI findings. First, activity in the right orbitofrontal cortex increased linearly as a function of attractiveness ratings. Second, activity in the left hippocampus increased as a function of subsequent memory (subsequent misses

A Graphical User Interface for Software-assisted Tracking of Protein Concentration in Dynamic Cellular Protrusions.

PubMed

Saha, Tanumoy; Rathmann, Isabel; Galic, Milos

2017-07-11

Filopodia are dynamic, finger-like cellular protrusions associated with migration and cell-cell communication. In order to better understand the complex signaling mechanisms underlying filopodial initiation, elongation and subsequent stabilization or retraction, it is crucial to determine the spatio-temporal protein activity in these dynamic structures. To analyze protein function in filopodia, we recently developed a semi-automated tracking algorithm that adapts to filopodial shape-changes, thus allowing parallel analysis of protrusion dynamics and relative protein concentration along the whole filopodial length. Here, we present a detailed step-by-step protocol for optimized cell handling, image acquisition and software analysis. We further provide instructions for the use of optional features during image analysis and data representation, as well as troubleshooting guidelines for all critical steps along the way. Finally, we also include a comparison of the described image analysis software with other programs available for filopodia quantification. Together, the presented protocol provides a framework for accurate analysis of protein dynamics in filopodial protrusions using image analysis software.

Systematic computation with functional gene-sets among leukemic and hematopoietic stem cells reveals a favorable prognostic signature for acute myeloid leukemia.

PubMed

Yang, Xinan Holly; Li, Meiyi; Wang, Bin; Zhu, Wanqi; Desgardin, Aurelie; Onel, Kenan; de Jong, Jill; Chen, Jianjun; Chen, Luonan; Cunningham, John M

2015-03-24

Genes that regulate stem cell function are suspected to exert adverse effects on prognosis in malignancy. However, diverse cancer stem cell signatures are difficult for physicians to interpret and apply clinically. To connect the transcriptome and stem cell biology, with potential clinical applications, we propose a novel computational "gene-to-function, snapshot-to-dynamics, and biology-to-clinic" framework to uncover core functional gene-sets signatures. This framework incorporates three function-centric gene-set analysis strategies: a meta-analysis of both microarray and RNA-seq data, novel dynamic network mechanism (DNM) identification, and a personalized prognostic indicator analysis. This work uses complex disease acute myeloid leukemia (AML) as a research platform. We introduced an adjustable "soft threshold" to a functional gene-set algorithm and found that two different analysis methods identified distinct gene-set signatures from the same samples. We identified a 30-gene cluster that characterizes leukemic stem cell (LSC)-depleted cells and a 25-gene cluster that characterizes LSC-enriched cells in parallel; both mark favorable-prognosis in AML. Genes within each signature significantly share common biological processes and/or molecular functions (empirical p = 6e-5 and 0.03 respectively). The 25-gene signature reflects the abnormal development of stem cells in AML, such as AURKA over-expression. We subsequently determined that the clinical relevance of both signatures is independent of known clinical risk classifications in 214 patients with cytogenetically normal AML. We successfully validated the prognosis of both signatures in two independent cohorts of 91 and 242 patients respectively (log-rank p < 0.0015 and 0.05; empirical p < 0.015 and 0.08). The proposed algorithms and computational framework will harness systems biology research because they efficiently translate gene-sets (rather than single genes) into biological discoveries about AML and other complex diseases.

Clinical Outcomes from Androgen Signaling-directed Therapy after Treatment with Abiraterone Acetate and Prednisone in Patients with Metastatic Castration-resistant Prostate Cancer: Post Hoc Analysis of COU-AA-302.

PubMed

Smith, Matthew R; Saad, Fred; Rathkopf, Dana E; Mulders, Peter F A; de Bono, Johann S; Small, Eric J; Shore, Neal D; Fizazi, Karim; Kheoh, Thian; Li, Jinhui; De Porre, Peter; Todd, Mary B; Yu, Margaret K; Ryan, Charles J

2017-07-01

In the COU-AA-302 trial, abiraterone acetate plus prednisone significantly increased overall survival for patients with chemotherapy-naïve metastatic castration-resistant prostate cancer (mCRPC). Limited information exists regarding response to subsequent androgen signaling-directed therapies following abiraterone acetate plus prednisone in patients with mCRPC. We investigated clinical outcomes associated with subsequent abiraterone acetate plus prednisone (55 patients) and enzalutamide (33 patients) in a post hoc analysis of COU-AA-302. Prostate-specific antigen (PSA) response was assessed. Median time to PSA progression was estimated using the Kaplan-Meier method. The PSA response rate (≥50% PSA decline, unconfirmed) was 44% and 67%, respectively. The median time to PSA progression was 3.9 mo (range 2.6-not estimable) for subsequent abiraterone acetate plus prednisone and 2.8 mo (range 1.8-not estimable) for subsequent enzalutamide. The majority of patients (68%) received intervening chemotherapy before subsequent abiraterone acetate plus prednisone or enzalutamide. While acknowledging the limitations of post hoc analyses and high censoring (>75%) in both treatment groups, these results suggest that subsequent therapy with abiraterone acetate plus prednisone or enzalutamide for patients who progressed on abiraterone acetate is associated with limited clinical benefit. This analysis showed limited clinical benefit for subsequent abiraterone acetate plus prednisone or enzalutamide in patients with metastatic castration-resistant prostate cancer following initial treatment with abiraterone acetate plus prednisone. This analysis does not support prioritization of subsequent abiraterone acetate plus prednisone or enzalutamide following initial therapy with abiraterone acetate plus prednisone. Copyright © 2017 European Association of Urology. Published by Elsevier B.V. All rights reserved.

Maintenance of soil functioning following erosion of microbial diversity.

PubMed

Wertz, Sophie; Degrange, Valérie; Prosser, James I; Poly, Franck; Commeaux, Claire; Freitag, Thomas; Guillaumaud, Nadine; Roux, Xavier Le

2006-12-01

The paradigm that soil microbial communities, being very diverse, have high functional redundancy levels, so that erosion of microbial diversity is less important for ecosystem functioning than erosion of plant or animal diversity, is often taken for granted. However, this has only been demonstrated for decomposition/respiration functions, performed by a large proportion of the total microbial community, but not for specialized microbial groups. Here, we determined the impact of a decrease in soil microbial diversity on soil ecosystem processes using a removal approach, in which less abundant species were removed preferentially. This was achieved by inoculation of sterile soil microcosms with serial dilutions of a suspension obtained from the same non-sterile soil and subsequent incubation, to enable recovery of community size. The sensitivity to diversity erosion was evaluated for three microbial functional groups with known contrasting taxonomic diversities (ammonia oxidizers < denitrifiers < heterotrophs). Diversity erosion within each functional group was characterized using molecular fingerprinting techniques: ribosomal intergenic spacer analysis (RISA) for the eubacterial community, denaturing gradient gel electrophoresis (DGGE) analysis of nirK genes for denitrifiers, and DGGE analysis of 16S rRNA genes for betaproteobacterial ammonia oxidizers. In addition, we simulated the impact of the removal approach by dilution on the number of soil bacterial species remaining in the inoculum using values of abundance distribution of bacterial species reported in the literature. The reduction of the diversity of the functional groups observed from genetic fingerprints did not impair the associated functioning of these groups, i.e. carbon mineralization, denitrification and nitrification. This was remarkable, because the amplitude of diversity erosion generated by the dilution approach was huge (level of bacterial species loss was estimated to be around 99.99% for the highest dilution). Our results demonstrate that the vast diversity of the soil microbiota makes soil ecosystem functioning largely insensitive to biodiversity erosion even for functions performed by specialized groups.

Application of isotope labeling experiments and (13)C flux analysis to enable rational pathway engineering.

PubMed

McAtee, Allison G; Jazmin, Lara J; Young, Jamey D

2015-12-01

Isotope labeling experiments (ILEs) and (13)C flux analysis provide actionable information for metabolic engineers to identify knockout, overexpression, and/or media optimization targets. ILEs have been used in both academic and industrial labs to increase product formation, discover novel metabolic functions in previously uncharacterized organisms, and enhance the metabolic efficiency of host cell factories. This review highlights specific examples of how ILEs have been used in conjunction with enzyme or metabolic engineering to elucidate host cell metabolism and improve product titer, rate, or yield in a directed manner. We discuss recent progress and future opportunities involving the use of ILEs and (13)C flux analysis to characterize non-model host organisms and to identify and subsequently eliminate wasteful byproduct pathways or metabolic bottlenecks. Copyright © 2015 Elsevier Ltd. All rights reserved.

Evolutionary and Comparative Genomics to Drive Rational Drug Design, with Particular Focus on Neuropeptide Seven-Transmembrane Receptors.

PubMed

Furlong, Michael; Seong, Jae Young

2017-01-01

Seven transmembrane receptors (7TMRs), also known as G protein-coupled receptors, are popular targets of drug development, particularly 7TMR systems that are activated by peptide ligands. Although many pharmaceutical drugs have been discovered via conventional bulk analysis techniques the increasing availability of structural and evolutionary data are facilitating change to rational, targeted drug design. This article discusses the appeal of neuropeptide-7TMR systems as drug targets and provides an overview of concepts in the evolution of vertebrate genomes and gene families. Subsequently, methods that use evolutionary concepts and comparative analysis techniques to aid in gene discovery, gene function identification, and novel drug design are provided along with case study examples.

[Value(s)].

PubMed

Vanbelle, G

2006-01-01

After a short explanation of the word value, the (cultural) value of teeth, the economic evaluation of dentistry and the payment criteria are being presented. The specific situation of health care as a service which deviates in quite a few aspects from the standard demand-supply model is being pointed out. Attention is drawn to key characteristics of the liberal professions such as the obligation to perform to the best of one's ability, not to a specific result. Function classification appears to offer possibilities for cataloguing the wide variation in practice settings. The well-known wage calculation of Professor De Lembre is being reviewed. Subsequently the analysis of cost variation and induced demand by extra services and profile shaping is being elaborated. Cost-benefit-analysis is the concluding item.

Evolutionary and Comparative Genomics to Drive Rational Drug Design, with Particular Focus on Neuropeptide Seven-Transmembrane Receptors

PubMed Central

Furlong, Michael; Seong, Jae Young

2017-01-01

Seven transmembrane receptors (7TMRs), also known as G protein-coupled receptors, are popular targets of drug development, particularly 7TMR systems that are activated by peptide ligands. Although many pharmaceutical drugs have been discovered via conventional bulk analysis techniques the increasing availability of structural and evolutionary data are facilitating change to rational, targeted drug design. This article discusses the appeal of neuropeptide-7TMR systems as drug targets and provides an overview of concepts in the evolution of vertebrate genomes and gene families. Subsequently, methods that use evolutionary concepts and comparative analysis techniques to aid in gene discovery, gene function identification, and novel drug design are provided along with case study examples. PMID:28035082

Genome-Wide Screening and Characterization of the Dof Gene Family in Physic Nut (Jatropha curcas L.).

PubMed

Wang, Peipei; Li, Jing; Gao, Xiaoyang; Zhang, Di; Li, Anlin; Liu, Changning

2018-05-29

Physic nut ( Jatropha curcas L.) is a species of flowering plant with great potential for biofuel production and as an emerging model organism for functional genomic analysis, particularly in the Euphorbiaceae family. DNA binding with one finger (Dof) transcription factors play critical roles in numerous biological processes in plants. Nevertheless, the knowledge about members, and the evolutionary and functional characteristics of the Dof gene family in physic nut is insufficient. Therefore, we performed a genome-wide screening and characterization of the Dof gene family within the physic nut draft genome. In total, 24 JcDof genes (encoding 33 JcDof proteins) were identified. All the JcDof genes were divided into three major groups based on phylogenetic inference, which was further validated by the subsequent gene structure and motif analysis. Genome comparison revealed that segmental duplication may have played crucial roles in the expansion of the JcDof gene family, and gene expansion was mainly subjected to positive selection. The expression profile demonstrated the broad involvement of JcDof genes in response to various abiotic stresses, hormonal treatments and functional divergence. This study provides valuable information for better understanding the evolution of JcDof genes, and lays a foundation for future functional exploration of JcDof genes.

Space Station data system analysis/architecture study. Task 1: Functional requirements definition, DR-5

NASA Technical Reports Server (NTRS)

1985-01-01

The initial task in the Space Station Data System (SSDS) Analysis/Architecture Study is the definition of the functional and key performance requirements for the SSDS. The SSDS is the set of hardware and software, both on the ground and in space, that provides the basic data management services for Space Station customers and systems. The primary purpose of the requirements development activity was to provide a coordinated, documented requirements set as a basis for the system definition of the SSDS and for other subsequent study activities. These requirements should also prove useful to other Space Station activities in that they provide an indication of the scope of the information services and systems that will be needed in the Space Station program. The major results of the requirements development task are as follows: (1) identification of a conceptual topology and architecture for the end-to-end Space Station Information Systems (SSIS); (2) development of a complete set of functional requirements and design drivers for the SSIS; (3) development of functional requirements and key performance requirements for the Space Station Data System (SSDS); and (4) definition of an operating concept for the SSIS. The operating concept was developed both from a Space Station payload customer and operator perspective in order to allow a requirements practicality assessment.

Biocompatibility of functionalized boron phosphate (BPO4) nanoparticles for boron neutron capture therapy (BNCT) application.

PubMed

Achilli, Cesare; Grandi, Stefania; Ciana, Annarita; Guidetti, Gianni F; Malara, Alessandro; Abbonante, Vittorio; Cansolino, Laura; Tomasi, Corrado; Balduini, Alessandra; Fagnoni, Maurizio; Merli, Daniele; Mustarelli, Piercarlo; Canobbio, Ilaria; Balduini, Cesare; Minetti, Giampaolo

2014-04-01

Boron neutron capture therapy (BNCT) is a radiotherapy treatment based on the accumulation in the tumor of a (10)B-containing drug and subsequent irradiation with low energy neutrons, which bring about the decay of (10)B to (7)Li and an α particle, causing the death of the neoplastic cell. The effectiveness of BNCT is limited by the low delivery and accumulation of the used boron-containing compounds. Here we report the development and the characterization of BPO4 nanoparticles (NPs) as a novel possible alternative drug for BNCT. An extensive analysis of BPO4 NP biocompatibility was performed using both mature blood cells (erythrocytes, neutrophils and platelets) and a model of hematopoietic progenitor cells. A time- and concentration-dependent cytotoxicity study was performed on neoplastic coloncarcinoma and osteosarcoma cell lines. BPO4 functionalization with folic acid, introduced to improve the uptake by tumor cells, appeared to effectively limit the unwanted effects of NPs on the analyzed blood components. Boron neutron capture therapy (BNCT) is a radiotherapy treatment modality based on the accumulation of a (10)B-containing drug and subsequent irradiation with low energy neutrons, inducing the decay of (10)B to (7)Li and an α particle, causing neoplastic cell death. This team of authors reports on a folic acid functionalized BPO4 nanoparticle with improved characteristics compared with conventional BNCT approaches, as demonstrated in tumor cell lines, and hopefully to be followed by translational human studies. © 2014.

Does change in cannabis use in established psychosis affect clinical outcome?

PubMed

Barrowclough, Christine; Emsley, Richard; Eisner, Emily; Beardmore, Ruth; Wykes, Til

2013-03-01

Cannabis use has been identified as a potent predictor of the earlier onset of psychosis, but meta-analysis has not indicated that it has a clear effect in established psychosis. To assess the association between cannabis and outcomes, including whether change in cannabis use affects symptoms and functioning, in a large sample of people with established nonaffective psychosis and comorbid substance misuse. One hundred and sixty participants whose substance use included cannabis were compared with other substance users (n = 167) on baseline demographic, clinical, and substance use variables. The cannabis using subgroup was examined prospectively with repeated measures of substance use and psychopathology at baseline, 12 months, and 24 months. We used generalized estimating equation models to estimate the effects of cannabis dose on subsequent clinical outcomes and whether change in cannabis use was associated with change in outcomes. Cannabis users showed cross-sectional differences from other substances users but not in terms of positive symptoms. Second, cannabis dose was not associated with subsequent severity of positive symptoms and change in cannabis dose did not predict change in positive symptom severity, even when patients became abstinent. However, greater cannabis exposure was associated with worse functioning, albeit with a small effect size. We did not find evidence of an association between cannabis dose and psychotic symptoms, although greater cannabis dose was associated with worse psychosocial functioning, albeit with small effect size. It would seem that within this population, not everyone will demonstrate durable symptomatic improvements from reducing cannabis.

Intraoperative Transesophageal Echocardiography and Right Ventricular Failure After Left Ventricular Assist Device Implantation.

PubMed

Silverton, Natalie A; Patel, Ravi; Zimmerman, Josh; Ma, Jianing; Stoddard, Greg; Selzman, Craig; Morrissey, Candice K

2018-02-15

To determine whether intraoperative measures of right ventricular (RV) function using transesophageal echocardiography are associated with subsequent RV failure after left ventricular assist device (LVAD) implantation. Retrospective, nonrandomized, observational study. Single tertiary-level, university-affiliated hospital. The study comprised 100 patients with systolic heart failure undergoing elective LVAD implantation. Transesophageal echocardiographic images before and after cardiopulmonary bypass were analyzed to quantify RV function using tricuspid annular plane systolic excursion (TAPSE), tricuspid annular systolic velocity (S'), fractional area change (FAC), RV global longitudinal strain, and RV free wall strain. A chart review was performed to determine which patients subsequently developed RV failure (right ventricular assist device placement or prolonged inotrope requirement ≥14 days). Nineteen patients (19%) subsequently developed RV failure. Postbypass FAC was the only measure of RV function that distinguished between the RV failure and non-RV failure groups (21.2% v 26.5%; p = 0.04). The sensitivity, specificity, and area under the curve of an abnormal RV FAC (<35%) for RV failure after LVAD implantation were 84%, 20%, and 0.52, respectively. No other intraoperative measure of RV function was associated with subsequent RV failure. RV failure increased ventilator time, intensive care unit and hospital length of stay, and mortality. Intraoperative measures of RV function such as tricuspid annular plane systolic excursion, tricuspid annular systolic velocity, and RV strain were not associated with RV failure after LVAD implantation. Decreased postbypass FAC was significantly associated with RV failure but showed poor discrimination. Copyright © 2018 Elsevier Inc. All rights reserved.

LncRNA and mRNA expression profiles of glioblastoma multiforme (GBM) reveal the potential roles of lncRNAs in GBM pathogenesis.

PubMed

Li, Qi; Jia, Hongmei; Li, Haowen; Dong, Chengya; Wang, Yajie; Zou, Zhongmei

2016-11-01

Glioblastoma multiforme (GBM) is the most common brain malignancy. Long non-coding RNAs (lncRNAs) are aberrantly expressed in many cancers and are involved in their cell proliferation, apoptosis, angiogenesis, and invasion. The functional roles of lncRNAs in GBM are less known. We analyzed a cohort of exon microarray datasets from The Cancer Genome Atlas. The differently expressed lncRNAs and mRNA were subjected to construct lncRNA-mRNA co-expression network. Probable functions for lncRNAs were predicted according to lncRNA-mRNA network and genomic adjacency by GO and pathway analysis. The expression of lncRNAs and mRNAs in GBM tissues versus normal brain tissues was examined by quantitative reverse transcription polymerase chain reaction. The 398 lncRNAs and 1995 mRNAs were identified as distinctively expressed in GBM. Probable functional roles for 98 lncRNAs were involved in 30 pathways and 32 gene functions related to tumorigenesis, development, and metastasis. The identified sets of key lncRNAs specific to GBM were subsequently verified by experiment in GBM tissues. Our reports predict the biological functions of a multitude of lncRNAs in GBM that could be potential diagnostic and prognostic biomarkers as well as therapeutic targets. Moreover, our research provides a road map for the identification and analysis of lncRNAs in tumors.

Cytocompatibility of polyethylene grafted with triethylenetetramine functionalized carbon nanoparticles

NASA Astrophysics Data System (ADS)

Žáková, Pavlína; Slepičková Kasálková, Nikola; Slepička, Petr; Kolská, Zdeňka; Karpíšková, Jana; Stibor, Ivan; Švorčík, Václav

2017-11-01

Various carbon nanostructures are widely researched as scaffolds for tissue engineering. We evaluated the surface properties and cell-substrate interactions of carbon nanoparticles functionalized with triethylenetetramine (CNPs) grafted polymer film. Two forms of polyethylene (HDPE, LDPE) were treated in an inert argon plasma discharge and, subsequently, grafted with CNPs. The surface properties were studied using multiple methods, including Raman spectroscopy, goniometry, atomic force microscopy, X-ray photoelectron spectroscopy and electrokinetic analysis. Cell-substrate interactions were determined in vitro by studying adhesion, proliferation and viability of vascular smooth muscle cells (VSMCs) from the aorta of a rat. Cell-substrate interactions on pristine and modified substrates were compared to standard tissue culture polystyrene. Our results show that CNPs affect surface morphology and wettability and therefore adhesion, proliferation and viability of cultured muscle cells.

Resolving TYK2 locus genotype-to-phenotype differences in autoimmunity.

PubMed

Dendrou, Calliope A; Cortes, Adrian; Shipman, Lydia; Evans, Hayley G; Attfield, Kathrine E; Jostins, Luke; Barber, Thomas; Kaur, Gurman; Kuttikkatte, Subita Balaram; Leach, Oliver A; Desel, Christiane; Faergeman, Soren L; Cheeseman, Jane; Neville, Matt J; Sawcer, Stephen; Compston, Alastair; Johnson, Adam R; Everett, Christine; Bell, John I; Karpe, Fredrik; Ultsch, Mark; Eigenbrot, Charles; McVean, Gil; Fugger, Lars

2016-11-02

Thousands of genetic variants have been identified, which contribute to the development of complex diseases, but determining how to elucidate their biological consequences for translation into clinical benefit is challenging. Conflicting evidence regarding the functional impact of genetic variants in the tyrosine kinase 2 (TYK2) gene, which is differentially associated with common autoimmune diseases, currently obscures the potential of TYK2 as a therapeutic target. We aimed to resolve this conflict by performing genetic meta-analysis across disorders; subsequent molecular, cellular, in vivo, and structural functional follow-up; and epidemiological studies. Our data revealed a protective homozygous effect that defined a signaling optimum between autoimmunity and immunodeficiency and identified TYK2 as a potential drug target for certain common autoimmune disorders. Copyright © 2016, American Association for the Advancement of Science.

Non-coding RNAs in virology: an RNA genomics approach.

PubMed

Isaac, Christopher; Patel, Trushar R; Zovoilis, Athanasios

2018-04-01

Advances in sequencing technologies and bioinformatic analysis techniques have greatly improved our understanding of various classes of RNAs and their functions. Despite not coding for proteins, non-coding RNAs (ncRNAs) are emerging as essential biomolecules fundamental for cellular functions and cell survival. Interestingly, ncRNAs produced by viruses not only control the expression of viral genes, but also influence host cell regulation and circumvent host innate immune response. Correspondingly, ncRNAs produced by the host genome can play a key role in host-virus interactions. In this article, we will first discuss a number of types of viral and mammalian ncRNAs associated with viral infections. Subsequently, we also describe the new possibilities and opportunities that RNA genomics and next-generation sequencing technologies provide for studying ncRNAs in virology.

Haplotype analysis and a novel allele-sharing method refines a chromosome 4p locus linked to bipolar affective disorder.

PubMed

Le Hellard, Stephanie; Lee, Andrew J; Underwood, Sarah; Thomson, Pippa A; Morris, Stewart W; Torrance, Helen S; Anderson, Susan M; Adams, Richard R; Navarro, Pau; Christoforou, Andrea; Houlihan, Lorna M; Detera-Wadleigh, Sevilla; Owen, Michael J; Asherson, Philip; Muir, Walter J; Blackwood, Douglas H R; Wray, Naomi R; Porteous, David J; Evans, Kathryn L

2007-03-15

Bipolar affective disorder (BPAD) and schizophrenia (SCZ) are common conditions. Their causes are unknown, but they include a substantial genetic component. Previously, we described significant linkage of BPAD to a chromosome 4p locus within a large pedigree (F22). Others subsequently have found evidence for linkage of BPAD and SCZ to this region. We constructed high-resolution haplotypes for four linked families, calculated logarithm of the odds (LOD) scores, and developed a novel method to assess the extent of allele sharing within genes between the families. We describe an increase in the F22 LOD score for this region. Definition and comparison of the linked haplotypes allowed us to prioritize two subregions of 3.8 and 4.4 Mb. Analysis of the extent of allele sharing within these subregions identified 200 kb that shows increased allele sharing between families. Linkage of BPAD to chromosome 4p has been strengthened. Haplotype analysis in the additional linked families refined the 20-Mb linkage region. Development of a novel allele-sharing method allowed us to bridge the gap between conventional linkage and association studies. Description of a 200-kb region of increased allele sharing prioritizes this region, which contains two functional candidate genes for BPAD, SLC2A9, and WDR1, for subsequent studies.

Tsunami Waves and Tsunami-Induced Natural Oscillations Determined by HF Radar in Ise Bay, Japan

NASA Astrophysics Data System (ADS)

Toguchi, Y.; Fujii, S.; Hinata, H.

2018-04-01

Tsunami waves and the subsequent natural oscillations generated by the 2011 Tohoku earthquake were observed by two high-frequency (HF) radars and four tidal gauge records in Ise Bay. The radial velocity components of both records increased abruptly at approximately 17:00 (JST) and continued for more than 24 h. This indicated that natural oscillations followed the tsunami in Ise Bay. The spectral analyses showed that the tsunami wave arrivals had periods of 16-19, 30-40, 60-90, and 120-140 min. The three longest periods were remarkably amplified. Time-frequency analysis also showed the energy increase and duration of these periods. We used an Empirical Orthogonal Function (EOF) to analyze the total velocity of the currents to find the underlying oscillation patterns in the three longest periods. To verify the physical properties of the EOF analysis results, we calculated the oscillation modes in Ise Bay using a numerical model proposed by Loomis. The results of EOF analysis showed that the oscillation modes of 120-140 and 60-90 min period bands were distributed widely, whereas the oscillation mode of the 30-40 min period band was distributed locally. The EOF spatial patterns of each period showed good agreement with the eigenmodes calculated by the method of Loomis (1975). Thus, the HF radars were capable of observing the tsunami arrival and the subsequent oscillations.

MONGKIE: an integrated tool for network analysis and visualization for multi-omics data.

PubMed

Jang, Yeongjun; Yu, Namhee; Seo, Jihae; Kim, Sun; Lee, Sanghyuk

2016-03-18

Network-based integrative analysis is a powerful technique for extracting biological insights from multilayered omics data such as somatic mutations, copy number variations, and gene expression data. However, integrated analysis of multi-omics data is quite complicated and can hardly be done in an automated way. Thus, a powerful interactive visual mining tool supporting diverse analysis algorithms for identification of driver genes and regulatory modules is much needed. Here, we present a software platform that integrates network visualization with omics data analysis tools seamlessly. The visualization unit supports various options for displaying multi-omics data as well as unique network models for describing sophisticated biological networks such as complex biomolecular reactions. In addition, we implemented diverse in-house algorithms for network analysis including network clustering and over-representation analysis. Novel functions include facile definition and optimized visualization of subgroups, comparison of a series of data sets in an identical network by data-to-visual mapping and subsequent overlaying function, and management of custom interaction networks. Utility of MONGKIE for network-based visual data mining of multi-omics data was demonstrated by analysis of the TCGA glioblastoma data. MONGKIE was developed in Java based on the NetBeans plugin architecture, thus being OS-independent with intrinsic support of module extension by third-party developers. We believe that MONGKIE would be a valuable addition to network analysis software by supporting many unique features and visualization options, especially for analysing multi-omics data sets in cancer and other diseases. .

Temporal manipulation of mitochondrial function by virulent Francisella tularensis to limit inflammation and control cell death.

PubMed

Jessop, Forrest; Schwarz, Benjamin; Heitmann, Emily; Buntyn, Robert; Wehrly, Tara; Bosio, Catharine M

2018-05-14

Francisella tularensis ssp tularensis (Ftt) is a highly pathogenic intracellular bacterium that suppresses host inflammation by impairing the metabolic shift from oxidative phosphorylation to glycolysis. Decreased mitochondrial metabolism is central to initiating a metabolic shift to glycolysis and regulating inflammation, but Ftt manipulation of host mitochondrial function has not been explored. We demonstrate using extracellular flux analysis that Ftt infection initially improves host macrophage mitochondrial bioenergetics in a capsule dependent manner. Enhancement of mitochondrial function by Ftt allowed for modest replication and inhibition of apoptosis early after infection. However, using live cell imaging we found that Ftt facilitated the loss of mitochondrial function at later time points during infection in a capsule independent fashion. This loss of function was paired with oncosis and rapid bacterial replication. Inhibition of oncosis reduced intracellular bacteria numbers, underscoring the requirement for this process during Ftt infection. These findings establish that temporal mitochondrial manipulation by Ftt is critical for maintenance of a non-inflammatory environment and subsequently aids in optimal replication and dissemination of this pathogenic organism. Copyright © 2018 American Society for Microbiology.

Neuronal dystonin isoform 2 is a mediator of endoplasmic reticulum structure and function.

PubMed

Ryan, Scott D; Ferrier, Andrew; Sato, Tadasu; O'Meara, Ryan W; De Repentigny, Yves; Jiang, Susan X; Hou, Sheng T; Kothary, Rashmi

2012-02-01

Dystonin/Bpag1 is a cytoskeletal linker protein whose loss of function in dystonia musculorum (dt) mice results in hereditary sensory neuropathy. Although loss of expression of neuronal dystonin isoforms (dystonin-a1/dystonin-a2) is sufficient to cause dt pathogenesis, the diverging function of each isoform and what pathological mechanisms are activated upon their loss remains unclear. Here we show that dt(27) mice manifest ultrastructural defects at the endoplasmic reticulum (ER) in sensory neurons corresponding to in vivo induction of ER stress proteins. ER stress subsequently leads to sensory neurodegeneration through induction of a proapoptotic caspase cascade. dt sensory neurons display neurodegenerative pathologies, including Ca(2+) dyshomeostasis, unfolded protein response (UPR) induction, caspase activation, and apoptosis. Isoform-specific loss-of-function analysis attributes these neurodegenerative pathologies to specific loss of dystonin-a2. Inhibition of either UPR or caspase signaling promotes the viability of cells deficient in dystonin. This study provides insight into the mechanism of dt neuropathology and proposes a role for dystonin-a2 as a mediator of normal ER structure and function.

Functionalized graphene sheets with poly(ionic liquid)s and high adsorption capacity of anionic dyes

NASA Astrophysics Data System (ADS)

Zhao, Weifeng; Tang, Yusheng; Xi, Jia; Kong, Jie

2015-01-01

Graphene sheets were covalently functionalized with poly(1-vinylimidazole) (PVI) type poly(ionic liquid), by utilizing a diazonium addition reaction and the subsequent grafting of PVI polymers onto the graphene sheet surface by a quaternarization reaction. The resultant modified graphene sheets showed improved dispersion property when being dissolved in DMF and ethanol. FTIR, XPS, XRD and TEM observations confirmed the success of the covalent functionalization, and thermogravimetric analysis revealed that the grafting ratio of PVI was ∼12 wt%. The obtained PVI-functionalized graphene showed a high capability for removing anionic dyes such as methyl blue (MB) from water solution. The experimental data of isotherm fitted well with the Langmuir adsorption model. The adsorption capacity of 1910 mg g-1 for methyl blue (MB) dye was observed for functionalized graphene sheets with poly(ionic liquid)s, which was higher than that of unmodified graphene. The high adsorption capacity observed in this study emphasizes that poly(ionic liquid)s-modified graphene materials have a great potential for water purification as they are highly efficient and stable adsorbents for sustainability.

Functional genomics analysis of low concentration of ethanol in human hepatocellular carcinoma (HepG2) cells. Role of genes involved in transcriptional and translational processes.

PubMed

Castaneda, Francisco; Rosin-Steiner, Sigrid; Jung, Klaus

2006-12-21

We previously found that ethanol at millimolar level (1 mM) activates the expression of transcription factors with subsequent regulation of apoptotic genes in human hepatocellular carcinoma (HCC) HepG2 cells. However, the role of ethanol on the expression of genes implicated in transcriptional and translational processes remains unknown. Therefore, the aim of this study was to characterize the effect of low concentration of ethanol on gene expression profiling in HepG2 cells using cDNA microarrays with especial interest in genes with transcriptional and translational function. The gene expression pattern observed in the ethanol-treated HepG2 cells revealed a relatively similar pattern to that found in the untreated control cells. The pairwise comparison analysis demonstrated four significantly up-regulated (COBRA1, ITGB4, STAU2, and HMGN3) genes and one down-regulated (ANK3) gene. All these genes exert their function on transcriptional and translational processes and until now none of these genes have been associated with ethanol. This functional genomic analysis demonstrates the reported interaction between ethanol and ethanol-regulated genes. Moreover, it confirms the relationship between ethanol-regulated genes and various signaling pathways associated with ethanol-induced apoptosis. The data presented in this study represents an important contribution toward the understanding of the molecular mechanisms of ethanol at low concentration in HepG2 cells, a HCC-derived cell line.

Functional genomics analysis of low concentration of ethanol in human hepatocellular carcinoma (HepG2) cells. Role of genes involved in transcriptional and translational processes

PubMed Central

Castaneda, Francisco; Rosin-Steiner, Sigrid; Jung, Klaus

2007-01-01

We previously found that ethanol at millimolar level (1 mM) activates the expression of transcription factors with subsequent regulation of apoptotic genes in human hepatocellular carcinoma (HCC) HepG2 cells. However, the role of ethanol on the expression of genes implicated in transcriptional and translational processes remains unknown. Therefore, the aim of this study was to characterize the effect of low concentration of ethanol on gene expression profiling in HepG2 cells using cDNA microarrays with especial interest in genes with transcriptional and translational function. The gene expression pattern observed in the ethanol-treated HepG2 cells revealed a relatively similar pattern to that found in the untreated control cells. The pairwise comparison analysis demonstrated four significantly up-regulated (COBRA1, ITGB4, STAU2, and HMGN3) genes and one down-regulated (ANK3) gene. All these genes exert their function on transcriptional and translational processes and until now none of these genes have been associated with ethanol. This functional genomic analysis demonstrates the reported interaction between ethanol and ethanol-regulated genes. Moreover, it confirms the relationship between ethanol-regulated genes and various signaling pathways associated with ethanol-induced apoptosis. The data presented in this study represents an important contribution toward the understanding of the molecular mechanisms of ethanol at low concentration in HepG2 cells, a HCC-derived cell line. PMID:17211498

Large-scale Granger causality analysis on resting-state functional MRI

NASA Astrophysics Data System (ADS)

D'Souza, Adora M.; Abidin, Anas Zainul; Leistritz, Lutz; Wismüller, Axel

2016-03-01

We demonstrate an approach to measure the information flow between each pair of time series in resting-state functional MRI (fMRI) data of the human brain and subsequently recover its underlying network structure. By integrating dimensionality reduction into predictive time series modeling, large-scale Granger Causality (lsGC) analysis method can reveal directed information flow suggestive of causal influence at an individual voxel level, unlike other multivariate approaches. This method quantifies the influence each voxel time series has on every other voxel time series in a multivariate sense and hence contains information about the underlying dynamics of the whole system, which can be used to reveal functionally connected networks within the brain. To identify such networks, we perform non-metric network clustering, such as accomplished by the Louvain method. We demonstrate the effectiveness of our approach to recover the motor and visual cortex from resting state human brain fMRI data and compare it with the network recovered from a visuomotor stimulation experiment, where the similarity is measured by the Dice Coefficient (DC). The best DC obtained was 0.59 implying a strong agreement between the two networks. In addition, we thoroughly study the effect of dimensionality reduction in lsGC analysis on network recovery. We conclude that our approach is capable of detecting causal influence between time series in a multivariate sense, which can be used to segment functionally connected networks in the resting-state fMRI.

Evolutionary conservation of the polyproline II conformation surrounding intrinsically disordered phosphorylation sites.

PubMed

Elam, W Austin; Schrank, Travis P; Campagnolo, Andrew J; Hilser, Vincent J

2013-04-01

Intrinsically disordered (ID) proteins function in the absence of a unique stable structure and appear to challenge the classic structure-function paradigm. The extent to which ID proteins take advantage of subtle conformational biases to perform functions, and whether signals for such mechanism can be identified in proteome-wide studies is not well understood. Of particular interest is the polyproline II (PII) conformation, suggested to be highly populated in unfolded proteins. We experimentally determine a complete calorimetric propensity scale for the PII conformation. Projection of the scale into representative eukaryotic proteomes reveals significant PII bias in regions coding for ID proteins. Importantly, enrichment of PII in ID proteins, or protein segments, is also captured by other PII scales, indicating that this enrichment is robustly encoded and universally detectable regardless of the method of PII propensity determination. Gene ontology (GO) terms obtained using our PII scale and other scales demonstrate a consensus for molecular functions performed by high PII proteins across the proteome. Perhaps the most striking result of the GO analysis is conserved enrichment (P < 10(-8) ) of phosphorylation sites in high PII regions found by all PII scales. Subsequent conformational analysis reveals a phosphorylation-dependent modulation of PII, suggestive of a conserved "tunability" within these regions. In summary, the application of an experimentally determined polyproline II (PII) propensity scale to proteome-wide sequence analysis and gene ontology reveals an enrichment of PII bias near disordered phosphorylation sites that is conserved throughout eukaryotes. Copyright © 2013 The Protein Society.

Mediator-dependent Nuclear Receptor Functions

PubMed Central

Chen, Wei; Roeder, Robert

2011-01-01

As gene-specific transcription factors, nuclear hormone receptors are broadly involved in many important biological processes. Their function on target genes requires the stepwise assembly of different coactivator complexes that facilitate chromatin remodeling and subsequent preinitiation complex (PIC) formation and function. Mediator has proved to be a crucial, and general, nuclear receptor-interacting coactivator, with demonstrated functions in transcription steps ranging from chromatin remodeling to subsequent PIC formation and function. Here we discuss (i) our current understanding of pathways that nuclear receptors and other interacting cofactors employ to recruit Mediator to target gene enhancers and promoters, including conditional requirements for the strong NR-Mediator interactions mediated by the NR AF2 domain and the MED1 LXXLLL motifs and (ii) mechanisms by which Mediator acts to transmit signals from enhancer-bound nuclear receptors to the general transcription machinery at core promoters to effect PIC formation and function. PMID:21854863

Organosilane functionalization of halloysite nanotubes for enhanced loading and controlled release.

PubMed

Yuan, Peng; Southon, Peter D; Liu, Zongwen; Kepert, Cameron J

2012-09-21

The surfaces of naturally occurring halloysite nanotubes were functionalized with γ-aminopropyltriethoxysilane (APTES), which was found to have a substantial effect on the loading and subsequent release of a model dye molecule. APTES was mostly anchored at the internal lumen surface of halloysite through covalent grafting, forming a functionalized surface covered by aminopropyl groups. The dye loading of the functionalized halloysite was 32% greater than that of the unmodified sample, and the release from the functionalized halloysite was dramatically prolonged as compared to that from the unmodified one. Dye release was prolonged at low pH and the release at pH 3.5 was approximately three times slower than that at pH 10.0. These results demonstrate that organosilane functionalization makes pH an external trigger for controlling the loading of guest on halloysite and the subsequent controlled release.

Acute toxicity of functionalized single wall carbon nanotubes: A biochemical, histopathologic and proteomics approach.

PubMed

Ahmadi, Homa; Ramezani, Mohammad; Yazdian-Robati, Rezvan; Behnam, Behzad; Razavi Azarkhiavi, Kamal; Hashem Nia, Azadeh; Mokhtarzadeh, Ahad; Matbou Riahi, Maryam; Razavi, Bibi Marjan; Abnous, Khalil

2017-09-25

Recently carbon nanotubes (CNTs) showed promising potentials in different biomedical applications but their safe use in humans and probable toxicities are still challenging. The aim of this study was to determine the acute toxicity of functionalized single walled carbon nanotubes (SWCNTs). In this project, PEGylated and Tween functionalized SWCNTs were prepared. BALB/c mice were randomly divided into nine groups, including PEGylated SWCNTs (75,150μg/mouse) and PEG, Tween80 suspended SWCNTs, Tween 80 and a control group (intact mice). One or 7 days after intravenous injection, the mice were killed and serum and livers were collected. The oxidative stress markers, biochemical and histopathological changes were studied. Subsequently, proteomics approach was used to investigate the alterations of protein expression profiles in the liver. Results showed that there were not any significant differences in malondealdehyde (MDA), glutathione (GSH) levels and biochemical enzymes (ALT and AST) between groups, while the histopathological observations of livers showed some injuries. The results of proteomics analysis revealed indolethylamine N-Methyltransferase (INMT), glycine N-Methyltransferase (GNMT), selenium binding protein (Selenbp), thioredoxin peroxidase (TPx), TNF receptor associated protein 1(Trap1), peroxiredoxin-6 (Prdx6), electron transport flavoprotein (Etf-α), regucalcin (Rgn) and ATP5b proteins were differentially expressed in functionalized SWCNTs groups. Western blot analyses confirmed that the changes in Prdx6 were consistent with 2-DE gel analysis. In summary, acute toxicological study on two functionalized SWCNTs did not show any significant toxicity at selected doses. Proteomics analysis also showed that following exposure to functionalized SWCNTs, the expression of some proteins with antioxidant activity and detoxifying properties were increased in liver tissue. Copyright © 2017 Elsevier B.V. All rights reserved.

Spatial memory tasks in rodents: what do they model?

PubMed

Morellini, Fabio

2013-10-01

The analysis of spatial learning and memory in rodents is commonly used to investigate the mechanisms underlying certain forms of human cognition and to model their dysfunction in neuropsychiatric and neurodegenerative diseases. Proper interpretation of rodent behavior in terms of spatial memory and as a model of human cognitive functions is only possible if various navigation strategies and factors controlling the performance of the animal in a spatial task are taken into consideration. The aim of this review is to describe the experimental approaches that are being used for the study of spatial memory in rats and mice and the way that they can be interpreted in terms of general memory functions. After an introduction to the classification of memory into various categories and respective underlying neuroanatomical substrates, I explain the concept of spatial memory and its measurement in rats and mice by analysis of their navigation strategies. Subsequently, I describe the most common paradigms for spatial memory assessment with specific focus on methodological issues relevant for the correct interpretation of the results in terms of cognitive function. Finally, I present recent advances in the use of spatial memory tasks to investigate episodic-like memory in mice.

SYNCHRONIZATION OF HETEROGENEOUS OSCILLATORS UNDER NETWORK MODIFICATIONS: PERTURBATION AND OPTIMIZATION OF THE SYNCHRONY ALIGNMENT FUNCTION

PubMed Central

Taylor, Dane; Skardal, Per Sebastian; Sun, Jie

2016-01-01

Synchronization is central to many complex systems in engineering physics (e.g., the power-grid, Josephson junction circuits, and electro-chemical oscillators) and biology (e.g., neuronal, circadian, and cardiac rhythms). Despite these widespread applications—for which proper functionality depends sensitively on the extent of synchronization—there remains a lack of understanding for how systems can best evolve and adapt to enhance or inhibit synchronization. We study how network modifications affect the synchronization properties of network-coupled dynamical systems that have heterogeneous node dynamics (e.g., phase oscillators with non-identical frequencies), which is often the case for real-world systems. Our approach relies on a synchrony alignment function (SAF) that quantifies the interplay between heterogeneity of the network and of the oscillators and provides an objective measure for a system’s ability to synchronize. We conduct a spectral perturbation analysis of the SAF for structural network modifications including the addition and removal of edges, which subsequently ranks the edges according to their importance to synchronization. Based on this analysis, we develop gradient-descent algorithms to efficiently solve optimization problems that aim to maximize phase synchronization via network modifications. We support these and other results with numerical experiments. PMID:27872501

Day-to-day relations between stress and sleep and the mediating role of perseverative cognition.

PubMed

Van Laethem, Michelle; Beckers, Debby G J; van Hooff, Madelon L M; Dijksterhuis, Ap; Geurts, Sabine A E

2016-08-01

The goals of this longitudinal diary-based study were to shed light on the day-level relationship between stress and subsequent sleep, and to examine whether perseverative cognition is a mediating factor in this relation. A total of 44 Dutch PhD students were followed during a two-month period, from one month before their public thesis defense (ie, a stressful life event), until one month thereafter. Participants completed short evening and morning questionnaires on eight occasions (in anticipation of and following the defense), including questions about day-level stress, sleep quality, and perseverative cognition. Objective sleep parameters were collected with the SenseWear Pro Armband. Multilevel analysis was used to analyze daily observations nested within individuals. Analyses revealed that day-level stress was not directly related to subsequent subjective sleep indicators or to subsequent objective sleep indicators. Day-level stress was significantly associated with day-level perseverative cognition, and daily variations in perseverative cognition were significantly related to several day-level objective sleep parameters (sleep efficiency, marginally to number of awakenings, and wake after sleep onset), and to several day-level subjective sleep parameters (sleep quality, number of awakenings, wake after sleep onset). Finally, mediation analyses using path analysis suggested that, on the day level, perseverative cognition functions as a mediator between stress and several sleep parameters, namely, subjective sleep quality, objective sleep efficiency, and subjective wake after sleep onset. Perseverative cognition is a promising explanatory mechanism linking day-level stress to subjective and objective measures of sleep. Copyright © 2016 Elsevier B.V. All rights reserved.

Equilibrium, quasi-equilibrium, and nonequilibrium freezing of mammalian embryos.

PubMed

Mazur, P

1990-08-01

The first successful freezing of early embryos to -196 degrees C in 1972 required that they be cooled slowly at approximately 1 degree C/min to about -70 degrees C. Subsequent observations and physical/chemical analyses indicate that embryos cooled at that rate dehydrate sufficiently to maintain the chemical potential of their intracellular water close to that of the water in the partly frozen extracellular solution. Consequently, such slow freezing is referred to as equilibrium freezing. In 1972 and since, a number of investigators have studied the responses of embryos to departures from equilibrium freezing. When disequilibrium is achieved by the use of higher constant cooling rates to -70 degrees C, the results is usually intracellular ice formation and embryo death. That result is quantitatively in accord with the predictions of the physical/chemical analysis of the kinetics of water loss as a function of cooling rate. However, other procedures involving rapid nonequilibrium cooling do not result in high mortality. One common element in these other nonequilibrium procedures is that, before the temperature has dropped to a level that permits intracellular ice formation, the embryo water content is reduced to the point at which the subsequent rapid nonequilibrium cooling results in either the formation of small innocuous intracellular ice crystals or the conversion of the intracellular solution into a glass. In both cases, high survival requires that subsequent warming be rapid, to prevent recrystallization or devitrification. The physical/chemical analysis developed for initially nondehydrated cells appears generally applicable to these other nonequilibrium procedures as well.

Ability to Walk 1/4 Mile Predicts Subsequent Disability, Mortality, and Health Care Costs

PubMed Central

Kang, Yihuang; Studenski, Stephanie A.; Degenholtz, Howard B.

2010-01-01

ABSTRACT Background Mobility, such as walking 1/4 mile, is a valuable but underutilized health indicator among older adults. For mobility to be successfully integrated into clinical practice and health policy, an easily assessed marker that predicts subsequent health outcomes is required. Objective To determine the association between mobility, defined as self-reported ability to walk 1/4 mile, and mortality, functional decline, and health care utilization and costs during the subsequent year. Design Analysis of longitudinal data from the 2003–2004 Medicare Current Beneficiary Survey, a nationally representative sample of Medicare beneficiaries. Participants Participants comprised 5895 community-dwelling adults aged 65 years or older enrolled in Medicare. Main Measures Mobility (self-reported ability to walk 1/4 mile), mortality, incident difficulty with activities of daily living (ADLs), total annual health care costs, and hospitalization rates. Key Results Among older adults, 28% reported difficulty and 17% inability to walk 1/4 mile at baseline. Compared to those without difficulty and adjusting for demographics, socioeconomic status, chronic conditions, and health behaviors, mortality was greater in those with difficulty [AOR (95% CI): 1.57 (1.10-2.24)] and inability [AOR (CI): 2.73 (1.79-4.15)]. New functional disability also occurred more frequently as self-reported ability to walk 1/4 mile declined (subsequent incident disability among those with no difficulty, difficulty, or inability to walk 1/4 mile at baseline was 11%, 29%, and 47% for instrumental ADLs, and 4%, 14%, and 23% for basic ADLs). Total annual health care costs were $2773 higher (95% CI $1443-4102) in persons with difficulty and $3919 higher (CI $1948-5890) in those who were unable. For each 100 persons, older adults reporting difficulty walking 1/4 mile at baseline experienced an additional 14 hospitalizations (95% CI 8-20), and those who were unable experienced an additional 22 hospitalizations (CI 14-30) during the follow-up period, compared to persons without walking difficulty. Conclusions Mobility disability, a simple self-report measure, is a powerful predictor of future health, function, and utilization independent of usual health and demographic indicators. Mobility disability may be used to target high-risk patients for care management and preventive interventions. PMID:20972641

Adiponectin is not associated with renal function decline in community-dwelling elderly adults.

PubMed

Kobayashi, Hiroki; Otsuka, Hiromasa; Yanai, Mitsuru; Haketa, Akira; Hara, Motohiko; Hishiki, Mikano; Abe, Masanori; Soma, Masayoshi

2018-05-01

Adiponectin secreted by adipocytes plays an important role in the regulation of glucose and fatty acid metabolism. Contrary to findings in patients with chronic kidney disease (CKD), no prospective data about the association of serum adiponectin with renal function decline in the general population have yet appeared. Our objective was to analyze the relationship of total and high molecular weight (HMW) adiponectin with renal function decline as measured by cystatin C in community-dwelling elderly adults without moderate or severe CKD.In a prospective observational analysis, a total of 216 healthy elderly volunteers with eGFRcys ≥60 mL/min/1.73 m underwent anthropometric and laboratory tests at baseline and at follow-up visits. A subgroup with serum samples collected 5 years apart was further analyzed.There were no differences in either total or HMW adiponectin level between subjects subsequently undergoing rapid renal function decline and subjects with normal physiologic renal function decline (P = .71, P = .81). On univariate linear regression, neither total nor HMW adiponectin were associated with annual renal function decline (β = -0.23; P = .71, β = -0.057; P = .90). Multivariate analysis did not show a significant contribution of either total or HMW adiponectin to annual renal function decline (β = -0.50; P = .46, β = 0.01; P = .98). In the logistic regression analysis, we did not observe any statistically significant association of serum adiponectin levels with rapid renal function decline or incidence of CKD.Contrary to findings in populations with CKD, neither total nor HMW adiponectin had a substantial association with renal function decline in an elderly population with eGFRcys ≥60 mL/min/1.73 m. Our results and conclusions should not be extrapolated to subjects with other characteristics.

Identification of candidate genes in osteoporosis by integrated microarray analysis.

PubMed

Li, J J; Wang, B Q; Fei, Q; Yang, Y; Li, D

2016-12-01

In order to screen the altered gene expression profile in peripheral blood mononuclear cells of patients with osteoporosis, we performed an integrated analysis of the online microarray studies of osteoporosis. We searched the Gene Expression Omnibus (GEO) database for microarray studies of peripheral blood mononuclear cells in patients with osteoporosis. Subsequently, we integrated gene expression data sets from multiple microarray studies to obtain differentially expressed genes (DEGs) between patients with osteoporosis and normal controls. Gene function analysis was performed to uncover the functions of identified DEGs. A total of three microarray studies were selected for integrated analysis. In all, 1125 genes were found to be significantly differentially expressed between osteoporosis patients and normal controls, with 373 upregulated and 752 downregulated genes. Positive regulation of the cellular amino metabolic process (gene ontology (GO): 0033240, false discovery rate (FDR) = 1.00E + 00) was significantly enriched under the GO category for biological processes, while for molecular functions, flavin adenine dinucleotide binding (GO: 0050660, FDR = 3.66E-01) and androgen receptor binding (GO: 0050681, FDR = 6.35E-01) were significantly enriched. DEGs were enriched in many osteoporosis-related signalling pathways, including those of mitogen-activated protein kinase (MAPK) and calcium. Protein-protein interaction (PPI) network analysis showed that the significant hub proteins contained ubiquitin specific peptidase 9, X-linked (Degree = 99), ubiquitin specific peptidase 19 (Degree = 57) and ubiquitin conjugating enzyme E2 B (Degree = 57). Analysis of gene function of identified differentially expressed genes may expand our understanding of fundamental mechanisms leading to osteoporosis. Moreover, significantly enriched pathways, such as MAPK and calcium, may involve in osteoporosis through osteoblastic differentiation and bone formation.Cite this article: J. J. Li, B. Q. Wang, Q. Fei, Y. Yang, D. Li. Identification of candidate genes in osteoporosis by integrated microarray analysis. Bone Joint Res 2016;5:594-601. DOI: 10.1302/2046-3758.512.BJR-2016-0073.R1. © 2016 Fei et al.

Adjusting the surface areal density of click-reactive azide groups by kinetic control of the azide substitution reaction on bromine-functional SAMs.

PubMed

Zhang, Shuo; Maidenberg, Yanir; Luo, Kai; Koberstein, Jeffrey T

2014-06-03

Azide-alkyne click chemistry has emerged as an important and versatile means for tethering a wide variety of guest molecules to virtually any substrate. In many of these applications, it is important to exercise control over the areal density of surface functional groups to achieve a desired areal density of the tethered guest molecule of interest. We demonstrate herein that the areal density of surface azide groups on flat germanium surfaces and nanoparticle substrates (silica and iron oxide) can be controlled kinetically by appropriately timed quenching of the S(N)2 substitution reaction of bromo-alkane-silane monolayers induced by the addition of sodium azide. The kinetics of the azide substitution reaction on monolayers formed on flat Ge substrates, determined by attenuated total reflection infrared spectroscopy (ATR-IR), are found to be identical to those for monolayers formed on both silica and iron oxide nanoparticles, the latter determined by transmission infrared spectroscopy. To validate the method, the percentages of surface bromine groups converted to azide groups after various reaction times were measured by quenching the S(N)2 reaction followed by analysis with ATR-IR (for Ge) and thermogravimetric analysis (after a subsequent click reaction with an alkyne-terminal polymer) for the nanoparticle substrates. The conversions found after quenching agree well with those expected from the standard kinetic curves. The latter result suggests that the kinetic method for the control of azide group areal density is a versatile means for functionalizing substrates with a prescribed areal density of azide groups for subsequent click reactions, and that the method is universal for any substrate, flat or nanoparticle, that can be modified with bromo-alkane-silane monolayers. Regardless of the surface geometry, we find that the azide substitution reaction is complete within 2-3 h, in sharp contrast to previous reports that indicate times of 48-60 h required for completion of the reaction.

The effects of presession manipulations on automatically maintained challenging behavior and task responding.

PubMed

Chung, Yi-Chieh; Cannella-Malone, Helen I

2010-11-01

This study examined the effects of presession exposure to attention, response blocking, attention with response blocking, and noninteraction conditions on subsequent engagement in automatically maintained challenging behavior and correct responding in four individuals with significant intellectual disabilities. Following a functional analysis, the effects of the four presession conditions were examined using multielement designs. Results varied across the 4 participants (e.g., presession noninteraction acted as an abolishing operation for 2 participants, but as an establishing operation for the other 2 participants). As such, both the results replicated and contradicted previous research examining the effects of motivating operations on automatically maintained challenging behavior. Although the results varied across participants, at least one condition resulting in a decrease in challenging behavior and an increase in correct responding were identified for each participant. These findings suggested that presession manipulations resulted in decreases in subsequent automatically maintained challenging behavior and simultaneous increases in correct responding might need to be individually identified when the maintaining contingencies cannot be identified.

A general diagrammatic algorithm for contraction and subsequent simplification of second-quantized expressions.

PubMed

Bochevarov, Arteum D; Sherrill, C David

2004-08-22

We present a general computer algorithm to contract an arbitrary number of second-quantized expressions and simplify the obtained analytical result. The functions that perform these operations are a part of the program Nostromo which facilitates the handling and analysis of the complicated mathematical formulas which are often encountered in modern quantum-chemical models. In contrast to existing codes of this kind, Nostromo is based solely on the Goldstone-diagrammatic representation of algebraic expressions in Fock space and has capabilities to work with operators as well as scalars. Each Goldstone diagram is internally represented by a line of text which is easy to interpret and transform. The calculation of matrix elements does not exploit Wick's theorem in a direct way, but uses diagrammatic techniques to produce only nonzero terms. The identification of equivalent expressions and their subsequent factorization in the final result is performed easily by analyzing the topological structure of the diagrammatic expressions. (c) 2004 American Institute of Physics

Assessing heterogeneity of peroxisomes: isolation of two subpopulations from rat liver.

PubMed

Islinger, Markus; Abdolzade-Bavil, Afsaneh; Liebler, Sven; Weber, Gerhardt; Völkl, Alfred

2012-01-01

Peroxisomes exhibit a heterogeneous morphological appearance in rat liver tissue. In this respect, the isolation and subsequent biochemical characterization of peroxisome species from different subcellular prefractions should help to solve the question of whether peroxisomes indeed diverge into functionally specialized subgroups in one tissue. As a means to address this question, we provide a detailed separation protocol for the isolation of peroxisomes from both the light (LM-Po) and the heavy (HM-Po) mitochondrial prefraction for their subsequent comparative analysis. Both isolation strategies rely on centrifugation in individually adapted Optiprep gradients. In case of the heavy mitochondrial fraction, free flow electrophoresis is appended as an additional separation step to yield peroxisomes of sufficient purity. In view of their morphology, peroxisomes isolated from both fractions are surrounded by a continuous single membrane and contain a gray-opaque inner matrix. However, beyond this overall similar appearance, HM-Po exhibit a smaller average diameter, float at lower density, and show a more negative average membrane charge when compared to LM-Po.

Portable Video/Digital Retinal Funduscope

NASA Technical Reports Server (NTRS)

Taylor, Gerald R.; Meehan, Richard; Hunter, Norwood; Caputo, Michael; Gibson, C. Robert

1991-01-01

Lightweight, inexpensive electronic and photographic instrument developed for detection, monitoring, and objective quantification of ocular/systemic disease or physiological alterations of retina, blood vessels, or other structures in anterior and posterior chambers of eye. Operated with little training. Functions with human or animal subject seated, recumbent, inverted, or in almost any other orientation; and in hospital, laboratory, field, or other environment. Produces video images viewed directly and/or digitized for simultaneous or subsequent analysis. Also equipped to produce photographs and/or fitted with adaptors to produce stereoscopic or magnified images of skin, nose, ear, throat, or mouth to detect lesions or diseases.

Risk Stratification in Arrhythmic Right Ventricular Cardiomyopathy Without Implantable Cardioverter-Defibrillators

PubMed Central

Brun, Francesca; Groeneweg, Judith A.; Gear, Kathleen; Sinagra, Gianfranco; van der Heijden, Jeroen; Mestroni, Luisa; Hauer, Richard N.; Borgstrom, Mark; Marcus, Frank I.; Hughes, Trina

2016-01-01

Objectives The primary objective of this study is risk stratification of patients with arrhythmic right ventricular cardiomyopathy (ARVC). Background There is a need to identify those who need an automatic implantable defibrillator (ICD) to prevent sudden death. Methods This is an analysis of 88 patients with ARVC from three centers who were not treated with an ICD. Results Risk factors for subsequent arrhythmic deaths were pre-enrollment sustained or nonsustained ventricular tachycardia (VT) and decreased left ventricular function. Conclusion These factors serve as proposed guidelines for implantation of an ICD in patients with ARVC to prevent sudden death. PMID:27790640

Determining relative error bounds for the CVBEM

USGS Publications Warehouse

Hromadka, T.V.

1985-01-01

The Complex Variable Boundary Element Methods provides a measure of relative error which can be utilized to subsequently reduce the error or provide information for further modeling analysis. By maximizing the relative error norm on each boundary element, a bound on the total relative error for each boundary element can be evaluated. This bound can be utilized to test CVBEM convergence, to analyze the effects of additional boundary nodal points in reducing the modeling error, and to evaluate the sensitivity of resulting modeling error within a boundary element from the error produced in another boundary element as a function of geometric distance. ?? 1985.

Supercomputer analysis of purine and pyrimidine metabolism leading to DNA synthesis.

PubMed

Heinmets, F

1989-06-01

A model-system is established to analyze purine and pyrimidine metabolism leading to DNA synthesis. The principal aim is to explore the flow and regulation of terminal deoxynucleoside triophosphates (dNTPs) in various input and parametric conditions. A series of flow equations are established, which are subsequently converted to differential equations. These are programmed (Fortran) and analyzed on a Cray chi-MP/48 supercomputer. The pool concentrations are presented as a function of time in conditions in which various pertinent parameters of the system are modified. The system is formulated by 100 differential equations.

Estimation of the probability of success in petroleum exploration

USGS Publications Warehouse

Davis, J.C.

1977-01-01

A probabilistic model for oil exploration can be developed by assessing the conditional relationship between perceived geologic variables and the subsequent discovery of petroleum. Such a model includes two probabilistic components, the first reflecting the association between a geologic condition (structural closure, for example) and the occurrence of oil, and the second reflecting the uncertainty associated with the estimation of geologic variables in areas of limited control. Estimates of the conditional relationship between geologic variables and subsequent production can be found by analyzing the exploration history of a "training area" judged to be geologically similar to the exploration area. The geologic variables are assessed over the training area using an historical subset of the available data, whose density corresponds to the present control density in the exploration area. The success or failure of wells drilled in the training area subsequent to the time corresponding to the historical subset provides empirical estimates of the probability of success conditional upon geology. Uncertainty in perception of geological conditions may be estimated from the distribution of errors made in geologic assessment using the historical subset of control wells. These errors may be expressed as a linear function of distance from available control. Alternatively, the uncertainty may be found by calculating the semivariogram of the geologic variables used in the analysis: the two procedures will yield approximately equivalent results. The empirical probability functions may then be transferred to the exploration area and used to estimate the likelihood of success of specific exploration plays. These estimates will reflect both the conditional relationship between the geological variables used to guide exploration and the uncertainty resulting from lack of control. The technique is illustrated with case histories from the mid-Continent area of the U.S.A. ?? 1977 Plenum Publishing Corp.

Factors affecting reorganisation of memory encoding networks in temporal lobe epilepsy

PubMed Central

Sidhu, M.K.; Stretton, J.; Winston, G.P.; Symms, M.; Thompson, P.J.; Koepp, M.J.; Duncan, J.S.

2015-01-01

Summary Aims In temporal lobe epilepsy (TLE) due to hippocampal sclerosis reorganisation in the memory encoding network has been consistently described. Distinct areas of reorganisation have been shown to be efficient when associated with successful subsequent memory formation or inefficient when not associated with successful subsequent memory. We investigated the effect of clinical parameters that modulate memory functions: age at onset of epilepsy, epilepsy duration and seizure frequency in a large cohort of patients. Methods We studied 53 patients with unilateral TLE and hippocampal sclerosis (29 left). All participants performed a functional magnetic resonance imaging memory encoding paradigm of faces and words. A continuous regression analysis was used to investigate the effects of age at onset of epilepsy, epilepsy duration and seizure frequency on the activation patterns in the memory encoding network. Results Earlier age at onset of epilepsy was associated with left posterior hippocampus activations that were involved in successful subsequent memory formation in left hippocampal sclerosis patients. No association of age at onset of epilepsy was seen with face encoding in right hippocampal sclerosis patients. In both left hippocampal sclerosis patients during word encoding and right hippocampal sclerosis patients during face encoding, shorter duration of epilepsy and lower seizure frequency were associated with medial temporal lobe activations that were involved in successful memory formation. Longer epilepsy duration and higher seizure frequency were associated with contralateral extra-temporal activations that were not associated with successful memory formation. Conclusion Age at onset of epilepsy influenced verbal memory encoding in patients with TLE due to hippocampal sclerosis in the speech-dominant hemisphere. Shorter duration of epilepsy and lower seizure frequency were associated with less disruption of the efficient memory encoding network whilst longer duration and higher seizure frequency were associated with greater, inefficient, extra-temporal reorganisation. PMID:25616449

Retail clinic visits and receipt of primary care.

PubMed

Reid, Rachel O; Ashwood, J Scott; Friedberg, Mark W; Weber, Ellerie S; Setodji, Claude M; Mehrotra, Ateev

2013-04-01

An increasing number of patients are visiting retail clinics for simple acute conditions. Physicians worry that visits to retail clinics will interfere with primary care relationships. No prior study has evaluated the impact of retail clinics on receipt of primary care. To assess the association between retail clinic use and receipt of key primary care functions. We performed a retrospective cohort analysis using commercial insurance claims from 2007 to 2009. We identified patients who had a visit for a simple acute condition in 2008, the "index visit". We divided these 127,358 patients into two cohorts according to the location of that index visit: primary care provider (PCP) versus retail clinic. We evaluated three functions of primary care: (1) where patients first sought care for subsequent simple acute conditions; (2) continuity of care using the Bice-Boxerman index; and (3) preventive care and diabetes management. Using a difference-in-differences approach, we compared care received in the 365 days following the index visit to care received in the 365 days prior, using propensity score weights to account for selection bias. Visiting a retail clinic instead of a PCP for the index visit was associated with a 27.7 visits per 100 patients differential reduction (p < 0 .001) in subsequent PCP visits for new simple acute conditions. Visiting a retail clinic instead of a PCP was also associated with decreased subsequent continuity of care (10.9 percentage-point differential reduction in Bice-Boxerman index, p < 0 .001). There was no differential change between the cohorts in receipt of preventive care or diabetes management. Retail clinics may disrupt two aspects of primary care: whether patients go to a PCP first for new conditions and continuity of care. However, they do not negatively impact preventive care or diabetes management.

Appropriate IMFs associated with cepstrum and envelope analysis for ball-bearing fault diagnosis

NASA Astrophysics Data System (ADS)

Tsao, Wen-Chang; Pan, Min-Chun

2014-03-01

The traditional envelope analysis is an effective method for the fault detection of rolling bearings. However, all the resonant frequency bands must be examined during the bearing-fault detection process. To handle the above deficiency, this paper proposes using the empirical mode decomposition (EMD) to select a proper intrinsic mode function (IMF) for the subsequent detection tools; here both envelope analysis and cepstrum analysis are employed and compared. By virtue of the band-pass filtering nature of EMD, the resonant frequency bands of structure to be measured are captured in the IMFs. As impulses arising from rolling elements striking bearing faults modulate with structure resonance, proper IMFs potentially enable to characterize fault signatures. In the study, faulty ball bearings are used to justify the proposed method, and comparisons with the traditional envelope analysis are made. Post the use of IMFs highlighting faultybearing features, the performance of using envelope analysis and cepstrum analysis to single out bearing faults is objectively compared and addressed; it is noted that generally envelope analysis offers better performance.

The role of lateral occipitotemporal junction and area MT/V5 in the visual analysis of upper-limb postures.

PubMed

Peigneux, P; Salmon, E; van der Linden, M; Garraux, G; Aerts, J; Delfiore, G; Degueldre, C; Luxen, A; Orban, G; Franck, G

2000-06-01

Humans, like numerous other species, strongly rely on the observation of gestures of other individuals in their everyday life. It is hypothesized that the visual processing of human gestures is sustained by a specific functional architecture, even at an early prelexical cognitive stage, different from that required for the processing of other visual entities. In the present PET study, the neural basis of visual gesture analysis was investigated with functional neuroimaging of brain activity during naming and orientation tasks performed on pictures of either static gestures (upper-limb postures) or tridimensional objects. To prevent automatic object-related cerebral activation during the visual processing of postures, only intransitive postures were selected, i. e., symbolic or meaningless postures which do not imply the handling of objects. Conversely, only intransitive objects which cannot be handled were selected to prevent gesture-related activation during their visual processing. Results clearly demonstrate a significant functional segregation between the processing of static intransitive postures and the processing of intransitive tridimensional objects. Visual processing of objects elicited mainly occipital and fusiform gyrus activity, while visual processing of postures strongly activated the lateral occipitotemporal junction, encroaching upon area MT/V5, involved in motion analysis. These findings suggest that the lateral occipitotemporal junction, working in association with area MT/V5, plays a prominent role in the high-level perceptual analysis of gesture, namely the construction of its visual representation, available for subsequent recognition or imitation. Copyright 2000 Academic Press.

Multiplex Quantitative Histologic Analysis of Human Breast Cancer Cell Signaling and Cell Fate

DTIC Science & Technology

2008-05-01

stains. 15. SUBJECT TERMS Breast cancer, cell signaling, cell proliferation, histology, image analysis 16. SECURITY CLASSIFICATION OF: 17...fluorescence, and these DAPI-stained nuclei are often not counted during subsequent image analysis ). To study two analytes in the same tumor section or...analytes (p-ERK, p-AKT, Ki67) and for epithelial cytokeratin (CK), so that tumor cells may be identified during subsequent automated image analysis (as

Global brain dynamics during social exclusion predict subsequent behavioral conformity

PubMed Central

Wasylyshyn, Nick; Hemenway Falk, Brett; Garcia, Javier O; Cascio, Christopher N; O’Donnell, Matthew Brook; Bingham, C Raymond; Simons-Morton, Bruce; Vettel, Jean M; Falk, Emily B

2018-01-01

Abstract Individuals react differently to social experiences; for example, people who are more sensitive to negative social experiences, such as being excluded, may be more likely to adapt their behavior to fit in with others. We examined whether functional brain connectivity during social exclusion in the fMRI scanner can be used to predict subsequent conformity to peer norms. Adolescent males (n = 57) completed a two-part study on teen driving risk: a social exclusion task (Cyberball) during an fMRI session and a subsequent driving simulator session in which they drove alone and in the presence of a peer who expressed risk-averse or risk-accepting driving norms. We computed the difference in functional connectivity between social exclusion and social inclusion from each node in the brain to nodes in two brain networks, one previously associated with mentalizing (medial prefrontal cortex, temporoparietal junction, precuneus, temporal poles) and another with social pain (dorsal anterior cingulate cortex, anterior insula). Using predictive modeling, this measure of global connectivity during exclusion predicted the extent of conformity to peer pressure during driving in the subsequent experimental session. These findings extend our understanding of how global neural dynamics guide social behavior, revealing functional network activity that captures individual differences. PMID:29529310

Comparative genomic analysis of retrogene repertoire in two green algae Volvox carteri and Chlamydomonas reinhardtii.

PubMed

Jąkalski, Marcin; Takeshita, Kazutaka; Deblieck, Mathieu; Koyanagi, Kanako O; Makałowska, Izabela; Watanabe, Hidemi; Makałowski, Wojciech

2016-08-04

Retroposition, one of the processes of copying the genetic material, is an important RNA-mediated mechanism leading to the emergence of new genes. Because the transcription controlling segments are usually not copied to the new location in this mechanism, the duplicated gene copies (retrocopies) become pseudogenized. However, few can still survive, e.g. by recruiting novel regulatory elements from the region of insertion. Subsequently, these duplicated genes can contribute to the formation of lineage-specific traits and phenotypic diversity. Despite the numerous studies of the functional retrocopies (retrogenes) in animals and plants, very little is known about their presence in green algae, including morphologically diverse species. The current availability of the genomes of both uni- and multicellular algae provides a good opportunity to conduct a genome-wide investigation in order to fill the knowledge gap in retroposition phenomenon in this lineage. Here we present a comparative genomic analysis of uni- and multicellular algae, Chlamydomonas reinhardtii and Volvox carteri, respectively, to explore their retrogene complements. By adopting a computational approach, we identified 141 retrogene candidates in total in both genomes, with their fraction being significantly higher in the multicellular Volvox. Majority of the retrogene candidates showed signatures of functional constraints, thus indicating their functionality. Detailed analyses of the identified retrogene candidates, their parental genes, and homologs of both, revealed that most of the retrogene candidates were derived from ancient retroposition events in the common ancestor of the two algae and that the parental genes were subsequently lost from the respective lineages, making many retrogenes 'orphan'. We revealed that the genomes of the green algae have maintained many possibly functional retrogenes in spite of experiencing various molecular evolutionary events during a long evolutionary time after the retroposition events. Our first report about the retrogene set in the green algae provides a good foundation for any future investigation of the repertoire of retrogenes and facilitates the assessment of the evolutionary impact of retroposition on diverse morphological traits in this lineage. This article was reviewed by William Martin and Piotr Zielenkiewicz.

Long-Term Functional Outcomes and Correlation with Regional Brain Connectivity by MRI Diffusion Tractography Metrics in a Near-Term Rabbit Model of Intrauterine Growth Restriction

PubMed Central

Illa, Miriam; Eixarch, Elisenda; Batalle, Dafnis; Arbat-Plana, Ariadna; Muñoz-Moreno, Emma; Figueras, Francesc; Gratacos, Eduard

2013-01-01

Background Intrauterine growth restriction (IUGR) affects 5–10% of all newborns and is associated with increased risk of memory, attention and anxiety problems in late childhood and adolescence. The neurostructural correlates of long-term abnormal neurodevelopment associated with IUGR are unknown. Thus, the aim of this study was to provide a comprehensive description of the long-term functional and neurostructural correlates of abnormal neurodevelopment associated with IUGR in a near-term rabbit model (delivered at 30 days of gestation) and evaluate the development of quantitative imaging biomarkers of abnormal neurodevelopment based on diffusion magnetic resonance imaging (MRI) parameters and connectivity. Methodology At +70 postnatal days, 10 cases and 11 controls were functionally evaluated with the Open Field Behavioral Test which evaluates anxiety and attention and the Object Recognition Task that evaluates short-term memory and attention. Subsequently, brains were collected, fixed and a high resolution MRI was performed. Differences in diffusion parameters were analyzed by means of voxel-based and connectivity analysis measuring the number of fibers reconstructed within anxiety, attention and short-term memory networks over the total fibers. Principal Findings The results of the neurobehavioral and cognitive assessment showed a significant higher degree of anxiety, attention and memory problems in cases compared to controls in most of the variables explored. Voxel-based analysis (VBA) revealed significant differences between groups in multiple brain regions mainly in grey matter structures, whereas connectivity analysis demonstrated lower ratios of fibers within the networks in cases, reaching the statistical significance only in the left hemisphere for both networks. Finally, VBA and connectivity results were also correlated with functional outcome. Conclusions The rabbit model used reproduced long-term functional impairments and their neurostructural correlates of abnormal neurodevelopment associated with IUGR. The description of the pattern of microstructural changes underlying functional defects may help to develop biomarkers based in diffusion MRI and connectivity analysis. PMID:24143189

Long-term functional outcomes and correlation with regional brain connectivity by MRI diffusion tractography metrics in a near-term rabbit model of intrauterine growth restriction.

PubMed

Illa, Miriam; Eixarch, Elisenda; Batalle, Dafnis; Arbat-Plana, Ariadna; Muñoz-Moreno, Emma; Figueras, Francesc; Gratacos, Eduard

2013-01-01

Intrauterine growth restriction (IUGR) affects 5-10% of all newborns and is associated with increased risk of memory, attention and anxiety problems in late childhood and adolescence. The neurostructural correlates of long-term abnormal neurodevelopment associated with IUGR are unknown. Thus, the aim of this study was to provide a comprehensive description of the long-term functional and neurostructural correlates of abnormal neurodevelopment associated with IUGR in a near-term rabbit model (delivered at 30 days of gestation) and evaluate the development of quantitative imaging biomarkers of abnormal neurodevelopment based on diffusion magnetic resonance imaging (MRI) parameters and connectivity. At +70 postnatal days, 10 cases and 11 controls were functionally evaluated with the Open Field Behavioral Test which evaluates anxiety and attention and the Object Recognition Task that evaluates short-term memory and attention. Subsequently, brains were collected, fixed and a high resolution MRI was performed. Differences in diffusion parameters were analyzed by means of voxel-based and connectivity analysis measuring the number of fibers reconstructed within anxiety, attention and short-term memory networks over the total fibers. The results of the neurobehavioral and cognitive assessment showed a significant higher degree of anxiety, attention and memory problems in cases compared to controls in most of the variables explored. Voxel-based analysis (VBA) revealed significant differences between groups in multiple brain regions mainly in grey matter structures, whereas connectivity analysis demonstrated lower ratios of fibers within the networks in cases, reaching the statistical significance only in the left hemisphere for both networks. Finally, VBA and connectivity results were also correlated with functional outcome. The rabbit model used reproduced long-term functional impairments and their neurostructural correlates of abnormal neurodevelopment associated with IUGR. The description of the pattern of microstructural changes underlying functional defects may help to develop biomarkers based in diffusion MRI and connectivity analysis.

The role of knee alignment in disease progression and functional decline in knee osteoarthritis.

PubMed

Sharma, L; Song, J; Felson, D T; Cahue, S; Shamiyeh, E; Dunlop, D D

2001-07-11

Knee osteoarthritis (OA) is a leading cause of disability in older persons. Few risk factors for disease progression or functional decline have been identified. Hip-knee-ankle alignment influences load distribution at the knee; varus and valgus alignment increase medial and lateral load, respectively. To test the hypotheses that (1) varus alignment increases risk of medial knee OA progression during the subsequent 18 months, (2) valgus alignment increases risk of subsequent lateral knee OA progression, (3) greater severity of malalignment is associated with greater subsequent loss of joint space, and (4) greater burden of malalignment is associated with greater subsequent decline in physical function. Prospective longitudinal cohort study conducted March 1997 to March 2000 at an academic medical center in Chicago, Ill. A total of 237 persons recruited from the community with primary knee OA, defined by presence of definite tibiofemoral osteophytes and at least some difficulty with knee-requiring activity; 230 (97%) completed the study. Progression of OA, defined as a 1-grade increase in severity of joint space narrowing on semiflexed, fluoroscopically confirmed knee radiographs; change in narrowest joint space width; and change in physical function between baseline and 18 months, compared by knee alignment at baseline. Varus alignment at baseline was associated with a 4-fold increase in the odds of medial progression, adjusting for age, sex, and body mass index (adjusted odds ratio [OR], 4.09; 95% confidence interval [CI], 2.20-7.62). Valgus alignment at baseline was associated with a nearly 5-fold increase in the odds of lateral progression (adjusted OR, 4.89; 95% CI, 2.13-11.20). Severity of varus correlated with greater medial joint space loss during the subsequent 18 months (R = 0.52; 95% CI, 0.40-0.62 in dominant knees), and severity of valgus correlated with greater subsequent lateral joint space loss (R = 0.35; 95% CI, 0.21-0.47 in dominant knees). Having alignment of more than 5 degrees (in either direction) in both knees at baseline was associated with significantly greater functional deterioration during the 18 months than having alignment of 5 degrees or less in both knees, after adjusting for age, sex, body mass index, and pain. This is, to our knowledge, the first demonstration that in primary knee OA varus alignment increases risk of medial OA progression, that valgus alignment increases risk of lateral OA progression, that burden of malalignment predicts decline in physical function, and that these effects can be detected after as little as 18 months of observation.

Evaluation of outpatients experiencing implantable cardioverter defibrillator shocks associated with minimal symptoms.

PubMed

Hamer, M E; Clair, W K; Wilkinson, W E; Greenfield, R A; Pritchett, E L; Page, R L

1994-05-01

Patients receiving minimally symptomatic shocks from their implantable cardioverter defibrillators were studied prospectively using transtelephonic ECG loop monitoring. The time course to the first subsequent shock was evaluated. Twenty-nine consecutive patients who received a shock preceded by mild palpitations or no symptoms were given a transtelephonic ECG loop monitor and instructed to activate the monitor if a subsequent shock occurred. Kaplan-Meier analysis was used to quantitate the time to first shock during the study period. The point estimate +/- standard error of patients receiving a shock during the study period was 31% +/- 9% at 30 days, 41% +/- 9% at 60 days, and 60% +/- 9% at 120 days. The ECG was successfully transmitted in 7 of 13 patients who had shocks in the 60-day monitoring period, and demonstrated inappropriate shocks in 6 of 7. Determination of the cause of shock led to a change in subsequent management in all 7 patients. We conclude that the incidence of inappropriate shocks may be higher than estimated previously in patients with minimal symptoms prior to the shock. There are thousands of patients with implantable cardioverter defibrillators that have no storage function for treated tachycardias; transtelephonic ECG loop monitoring can determine the cause of implantable cardioverter defibrillator discharge in these patients, and the diagnosis is invaluable in their management.

Mental disorders and subsequent educational attainment in a US national sample.

PubMed

Breslau, Joshua; Lane, Michael; Sampson, Nancy; Kessler, Ronald C

2008-07-01

As part of a larger investigation of the adverse effects of mental disorders on role functioning, we examined the associations of early-onset mental disorders with subsequent educational attainment in a large nationally representative survey of the US adult population. Diagnoses and age of onset for each of 17 DSM-IV disorders were assessed through retrospective self-report with the fully structured WHO Composite International Diagnostic Instrument (CIDI). Survival analysis was used to examine the associations between early-onset DSM-IV/CIDI disorders and subsequent termination of schooling with controls for socio-demographic characteristics and childhood adversities (i.e. childhood traumatic events, childhood neglect, parental mental illness, family disruption, and low parental educational attainment). Mental disorders were found to be significantly associated with termination of schooling prior to completion of each of four educational milestones (primary school graduation, high school graduation, college entry, college graduation), with odds ratios in the range of 1.3-7.0. The proportion of school terminations attributable to mental disorders was largest for high school graduation (10.2%) but also meaningful for primary school graduation (3.8%), college entry (4.4%) and college graduation (2.6%). These results add to a growing body of evidence documenting a wide variety of adverse life course effects of mental disorders.

Idea Density Measured in Late Life Predicts Subsequent Cognitive Trajectories: Implications for the Measurement of Cognitive Reserve

PubMed Central

Chand, Vineeta; Bonnici, Lisa; Baynes, Kathleen; Harvey, Danielle; Mungas, Dan; Simon, Christa; Reed, Bruce

2012-01-01

Objective. The Nun Study showed that lower linguistic ability in young adulthood, measured by idea density (ID), increased the risk of dementia in late life. The present study examined whether ID measured in late life continues to predict the trajectory of cognitive change. Method. ID was measured in 81 older adults who were followed longitudinally for an average of 4.3 years. Changes in global cognition and 4 specific neuropsychological domains (episodic memory, semantic memory, spatial abilities, and executive function) were examined as outcomes. Separate random effects models tested the effect of ID on longitudinal change in outcomes, adjusted for age and education. Results. Lower ID was associated with greater subsequent decline in global cognition, semantic memory, episodic memory, and spatial abilities. When analysis was restricted to only participants without dementia at the time ID was collected, results were similar. Discussion. Linguistic ability in young adulthood, as measured by ID, has been previously proposed as an index of neurocognitive development and/or cognitive reserve. The present study provides evidence that even when ID is measured in old age, it continues to be associated with subsequent cognitive decline and as such may continue to provide a marker of cognitive reserve. PMID:22357642

Identification of differentially expressed genes through RNA sequencing in goats (Capra hircus) at different postnatal stages

PubMed Central

Li, Qian; Lin, Sen

2017-01-01

Intramuscular fat (IMF) content and fatty acid composition of longissimus dorsi muscle (LM) change with growth, which partially determines the flavor and nutritional value of goat (Capra hircus) meat. However, unlike cattle, little information is available on the transcriptome-wide changes during different postnatal stages in small ruminants, especially goats. In this study, the sequencing reads of goat LM tissues collected from kid, youth, and adult period were mapped to the goat genome. Results showed that out of total 24 689 Unigenes, 20 435 Unigenes were annotated. Based on expected number of fragments per kilobase of transcript sequence per million base pairs sequenced (FPKM), 111 annotated differentially expressed genes (DEGs) were identified among different postnatal stages, which were subsequently assigned to 16 possible expression patterns by series-cluster analysis. Functional classification by Gene Ontology (GO) analysis was used for selecting the genes showing highest expression related to lipid metabolism. Finally, we identified the node genes for lipid metabolism regulation using co-expression analysis. In conclusion, these data may uncover candidate genes having functional roles in regulation of goat muscle development and lipid metabolism during the various growth stages in goats. PMID:28800357

Identification of differentially expressed genes through RNA sequencing in goats (Capra hircus) at different postnatal stages.

PubMed

Lin, Yaqiu; Zhu, Jiangjiang; Wang, Yong; Li, Qian; Lin, Sen

2017-01-01

Intramuscular fat (IMF) content and fatty acid composition of longissimus dorsi muscle (LM) change with growth, which partially determines the flavor and nutritional value of goat (Capra hircus) meat. However, unlike cattle, little information is available on the transcriptome-wide changes during different postnatal stages in small ruminants, especially goats. In this study, the sequencing reads of goat LM tissues collected from kid, youth, and adult period were mapped to the goat genome. Results showed that out of total 24 689 Unigenes, 20 435 Unigenes were annotated. Based on expected number of fragments per kilobase of transcript sequence per million base pairs sequenced (FPKM), 111 annotated differentially expressed genes (DEGs) were identified among different postnatal stages, which were subsequently assigned to 16 possible expression patterns by series-cluster analysis. Functional classification by Gene Ontology (GO) analysis was used for selecting the genes showing highest expression related to lipid metabolism. Finally, we identified the node genes for lipid metabolism regulation using co-expression analysis. In conclusion, these data may uncover candidate genes having functional roles in regulation of goat muscle development and lipid metabolism during the various growth stages in goats.

Abnormal Current–Voltage Hysteresis Induced by Reverse Bias in Organic–Inorganic Hybrid Perovskite Photovoltaics

DOE PAGES

Rajagopal, Adharsh; Williams, Spencer T.; Chueh, Chu-Chen; ...

2016-02-29

In this study, reverse bias (RB)-induced abnormal hysteresis is investigated in perovskite solar cells (PVSCs) with nickel oxide (NiOx)/methylammonium lead iodide (CH 3NH 3PbI 3) interfaces. Through comprehensive current-voltage (I-V) characterization and bias-dependent external quantum efficiency (EQE) measurements, we demonstrate that this phenomenon is caused by the interfacial ion accumulation intrinsic to CH 3NH 3PbI 3. Subsequently, via systematic analysis we discover that the abnormal I-V behavior is remarkably similar to tunnel diode I-V characteristics and is due to the formation of a transient tunnel junction at NiO x/CH 3NH 3PbI 3 interfaces under RB. The detailed analysis navigating themore » complexities of I-V behavior in CH 3NH 3PbI 3-based solar cells provided here ultimately illuminates possibilities in modulating ion motion and hysteresis via interfacial engineering in PVSCs. Moreover, this work shows that RB can alter how CH 3NH 3PbI 3 contributes to the functional nature of devices and provides the first steps toward approaching functional perovskite interfaces in new ways for metrology and analysis of complex transient processes.« less

Recurrence Quantification Analysis of Sentence-Level Speech Kinematics.

PubMed

Jackson, Eric S; Tiede, Mark; Riley, Michael A; Whalen, D H

2016-12-01

Current approaches to assessing sentence-level speech variability rely on measures that quantify variability across utterances and use normalization procedures that alter raw trajectory data. The current work tests the feasibility of a less restrictive nonlinear approach-recurrence quantification analysis (RQA)-via a procedural example and subsequent analysis of kinematic data. To test the feasibility of RQA, lip aperture (i.e., the Euclidean distance between lip-tracking sensors) was recorded for 21 typically developing adult speakers during production of a simple utterance. The utterance was produced in isolation and in carrier structures differing just in length or in length and complexity. Four RQA indices were calculated: percent recurrence (%REC), percent determinism (%DET), stability (MAXLINE), and stationarity (TREND). Percent determinism (%DET) decreased only for the most linguistically complex sentence; MAXLINE decreased as a function of linguistic complexity but increased for the longer-only sentence; TREND decreased as a function of both length and linguistic complexity. This research note demonstrates the feasibility of using RQA as a tool to compare speech variability across speakers and groups. RQA offers promise as a technique to assess effects of potential stressors (e.g., linguistic or cognitive factors) on the speech production system.

Analyzing psychotherapy process as intersubjective sensemaking: an approach based on discourse analysis and neural networks.

PubMed

Nitti, Mariangela; Ciavolino, Enrico; Salvatore, Sergio; Gennaro, Alessandro

2010-09-01

The authors propose a method for analyzing the psychotherapy process: discourse flow analysis (DFA). DFA is a technique representing the verbal interaction between therapist and patient as a discourse network, aimed at measuring the therapist-patient discourse ability to generate new meanings through time. DFA assumes that the main function of psychotherapy is to produce semiotic novelty. DFA is applied to the verbatim transcript of the psychotherapy. It defines the main meanings active within the therapeutic discourse by means of the combined use of text analysis and statistical techniques. Subsequently, it represents the dynamic interconnections among these meanings in terms of a "discursive network." The dynamic and structural indexes of the discursive network have been shown to provide a valid representation of the patient-therapist communicative flow as well as an estimation of its clinical quality. Finally, a neural network is designed specifically to identify patterns of functioning of the discursive network and to verify the clinical validity of these patterns in terms of their association with specific phases of the psychotherapy process. An application of the DFA to a case of psychotherapy is provided to illustrate the method and the kinds of results it produces.

Recurrence Quantification Analysis of Sentence-Level Speech Kinematics

PubMed Central

Tiede, Mark; Riley, Michael A.; Whalen, D. H.

2016-01-01

Purpose Current approaches to assessing sentence-level speech variability rely on measures that quantify variability across utterances and use normalization procedures that alter raw trajectory data. The current work tests the feasibility of a less restrictive nonlinear approach—recurrence quantification analysis (RQA)—via a procedural example and subsequent analysis of kinematic data. Method To test the feasibility of RQA, lip aperture (i.e., the Euclidean distance between lip-tracking sensors) was recorded for 21 typically developing adult speakers during production of a simple utterance. The utterance was produced in isolation and in carrier structures differing just in length or in length and complexity. Four RQA indices were calculated: percent recurrence (%REC), percent determinism (%DET), stability (MAXLINE), and stationarity (TREND). Results Percent determinism (%DET) decreased only for the most linguistically complex sentence; MAXLINE decreased as a function of linguistic complexity but increased for the longer-only sentence; TREND decreased as a function of both length and linguistic complexity. Conclusions This research note demonstrates the feasibility of using RQA as a tool to compare speech variability across speakers and groups. RQA offers promise as a technique to assess effects of potential stressors (e.g., linguistic or cognitive factors) on the speech production system. PMID:27824987

Anatomic and functional imaging of tagged molecules in animals

DOEpatents

Weisenberger, Andrew G [Yorktown, VA; Majewski, Stanislaw [Grafton, VA; Paulus, Michael J [Knoxville, TN; Gleason, Shaun S [Knoxville, VA

2007-04-24

A novel functional imaging system for use in the imaging of unrestrained and non-anesthetized small animals or other subjects and a method for acquiring such images and further registering them with anatomical X-ray images previously or subsequently acquired. The apparatus comprises a combination of an IR laser profilometry system and gamma, PET and/or SPECT, imaging system, all mounted on a rotating gantry, that permits simultaneous acquisition of positional and orientational information and functional images of an unrestrained subject that are registered, i.e. integrated, using image processing software to produce a functional image of the subject without the use of restraints or anesthesia. The functional image thus obtained can be registered with a previously or subsequently obtained X-ray CT image of the subject. The use of the system described herein permits functional imaging of a subject in an unrestrained/non-anesthetized condition thereby reducing the stress on the subject and eliminating any potential interference with the functional testing that such stress might induce.

The Optics and Alignment of the Divergent Beam Laboratory X-ray Powder Diffractometer and its Calibration Using NIST Standard Reference Materials.

PubMed

Cline, James P; Mendenhall, Marcus H; Black, David; Windover, Donald; Henins, Albert

2015-01-01

The laboratory X-ray powder diffractometer is one of the primary analytical tools in materials science. It is applicable to nearly any crystalline material, and with advanced data analysis methods, it can provide a wealth of information concerning sample character. Data from these machines, however, are beset by a complex aberration function that can be addressed through calibration with the use of NIST Standard Reference Materials (SRMs). Laboratory diffractometers can be set up in a range of optical geometries; considered herein are those of Bragg-Brentano divergent beam configuration using both incident and diffracted beam monochromators. We review the origin of the various aberrations affecting instruments of this geometry and the methods developed at NIST to align these machines in a first principles context. Data analysis methods are considered as being in two distinct categories: those that use empirical methods to parameterize the nature of the data for subsequent analysis, and those that use model functions to link the observation directly to a specific aspect of the experiment. We consider a multifaceted approach to instrument calibration using both the empirical and model based data analysis methods. The particular benefits of the fundamental parameters approach are reviewed.

Structural neural correlates of impaired mobility and subsequent decline in executive functions: A 12-month prospective study

PubMed Central

Hsu, Chun Liang; Best, John R.; Chiu, Bryan K.; Nagamatsu, Lindsay S; Voss, Michelle W.; Handy, Todd C.; Bolandzadeh, Niousha; Liu-Ambrose, Teresa

2016-01-01

Impaired mobility, such as falls, may be an early biomarker of subsequent cognitive decline and is associated with subclinical alterations in both brain structure and function. In this 12-month prospective study, we examined whether there are volumetric differences in gray matter and subcortical regions, as well as cerebral white matter, between older fallers and non-fallers. In addition, we assessed whether these baseline volumetric differences are associated with changes in cognitive function over 12 months. A total of 66 community-dwelling older adults were recruited and categorized by their falls status. Magnetic resonance imaging occurred at baseline and participants’ physical and cognitive performances were assessed at baseline and 12-months. At baseline, fallers showed significantly lower volumes in gray matter, subcortical regions, and cerebral white matter compared with non-fallers. Notably, fallers had significantly lower left lateral orbitofrontal white matter volume. Moreover, lower left lateral orbitofrontal white matter volume at baseline was associated with greater decline in set-shifting performance over 12 months. Our data suggest that falls may indicate subclinical alterations in regional brain volume that are associated with subsequent decline in executive functions. PMID:27079333

Whole brain resting-state analysis reveals decreased functional connectivity in major depression.

PubMed

Veer, Ilya M; Beckmann, Christian F; van Tol, Marie-José; Ferrarini, Luca; Milles, Julien; Veltman, Dick J; Aleman, André; van Buchem, Mark A; van der Wee, Nic J; Rombouts, Serge A R B

2010-01-01

Recently, both increases and decreases in resting-state functional connectivity have been found in major depression. However, these studies only assessed functional connectivity within a specific network or between a few regions of interest, while comorbidity and use of medication was not always controlled for. Therefore, the aim of the current study was to investigate whole-brain functional connectivity, unbiased by a priori definition of regions or networks of interest, in medication-free depressive patients without comorbidity. We analyzed resting-state fMRI data of 19 medication-free patients with a recent diagnosis of major depression (within 6 months before inclusion) and no comorbidity, and 19 age- and gender-matched controls. Independent component analysis was employed on the concatenated data sets of all participants. Thirteen functionally relevant networks were identified, describing the entire study sample. Next, individual representations of the networks were created using a dual regression method. Statistical inference was subsequently done on these spatial maps using voxel-wise permutation tests. Abnormal functional connectivity was found within three resting-state networks in depression: (1) decreased bilateral amygdala and left anterior insula connectivity in an affective network, (2) reduced connectivity of the left frontal pole in a network associated with attention and working memory, and (3) decreased bilateral lingual gyrus connectivity within ventromedial visual regions. None of these effects were associated with symptom severity or gray matter density. We found abnormal resting-state functional connectivity not previously associated with major depression, which might relate to abnormal affect regulation and mild cognitive deficits, both associated with the symptomatology of the disorder.

Whole Brain Resting-State Analysis Reveals Decreased Functional Connectivity in Major Depression

PubMed Central

Veer, Ilya M.; Beckmann, Christian F.; van Tol, Marie-José; Ferrarini, Luca; Milles, Julien; Veltman, Dick J.; Aleman, André; van Buchem, Mark A.; van der Wee, Nic J.; Rombouts, Serge A.R.B.

2010-01-01

Recently, both increases and decreases in resting-state functional connectivity have been found in major depression. However, these studies only assessed functional connectivity within a specific network or between a few regions of interest, while comorbidity and use of medication was not always controlled for. Therefore, the aim of the current study was to investigate whole-brain functional connectivity, unbiased by a priori definition of regions or networks of interest, in medication-free depressive patients without comorbidity. We analyzed resting-state fMRI data of 19 medication-free patients with a recent diagnosis of major depression (within 6 months before inclusion) and no comorbidity, and 19 age- and gender-matched controls. Independent component analysis was employed on the concatenated data sets of all participants. Thirteen functionally relevant networks were identified, describing the entire study sample. Next, individual representations of the networks were created using a dual regression method. Statistical inference was subsequently done on these spatial maps using voxel-wise permutation tests. Abnormal functional connectivity was found within three resting-state networks in depression: (1) decreased bilateral amygdala and left anterior insula connectivity in an affective network, (2) reduced connectivity of the left frontal pole in a network associated with attention and working memory, and (3) decreased bilateral lingual gyrus connectivity within ventromedial visual regions. None of these effects were associated with symptom severity or gray matter density. We found abnormal resting-state functional connectivity not previously associated with major depression, which might relate to abnormal affect regulation and mild cognitive deficits, both associated with the symptomatology of the disorder. PMID:20941370

Structure-based functional annotation of putative conserved proteins having lyase activity from Haemophilus influenzae.

PubMed

Shahbaaz, Mohd; Ahmad, Faizan; Imtaiyaz Hassan, Md

2015-06-01

Haemophilus influenzae is a small pleomorphic Gram-negative bacteria which causes several chronic diseases, including bacteremia, meningitis, cellulitis, epiglottitis, septic arthritis, pneumonia, and empyema. Here we extensively analyzed the sequenced genome of H. influenzae strain Rd KW20 using protein family databases, protein structure prediction, pathways and genome context methods to assign a precise function to proteins whose functions are unknown. These proteins are termed as hypothetical proteins (HPs), for which no experimental information is available. Function prediction of these proteins would surely be supportive to precisely understand the biochemical pathways and mechanism of pathogenesis of Haemophilus influenzae. During the extensive analysis of H. influenzae genome, we found the presence of eight HPs showing lyase activity. Subsequently, we modeled and analyzed three-dimensional structure of all these HPs to determine their functions more precisely. We found these HPs possess cystathionine-β-synthase, cyclase, carboxymuconolactone decarboxylase, pseudouridine synthase A and C, D-tagatose-1,6-bisphosphate aldolase and aminodeoxychorismate lyase-like features, indicating their corresponding functions in the H. influenzae. Lyases are actively involved in the regulation of biosynthesis of various hormones, metabolic pathways, signal transduction, and DNA repair. Lyases are also considered as a key player for various biological processes. These enzymes are critically essential for the survival and pathogenesis of H. influenzae and, therefore, these enzymes may be considered as a potential target for structure-based rational drug design. Our structure-function relationship analysis will be useful to search and design potential lead molecules based on the structure of these lyases, for drug design and discovery.

Automated extraction of direct, reactive, and vat dyes from cellulosic fibers for forensic analysis by capillary electrophoresis.

PubMed

Dockery, C R; Stefan, A R; Nieuwland, A A; Roberson, S N; Baguley, B M; Hendrix, J E; Morgan, S L

2009-08-01

Systematic designed experiments were employed to find the optimum conditions for extraction of direct, reactive, and vat dyes from cotton fibers prior to forensic characterization. Automated microextractions were coupled with measurements of extraction efficiencies on a microplate reader UV-visible spectrophotometer to enable rapid screening of extraction efficiency as a function of solvent composition. Solvent extraction conditions were also developed to be compatible with subsequent forensic characterization of extracted dyes by capillary electrophoresis with UV-visible diode array detection. The capillary electrophoresis electrolyte successfully used in this work consists of 5 mM ammonium acetate in 40:60 acetonitrile-water at pH 9.3, with the addition of sodium dithionite reducing agent to facilitate analysis of vat dyes. The ultimate goal of these research efforts is enhanced discrimination of trace fiber evidence by analysis of extracted dyes.

Dynamic functional connectivity analysis reveals transient states of dysconnectivity in schizophrenia.

PubMed

Damaraju, E; Allen, E A; Belger, A; Ford, J M; McEwen, S; Mathalon, D H; Mueller, B A; Pearlson, G D; Potkin, S G; Preda, A; Turner, J A; Vaidya, J G; van Erp, T G; Calhoun, V D

2014-01-01

Schizophrenia is a psychotic disorder characterized by functional dysconnectivity or abnormal integration between distant brain regions. Recent functional imaging studies have implicated large-scale thalamo-cortical connectivity as being disrupted in patients. However, observed connectivity differences in schizophrenia have been inconsistent between studies, with reports of hyperconnectivity and hypoconnectivity between the same brain regions. Using resting state eyes-closed functional imaging and independent component analysis on a multi-site data that included 151 schizophrenia patients and 163 age- and gender matched healthy controls, we decomposed the functional brain data into 100 components and identified 47 as functionally relevant intrinsic connectivity networks. We subsequently evaluated group differences in functional network connectivity, both in a static sense, computed as the pairwise Pearson correlations between the full network time courses (5.4 minutes in length), and a dynamic sense, computed using sliding windows (44 s in length) and k-means clustering to characterize five discrete functional connectivity states. Static connectivity analysis revealed that compared to healthy controls, patients show significantly stronger connectivity, i.e., hyperconnectivity, between the thalamus and sensory networks (auditory, motor and visual), as well as reduced connectivity (hypoconnectivity) between sensory networks from all modalities. Dynamic analysis suggests that (1), on average, schizophrenia patients spend much less time than healthy controls in states typified by strong, large-scale connectivity, and (2), that abnormal connectivity patterns are more pronounced during these connectivity states. In particular, states exhibiting cortical-subcortical antagonism (anti-correlations) and strong positive connectivity between sensory networks are those that show the group differences of thalamic hyperconnectivity and sensory hypoconnectivity. Group differences are weak or absent during other connectivity states. Dynamic analysis also revealed hypoconnectivity between the putamen and sensory networks during the same states of thalamic hyperconnectivity; notably, this finding cannot be observed in the static connectivity analysis. Finally, in post-hoc analyses we observed that the relationships between sub-cortical low frequency power and connectivity with sensory networks is altered in patients, suggesting different functional interactions between sub-cortical nuclei and sensorimotor cortex during specific connectivity states. While important differences between patients with schizophrenia and healthy controls have been identified, one should interpret the results with caution given the history of medication in patients. Taken together, our results support and expand current knowledge regarding dysconnectivity in schizophrenia, and strongly advocate the use of dynamic analyses to better account for and understand functional connectivity differences.

Dynamic functional connectivity analysis reveals transient states of dysconnectivity in schizophrenia

PubMed Central

Damaraju, E.; Allen, E.A.; Belger, A.; Ford, J.M.; McEwen, S.; Mathalon, D.H.; Mueller, B.A.; Pearlson, G.D.; Potkin, S.G.; Preda, A.; Turner, J.A.; Vaidya, J.G.; van Erp, T.G.; Calhoun, V.D.

2014-01-01

Schizophrenia is a psychotic disorder characterized by functional dysconnectivity or abnormal integration between distant brain regions. Recent functional imaging studies have implicated large-scale thalamo-cortical connectivity as being disrupted in patients. However, observed connectivity differences in schizophrenia have been inconsistent between studies, with reports of hyperconnectivity and hypoconnectivity between the same brain regions. Using resting state eyes-closed functional imaging and independent component analysis on a multi-site data that included 151 schizophrenia patients and 163 age- and gender matched healthy controls, we decomposed the functional brain data into 100 components and identified 47 as functionally relevant intrinsic connectivity networks. We subsequently evaluated group differences in functional network connectivity, both in a static sense, computed as the pairwise Pearson correlations between the full network time courses (5.4 minutes in length), and a dynamic sense, computed using sliding windows (44 s in length) and k-means clustering to characterize five discrete functional connectivity states. Static connectivity analysis revealed that compared to healthy controls, patients show significantly stronger connectivity, i.e., hyperconnectivity, between the thalamus and sensory networks (auditory, motor and visual), as well as reduced connectivity (hypoconnectivity) between sensory networks from all modalities. Dynamic analysis suggests that (1), on average, schizophrenia patients spend much less time than healthy controls in states typified by strong, large-scale connectivity, and (2), that abnormal connectivity patterns are more pronounced during these connectivity states. In particular, states exhibiting cortical–subcortical antagonism (anti-correlations) and strong positive connectivity between sensory networks are those that show the group differences of thalamic hyperconnectivity and sensory hypoconnectivity. Group differences are weak or absent during other connectivity states. Dynamic analysis also revealed hypoconnectivity between the putamen and sensory networks during the same states of thalamic hyperconnectivity; notably, this finding cannot be observed in the static connectivity analysis. Finally, in post-hoc analyses we observed that the relationships between sub-cortical low frequency power and connectivity with sensory networks is altered in patients, suggesting different functional interactions between sub-cortical nuclei and sensorimotor cortex during specific connectivity states. While important differences between patients with schizophrenia and healthy controls have been identified, one should interpret the results with caution given the history of medication in patients. Taken together, our results support and expand current knowledge regarding dysconnectivity in schizophrenia, and strongly advocate the use of dynamic analyses to better account for and understand functional connectivity differences. PMID:25161896

Doping Level of Boron-Doped Diamond Electrodes Controls the Grafting Density of Functional Groups for DNA Assays.

PubMed

Švorc, Ĺubomír; Jambrec, Daliborka; Vojs, Marian; Barwe, Stefan; Clausmeyer, Jan; Michniak, Pavol; Marton, Marián; Schuhmann, Wolfgang

2015-09-02

The impact of different doping levels of boron-doped diamond on the surface functionalization was investigated by means of electrochemical reduction of aryldiazonium salts. The grafting efficiency of 4-nitrophenyl groups increased with the boron levels (B/C ratio from 0 to 20,000 ppm). Controlled grafting of nitrophenyldiazonium was used to adjust the amount of immobilized single-stranded DNA strands at the surface and further on the hybridization yield in dependence on the boron doping level. The grafted nitro functions were electrochemically reduced to the amine moieties. Subsequent functionalization with a succinic acid introduced carboxyl groups for subsequent binding of an amino-terminated DNA probe. DNA hybridization significantly depends on the probe density which is in turn dependent on the boron doping level. The proposed approach opens new insights for the design and control of doped diamond surface functionalization for the construction of DNA hybridization assays.

Bioinformatics of cardiovascular miRNA biology.

PubMed

Kunz, Meik; Xiao, Ke; Liang, Chunguang; Viereck, Janika; Pachel, Christina; Frantz, Stefan; Thum, Thomas; Dandekar, Thomas

2015-12-01

MicroRNAs (miRNAs) are small ~22 nucleotide non-coding RNAs and are highly conserved among species. Moreover, miRNAs regulate gene expression of a large number of genes associated with important biological functions and signaling pathways. Recently, several miRNAs have been found to be associated with cardiovascular diseases. Thus, investigating the complex regulatory effect of miRNAs may lead to a better understanding of their functional role in the heart. To achieve this, bioinformatics approaches have to be coupled with validation and screening experiments to understand the complex interactions of miRNAs with the genome. This will boost the subsequent development of diagnostic markers and our understanding of the physiological and therapeutic role of miRNAs in cardiac remodeling. In this review, we focus on and explain different bioinformatics strategies and algorithms for the identification and analysis of miRNAs and their regulatory elements to better understand cardiac miRNA biology. Starting with the biogenesis of miRNAs, we present approaches such as LocARNA and miRBase for combining sequence and structure analysis including phylogenetic comparisons as well as detailed analysis of RNA folding patterns, functional target prediction, signaling pathway as well as functional analysis. We also show how far bioinformatics helps to tackle the unprecedented level of complexity and systemic effects by miRNA, underlining the strong therapeutic potential of miRNA and miRNA target structures in cardiovascular disease. In addition, we discuss drawbacks and limitations of bioinformatics algorithms and the necessity of experimental approaches for miRNA target identification. This article is part of a Special Issue entitled 'Non-coding RNAs'. Copyright © 2014 Elsevier Ltd. All rights reserved.

Memory and executive functions in persons with type 2 diabetes: a meta-analysis.

PubMed

Sadanand, Shilpa; Balachandar, Rakesh; Bharath, Srikala

2016-02-01

Literature suggests that persons with type 2 diabetes mellitus (T2DM) are at risk for cognitive impairment, hence dementia. Common domains reported to be affected in those with T2DM are memory and executive functions. The extent of influence of T2DM on these domains has varied among studies. A systematic review and meta-analysis was carried out to understand whether sub-domains contributed to the variations observed in published research. We searched 'PubMed', 'ScienceDirect', 'SciVerseHub', 'Psychinfo', 'Proquest' 'Ebsco' and 'J-gate Plus' databases for published studies on cognition and T2DM among persons aged 50 years and older. Memory, executive functions and processing speed domain and sub-domain scores were extracted; effect sizes (Cohen's d) were calculated and analysed. Eight hundred seventeen articles were found. After various levels of filtering, 15 articles met the inclusion criteria for quantitative analyses. The analyses indicated that in comparison to controls, persons with T2DM showed decrements in episodic memory (d = -0.51), logical memory (d = -0.24), sub-domain of executive functions which included phonemic fluency (d = -0.35) and cognitive flexibility (d = 0.52), and speed of processing (d = -0.22). We found no difference in the sub-domains of verbal short-term memory and working memory. The meta-analysis revealed a detrimental effect of T2DM on cognitive sub-domains, namely, episodic memory and cognitive flexibility. There was a trend for the logical memory, phonemic fluency and processing speed to be affected. The analysis indicates that T2DM is a detrimental factor on certain cognitive sub-domains, rendering the person vulnerable to subsequent dementia. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2015 John Wiley & Sons, Ltd.

Problems in female development. Comments on the analysis of an early latency-age girl.

PubMed

Frenkel, R S

1993-01-01

A 6 1/2-year-old girl's clinical material relevant to the emergence of clitoral and vaginal masturbation and masturbation fantasies during analytic sessions is presented. The intense genital excitation, which she called "jeebies," often overwhelmed her ego functioning. She assumed the jeebies and the fantasies that precipitated and accompanied them would cause bad things to happen to her. External events and the nature of her object relations reinforced and confirmed her belief that being only female was unacceptable. Her penis envy, a wish to be a boy-girl, had multiple determinants. A detailed description of her evaluation and subsequent treatment reveals how her unconscious conflicts were resolved in analysis through the evolution and resolution of her transference neurosis, validating the psychoanalytic approach.

Evolution of a terrestrial magma ocean: Thermodynamics, kinetics, rheology, convection, differentiation

NASA Technical Reports Server (NTRS)

Solomatov, V. S.; Stevenson, D. J.

1992-01-01

The evolution of an initially totally molten magma ocean is constrained on the basis of analysis of various physical problems in the magma ocean. First of all an equilibrium thermodynamics of the magma ocean is developed in the melting temperature range. The equilibrium thermodynamical parameters are found as functions only of temperature and pressure and are used in the subsequent models of kinetics and convection. Kinematic processes determine the crystal size and also determine a non-equilibrium thermodynamics of the system. Rheology controls all dynamical regimes of the magma ocean. The thermal convection models for different rheological laws are developed for both the laminar convection and for turbulent convection in the case of equilibrium thermodynamics of the multiphase system. The evolution is estimated on the basis of all the above analysis.

Glycerol-3-phosphate O-acyltransferase is required for PBAN-induced sex pheromone biosynthesis in Bombyx mori

PubMed Central

Du, Mengfang; Liu, Xiaoguang; Liu, Xiaoming; Yin, Xinming; Han, Shuangyin; Song, Qisheng; An, Shiheng

2015-01-01

Female moths employ their own pheromone blends as a communicational medium in mating behavior. The biosynthesis and release of sex pheromone in female moths are regulated by pheromone biosynthesis activating neuropeptide (PBAN) and the corresponding action of PBAN has been well elucidated in Bombyx mori. However, very little is known about the molecular mechanism regarding the biosynthesis of sex pheromone precursor. In this study, quantitative proteomics was utilized to comprehensively elucidate the expression dynamics of pheromone glands (PGs) during development. Proteomic analysis revealed a serial of differentially expressed sex pheromone biosynthesis-associated proteins at the different time points of B. mori development. Most interestingly B. mori glycerol-3-phosphate O-acyltransferase (BmGPAT) was found to be expressed during the key periods of sex pheromone biosynthesis. RNAi knockdown of BmGPAT confirmed the important function of this protein in the biosynthesis of sex pheromone precursor, triacylglcerol (TAG), and subsequently PBAN-induced production of sex pheromone, bombykol. Behavioral analysis showed that RNAi knockdown of GPAT significantly impaired the ability of females to attract males. Our findings indicate that GPAT acts to regulate the biosynthesis of sex pheromone precursor, TAG, thus influencing PBAN-induced sex pheromone production and subsequent mating behavior. PMID:25630665

Subsequent Chemotherapy and Treatment Patterns After Abiraterone Acetate in Patients with Metastatic Castration-resistant Prostate Cancer: Post Hoc Analysis of COU-AA-302.

PubMed

de Bono, Johann S; Smith, Matthew R; Saad, Fred; Rathkopf, Dana E; Mulders, Peter F A; Small, Eric J; Shore, Neal D; Fizazi, Karim; De Porre, Peter; Kheoh, Thian; Li, Jinhui; Todd, Mary B; Ryan, Charles J; Flaig, Thomas W

2017-04-01

Treatment patterns for metastatic castration-resistant prostate cancer (mCRPC) have changed substantially in the last few years. In trial COU-AA-302 (chemotherapy-naïve men with mCRPC), abiraterone acetate plus prednisone (AA) significantly improved radiographic progression-free survival and overall survival (OS) when compared to placebo plus prednisone (P). This post hoc analysis investigated clinical responses to docetaxel as first subsequent therapy (FST) among patients who progressed following protocol-specified treatment with AA, and characterized subsequent treatment patterns among older (≥75 yr) and younger (<75 yr) patient subgroups. Data were collected at the final OS analysis (96% of expected death events). Subsequent therapy data were prospectively collected, while response and discontinuation data were collected retrospectively following discontinuation of the study drug. At the discretion of the investigator, 67% (365/546) of patients from the AA arm received subsequent treatment with one or more agents approved for mCRPC. Efficacy analysis was performed for patients for whom baseline and at least one post-baseline prostate-specific antigen (PSA) values were available. Baseline and at least one post-baseline PSA values were available for 100 AA patients who received docetaxel as FST. While acknowledging the limitations of post hoc analyses, 40% (40/100) of these patients had an unconfirmed ≥50% PSA decline with first subsequent docetaxel therapy, and 27% (27/100) had a confirmed ≥50% PSA decline. The median docetaxel treatment duration among these 100 patients was 4.2 mo. Docetaxel was the most common FST among older and younger patients from each treatment arm. However, 43% (79/185) of older patients who progressed on AA received no subsequent therapy for mCRPC, compared with 17% (60/361) of younger patients. Patients with mCRPC who progress with AA treatment may still derive benefit from subsequent docetaxel therapy. These data support further assessment of treatment patterns following AA treatment for mCRPC, particularly among older patients. ClinicalTrials.gov NCT00887198. Treatment patterns for advanced prostate cancer have changed substantially in the last few years. This additional analysis provides evidence of clinical benefit for subsequent chemotherapy in men with advanced prostate cancer whose disease progressed after treatment with abiraterone acetate. Older patients were less likely to be treated with subsequent therapy. Copyright © 2016 European Association of Urology. Published by Elsevier B.V. All rights reserved.

Comparative analysis of gene expression profiles of OPN signaling pathway in four kinds of liver diseases.

PubMed

Wang, Gaiping; Chen, Shasha; Zhao, Congcong; Li, Xiaofang; Zhao, Weiming; Yang, Jing; Chang, Cuifang; Xu, Cunshuan

2016-09-01

To explore the relevance of OPN signalling pathway to the occurrence and development of nonalcoholic fatty liver disease (NAFLD), liver cirrhosis (LC), hepatic cancer (HC) and acute hepatic failure (AHF) at transcriptional level, Rat Genome 230 2.0 Array was used to detect expression profiles of OPN signalling pathway-related genes in four kinds of liver diseases. The results showed that 23, 33, 59 and 74 genes were significantly changed in the above four kinds of liver diseases, respectively. H-clustering analysis showed that the expression profiles of OPN signalling-related genes were notably different in four kinds of liver diseases. Subsequently, a total of above-mentioned 147 genes were categorized into four clusters by k-means according to the similarity of gene expression, and expression analysis systematic explorer (EASE) functional enrichment analysis revealed that OPN signalling pathway-related genes were involved in cell adhesion and migration, cell proliferation, apoptosis, stress and inflammatory reaction, etc. Finally, ingenuity pathway analysis (IPA) software was used to predict the functions of OPN signalling-related genes, and the results indicated that the activities of ROS production, cell adhesion and migration, cell proliferation were remarkably increased, while that of apoptosis, stress and inflammatory reaction were reduced in four kinds of liver diseases. In summary, the above physiological activities changed more obviously in LC, HC and AHF than in NAFLD.

Modeling cation/anion-water interactions in functional aluminosilicate structures.

PubMed

Richards, A J; Barnes, P; Collins, D R; Christodoulos, F; Clark, S M

1995-02-01

A need for the computer simulation of hydration/dehydration processes in functional aluminosilicate structures has been noted. Full and realistic simulations of these systems can be somewhat ambitious and require the aid of interactive computer graphics to identify key structural/chemical units, both in the devising of suitable water-ion simulation potentials and in the analysis of hydrogen-bonding schemes in the subsequent simulation studies. In this article, the former is demonstrated by the assembling of a range of essential water-ion potentials. These span the range of formal charges from +4e to -2e, and are evaluated in the context of three types of structure: a porous zeolite, calcium silicate cement, and layered clay. As an example of the latter, the computer graphics output from Monte Carlo computer simulation studies of hydration/dehydration in calcium-zeolite A is presented.

Missing data exploration: highlighting graphical presentation of missing pattern.

PubMed

Zhang, Zhongheng

2015-12-01

Functions shipped with R base can fulfill many tasks of missing data handling. However, because the data volume of electronic medical record (EMR) system is always very large, more sophisticated methods may be helpful in data management. The article focuses on missing data handling by using advanced techniques. There are three types of missing data, that is, missing completely at random (MCAR), missing at random (MAR) and not missing at random (NMAR). This classification system depends on how missing values are generated. Two packages, Multivariate Imputation by Chained Equations (MICE) and Visualization and Imputation of Missing Values (VIM), provide sophisticated functions to explore missing data pattern. In particular, the VIM package is especially helpful in visual inspection of missing data. Finally, correlation analysis provides information on the dependence of missing data on other variables. Such information is useful in subsequent imputations.

How Hot are Your Ions in TWAVE Ion Mobility Spectrometry?

PubMed Central

Merenbloom, Samuel I.; Flick, Tawnya G.; Williams, Evan R.

2012-01-01

Effective temperatures of ions during traveling wave ion mobility spectrometry (TWIMS) analysis were measured using singly protonated leucine enkephalin dimer as a chemical thermometer by monitoring dissociation of the dimer into monomer, as well as the subsequent dissociation of monomer into a-, b-, and y-ions, as a function of instrumental parameters. At fixed helium cell and TWIMS cell gas flow rates, the extent of dissociation does not vary significantly with either the wave velocity or wave height, except at low (<500 m/s) wave velocities that are not commonly used. Increasing the flow rate of nitrogen gas into the TWIMS cell and decreasing the flow rate of helium gas into the helium cell resulted in greater dissociation. However, the mobility distributions of the fragment ions formed by dissociation of the dimer upon injection into the TWIMS cell are nearly indistinguishable from those of fragment ions formed in the collision cell prior to TWIMS analysis for all TWIMS experiments. These results indicate that heating and dissociation occur when ions are injected into the TWIMS cell, and that the effective temperature subsequently decreases to a point at which no further dissociation is observed during the TWIMS analysis. An upper limit to the effective ion temperature of 449 K during TWIMS analysis is obtained at a helium flow rate of 180 mL/min, TWIMS flow rate of 80 mL/min and traveling wave height of 40 V, which is well below previously reported values. Effects of ion heating in TWIMS on gas-phase protein conformation are presented. PMID:22203576

Elimination of ``memory`` from sample handling and inlet system of a mass spectrometer

DOEpatents

Chastgner, P.

1991-05-08

This paper describes a method for preparing the sample handling and inlet system of a mass spectrometer for analysis of a subsequent sample following analysis of a previous sample comprising the flushing of the system interior with supercritical CO{sub 2} and venting the interior. The method eliminates the effect of system ``memory`` on the subsequent analysis, especially following persistent samples such as xenon and krypton.

Prediction of recovery of motor function after stroke.

PubMed

Stinear, Cathy

2010-12-01

Stroke is a leading cause of disability. The ability to live independently after stroke depends largely on the reduction of motor impairment and the recovery of motor function. Accurate prediction of motor recovery assists rehabilitation planning and supports realistic goal setting by clinicians and patients. Initial impairment is negatively related to degree of recovery, but inter-individual variability makes accurate prediction difficult. Neuroimaging and neurophysiological assessments can be used to measure the extent of stroke damage to the motor system and predict subsequent recovery of function, but these techniques are not yet used routinely. The use of motor impairment scores and neuroimaging has been refined by two recent studies in which these investigations were used at multiple time points early after stroke. Voluntary finger extension and shoulder abduction within 5 days of stroke predicted subsequent recovery of upper-limb function. Diffusion-weighted imaging within 7 days detected the effects of stroke on caudal motor pathways and was predictive of lasting motor impairment. Thus, investigations done soon after stroke had good prognostic value. The potential prognostic value of cortical activation and neural plasticity has been explored for the first time by two recent studies. Functional MRI detected a pattern of cortical activation at the acute stage that was related to subsequent reduction in motor impairment. Transcranial magnetic stimulation enabled measurement of neural plasticity in the primary motor cortex, which was related to subsequent disability. These studies open interesting new lines of enquiry. WHERE NEXT?: The accuracy of prediction might be increased by taking into account the motor system's capacity for functional reorganisation in response to therapy, in addition to the extent of stroke-related damage. Improved prognostic accuracy could also be gained by combining simple tests of motor impairment with neuroimaging, genotyping, and neurophysiological assessment of neural plasticity. The development of algorithms to guide the sequential combinations of these assessments could also further increase accuracy, in addition to improving rehabilitation planning and outcomes. Copyright © 2010 Elsevier Ltd. All rights reserved.

Hemorrhage and Subsequent Allogenic Red Blood Cell Transfusion are Associated With Characteristic Monocyte Messenger RNA Expression Patterns in Patients After Multiple Injury—A Genome Wide View

PubMed Central

Bogner, Viktoria; Baker, Henry V.; Kanz, Karl-Georg; Moldawer, L. L.; Mutschler, Wolf; Biberthaler, Peter

2014-01-01

Introduction As outcome to severe trauma is frequently affected by massive blood loss and consecutive hemorrhagic shock, replacement of red blood cell (RBC) units remains indispensable. Administration of RBC units is an independent risk factor for adverse outcome in patients with trauma. The impact of massive blood transfusion or uncrossmatched blood transfusion on the patients’ immune response in the early posttraumatic period remains unclear. Material Thirteen patients presenting with blunt multiple injuries (Injury Severity Score >16) were studied. Monocytes were obtained on admission and at 6, 12, 24, 48, and 72 hours after trauma. Biotinylated complementary RNA targets were hybridized to Affymetrix HG U 133A microarrays. The data were analyzed by a supervised analysis based on whether the patients received massive blood transfusions, and then subsequently, by hierarchical clustering, and by Ingenuity pathway analysis. Results Supervised analysis identified 224 probe sets to be differentially expressed (p < 0.001) in patients who received massive blood transfusion, when compared with those who did not. In addition, 331 probe sets were found differentially expressed (p < 0.001) in patients who received uncrossmatched RBC units in comparison with those who exclusively gained crossmatched ones. Functional pathway analysis of the respectively identified gene expression profiles suggests a contributory role by the AKT/PI3Kinase pathway, the mitogen-activated protein-kinase pathway, the Ubiquitin pathway, and the diverse inflammatory networks. Conclusion We exhibited for the first time a serial, sequential screening analysis of monocyte messenger RNA expression patterns in patients with multiple trauma indicating a strongly significant association between the patients’ genomic response in blood monocytes and massive or uncross-matched RBC substitution. PMID:19820587

The interaction of nifedipine with selected cyclodextrins and the subsequent solubility-permeability trade-off.

PubMed

Beig, Avital; Miller, Jonathan M; Dahan, Arik

2013-11-01

The purpose of this study was to investigate the interaction of 2-hydroxypropyl-β-cyclodextrin (HPβCD) and 2,6-dimethyl-β-cyclodextrin (DMβCD) with the lipophilic drug nifedipine and to investigate the subsequent solubility-permeability interplay. Solubility curves of nifedipine with HPβCD and DMβCD in MES buffer were evaluated using phase solubility methods. Then, the apparent permeability of nifedipine was investigated as a function of increasing HPβCD/DMβCD concentration in the hexadecane-based PAMPA model. The interaction with nifedipine was CD dependent; significantly higher stability constant was obtained for DMβCD in comparison with HPβCD. Moreover, nifedipine displays different type of interaction with these CDs; a 1:1 stoichiometric inclusion complex was apparent with HPβCD, while 1:2 stoichiometry was apparent for DMβCD. In all cases, decreased apparent intestinal permeability of nifedipine as a function of increasing CD level and nifedipine apparent solubility was obtained. A quasi-equilibrium mass transport analysis was developed to explain this solubility-permeability interplay; the model enabled excellent quantitative prediction of nifedipine's permeability as a function of CD concentrations. This work demonstrates that when using CDs in solubility-enabling formulations, a trade-off exists between solubility increase and permeability decrease that must not be overlooked. This trade-off was found to be independent of the type of CD-drug interaction. The transport model presented here can aid in striking the appropriate solubility-permeability balance in order to achieve optimal overall absorption. Copyright © 2013 Elsevier B.V. All rights reserved.

AaCAT1 of the Yellow Fever Mosquito, Aedes aegypti

PubMed Central

Hansen, Immo A.; Boudko, Dmitri Y.; Shiao, Shin-Hong; Voronov, Dmitri A.; Meleshkevitch, Ella A.; Drake, Lisa L.; Aguirre, Sarah E.; Fox, Jeffrey M.; Attardo, Geoffrey M.; Raikhel, Alexander S.

2011-01-01

Insect yolk protein precursor gene expression is regulated by nutritional and endocrine signals. A surge of amino acids in the hemolymph of blood-fed female mosquitoes activates a nutrient signaling system in the fat bodies, which subsequently derepresses yolk protein precursor genes and makes them responsive to activation by steroid hormones. Orphan transporters of the SLC7 family were identified as essential upstream components of the nutrient signaling system in the fat body of fruit flies and the yellow fever mosquito, Aedes aegypti. However, the transport function of these proteins was unknown. We report expression and functional characterization of AaCAT1, cloned from the fat body of A. aegypti. Expression of AaCAT1 transcript and protein undergoes dynamic changes during postembryonic development of the mosquito. Transcript expression was especially high in the third and fourth larval stages; however, the AaCAT1 protein was detected only in pupa and adult stages. Functional expression and analysis of AaCAT1 in Xenopus oocytes revealed that it acts as a sodium-independent cationic amino acid transporter, with unique selectivity to l-histidine at neutral pH (K0.5l-His = 0.34 ± 0.07 mm, pH 7.2). Acidification to pH 6.2 dramatically increases AaCAT1-specific His+-induced current. RNAi-mediated silencing of AaCAT1 reduces egg yield of subsequent ovipositions. Our data show that AaCAT1 has notable differences in its transport mechanism when compared with related mammalian cationic amino acid transporters. It may execute histidine-specific transport and signaling in mosquito tissues. PMID:21262963

KDR (VEGFR2) identifies a conserved human and murine hepatic progenitor and instructs early liver development

PubMed Central

Goldman, Orit; Han, Songyan; Sourrisseau, Marion; Dziedzic, Noelle; Hamou, Wissam; Corneo, Barbara; D’Souza, Sunita; Sato, Thomas; Kotton, Darrell N.; Bissig, Karl-Dimiter; Kalir, Tamara; Jacobs, Adam; Evans, Todd; Evans, Matthew J.; Gouon-Evans, Valerie

2013-01-01

SUMMARY Understanding the fetal hepatic niche is essential for optimizing the generation of functional hepatocyte-like (hepatic) cells from human embryonic stem cells (hESCs). Here, we show that KDR (VEGFR2), previously assumed to be mostly restricted to mesodermal lineages, marks a hESC-derived hepatic progenitor. hESC-derived endoderm cells do not express KDR, but when cultured in media supporting hepatic differentiation, generate KDR+ hepatic progenitors and KDR- hepatic cells. KDR+ progenitors require active KDR signaling both to instruct their own differentiation into hepatic cells, and to support non-cell-autonomously the functional maturation of co-cultured KDR- hepatic cells. Analysis of human fetal livers suggests that similar progenitors are present in human livers. Lineage tracing in mice provides in vivo evidence of a KDR+ hepatic progenitor for fetal hepatoblasts and subsequently adult hepatocytes and cholangiocytes. Altogether, our findings reveal that KDR is a conserved marker for endoderm-derived hepatic progenitors, and a functional receptor instructing early liver development. PMID:23746980

Photogenerated Lectin Sensors Produced by Thiol-Ene/Yne Photo-Click Chemistry in Aqueous Solution

PubMed Central

Norberg, Oscar; Lee, Irene H.; Aastrup, Teodor; Yan, Mingdi; Ramström, Olof

2012-01-01

The photoinitiated radical reactions between thiols and alkenes/alkynes (thiol-ene and thiol-yne chemistry) have been applied to a functionalization methodology to produce carbohydrate-presenting surfaces for analyses of biomolecular interactions. Polymer-coated quartz surfaces were functionalized with alkenes or alkynes in a straightforward photochemical procedure utilizing perfluorophenylazide (PFPA) chemistry. The alkene/alkyne surfaces were subsequently allowed to react with carbohydrate thiols in water under UV-irradiation. The reaction can be carried out in a drop of water directly on the surface without photoinitiator and any disulfide side products were easily washed away after the functionalization process. The resulting carbohydrate-presenting surfaces were evaluated in real-time studies of protein-carbohydrate interactions using a quartz crystal microbalance flow-through system with recurring injections of selected lectins with intermediate regeneration steps using low pH buffer. The resulting methodology proved fast, efficient and scalable to high-throughput analysis formats, and the produced surfaces showed significant protein binding with expected selectivities of the lectins used in the study. PMID:22341757

Response of soil bacterial community to repeated applications of carbendazim.

PubMed

Wang, Xiuguo; Song, Min; Wang, Yiqi; Gao, Chunming; Zhang, Qun; Chu, Xiaoqiang; Fang, Hua; Yu, Yunlong

2012-01-01

The effect of repeated carbendazim applications on functional diversity of culturable microorganisms and bacterial community composition was studied under field conditions. The functional diversity of soil culturable microbial community (Shannon index, H') reduced significantly (P<0.05) after the first introduction of carbendazim at levels of 0.94, 1.88 and 4.70 kg active ingredient (a.i.)ha(-1) and then recovered to that in the control with subsequent applications. An evident (P<0.01) difference in the bacterial community composition was observed after the second carbendazim application by Temperature Gradient Gel Electrophoresis (TGGE) analysis of 16S rRNA genes amplified from treated and control soils, which remained after the third and fourth treatments. Our results indicated that repeated carbendazim applications have a transient harmful effect on functional diversity of soil culturable microbial community and result in an alteration in bacterial community composition largely due to one species within the γ-proteobacterium. Copyright © 2011 Elsevier Inc. All rights reserved.

Differentiated thyroid carcinoma with functional autonomy.

PubMed

Yaturu, Subhashini; Fowler, Marjorie R

2002-01-01

To present a case of papillary carcinoma in an autonomously hyperfunctioning thyroid nodule. We chronicle the clinical and laboratory findings in a patient with a painless neck mass, with a particular focus on the pathologic findings after surgical removal of the right thyroid lobe. A 39-year-old woman had an enlarging nodule of the right thyroid lobe. Results of thyroid function tests suggested subclinical hyperthyroidism. Two months later, the patient complained of increasing swelling in the neck (but still had no symptoms suggestive of hyperthyroidism). Thus, resection of the right thyroid lobe was performed. Pathologic analysis disclosed low-grade papillary thyroid carcinoma within the nodule, with a small rim of compressed inactive-appearing thyroid tissue surrounding the nodule. Subsequently, she underwent total thyroidectomy and follow-up care for thyroid carcinoma. Although solitary hyperfunctioning nodules of the thyroid gland are usually considered benign, the current case suggests that the diagnosis of autonomous thyroid nodules does not preclude thyroid carcinoma in a functioning nodule.

Bim, a Proapoptotic Protein, Up-regulated via Transcription Factor E2F1-dependent Mechanism, Functions as a Prosurvival Molecule in Cancer*

PubMed Central

Gogada, Raghu; Yadav, Neelu; Liu, Junwei; Tang, Shaohua; Zhang, Dianmu; Schneider, Andrea; Seshadri, Athul; Sun, Leimin; Aldaz, C. Marcelo; Tang, Dean G.; Chandra, Dhyan

2013-01-01

Proapoptotic Bcl-2 homology 3-only protein Bim plays an important role in Bax/Bak-mediated cytochrome c release and apoptosis. Here, we provide evidence for a novel prosurvival function of Bim in cancer cells. Bim was constitutively overexpressed in multiple prostate and breast cancer cells as well as in primary tumor cells. Quantitative real time PCR analysis showed that Bim was transcriptionally up-regulated. We have identified eight endogenous E2F1-binding sites on the Bim promoter using in silico analysis. Luciferase assay demonstrated that Bim expression was E2F1-dependent as mutation of the E2F1-binding sites on the Bim promoter inhibited luciferase activities. In support, E2F1 silencing led to the loss of Bim expression in cancer cells. Bim primarily localized to mitochondrial and cytoskeleton-associated fractions. Bim silencing or microinjection of anti-Bim antibodies into the cell cytoplasm resulted in cell rounding, detachment, and subsequent apoptosis. We observed up-regulation of prosurvival proteins Bcl-xL and Mcl-1, which sequester Bim in cancer cells. In addition, a phosphorylated form of Bim was also elevated in cancer cells. These findings suggest that the constitutively overexpressed Bim may function as a prosurvival molecule in epithelial cancer cells, and phosphorylation and association with Bcl-xL/Mcl-1 block its proapoptotic functions. PMID:23152504

Higher-Order Theory for Functionally Graded Materials

NASA Technical Reports Server (NTRS)

Aboudi, J.; Pindera, M. J.; Arnold, Steven M.

2001-01-01

Functionally graded materials (FGM's) are a new generation of engineered materials wherein the microstructural details are spatially varied through nonuniform distribution of the reinforcement phase(s). Engineers accomplish this by using reinforcements with different properties, sizes, and shapes, as well as by interchanging the roles of the reinforcement and matrix phases in a continuous manner (ref. 1). The result is a microstructure that produces continuously or discretely changing thermal and mechanical properties at the macroscopic or continuum scale. This new concept of engineering the material's microstructure marks the beginning of a revolution both in the materials science and mechanics of materials areas since it allows one, for the first time, to fully integrate the material and structural considerations into the final design of structural components. Functionally graded materials are ideal candidates for applications involving severe thermal gradients, ranging from thermal structures in advanced aircraft and aerospace engines to computer circuit boards. Owing to the many variables that control the design of functionally graded microstructures, full exploitation of the FGM's potential requires the development of appropriate modeling strategies for their response to combined thermomechanical loads. Previously, most computational strategies for the response of FGM's did not explicitly couple the material's heterogeneous microstructure with the structural global analysis. Rather, local effective or macroscopic properties at a given point within the FGM were first obtained through homogenization based on a chosen micromechanics scheme and then subsequently used in a global thermomechanical analysis.

Controlled growth of silica-titania hybrid functional nanoparticles through a multistep microfluidic approach.

PubMed

Shiba, K; Sugiyama, T; Takei, T; Yoshikawa, G

2015-11-11

Silica/titania-based functional nanoparticles were prepared through controlled nucleation of titania and subsequent encapsulation by silica through a multistep microfluidic approach, which was successfully applied to obtaining aminopropyl-functionalized silica/titania nanoparticles for a highly sensitive humidity sensor.

Synthesis and characterization of (3-Aminopropyl)trimethoxy-silane (APTMS) functionalized Gd2O3:Eu(3+) red phosphor with enhanced quantum yield.

PubMed

Jain, Akhil; Hirata, G A; Farías, M H; Castillón, F F

2016-02-12

We report the surface modification of nanocrystalline Gd2O3:Eu(3+) phosphor by (3-Aminopropyl)trimethoxysilane (APTMS). The nanoparticles were first coated with silica using the Stöber process, and then annealed at 650 °C for 2 h. Afterwards, APTMS was functionalized onto the silica layer to obtain Gd2O3:Eu(3+) nanoparticles bearing amine groups on the surface. The effect of silica coating, and the subsequent annealing process on the crystallization of the nanophosphor were analyzed by x-ray diffraction (XRD). High-resolution transmission electron microscopy (HR-TEM) confirmed the presence of a silica layer of ∼45 nm thickness. X-ray photoelectron (XPS) and Fourier transform infrared (FTIR) spectroscopy confirmed the presence of silica and the amine groups. Photoluminescence (PL) analysis demonstrated an increased emission after functionalization of nanoparticles. Absolute quantum yield (QY) measurements revealed an 18% enhancement in QY in functionalized nanoparticles compared with unmodified nanoparticles, which is of great importance for their biomedical applications.

Synthesis and characterization of (3-Aminopropyl)trimethoxy-silane (APTMS) functionalized Gd2O3:Eu3+ red phosphor with enhanced quantum yield

NASA Astrophysics Data System (ADS)

Jain, Akhil; Hirata, G. A.; Farías, M. H.; Castillón, F. F.

2016-02-01

We report the surface modification of nanocrystalline Gd2O3:Eu3+ phosphor by (3-Aminopropyl)trimethoxysilane (APTMS). The nanoparticles were first coated with silica using the Stöber process, and then annealed at 650 °C for 2 h. Afterwards, APTMS was functionalized onto the silica layer to obtain Gd2O3:Eu3+ nanoparticles bearing amine groups on the surface. The effect of silica coating, and the subsequent annealing process on the crystallization of the nanophosphor were analyzed by x-ray diffraction (XRD). High-resolution transmission electron microscopy (HR-TEM) confirmed the presence of a silica layer of ∼45 nm thickness. X-ray photoelectron (XPS) and Fourier transform infrared (FTIR) spectroscopy confirmed the presence of silica and the amine groups. Photoluminescence (PL) analysis demonstrated an increased emission after functionalization of nanoparticles. Absolute quantum yield (QY) measurements revealed an 18% enhancement in QY in functionalized nanoparticles compared with unmodified nanoparticles, which is of great importance for their biomedical applications.

N-heterocyclic carbene gold(I) and silver(I) complexes bearing functional groups for bio-conjugation

PubMed Central

Garner, Mary E.; Niu, Weijia; Chen, Xigao; Ghiviriga, Ion; Tan, Weihong; Veige, Adam S.

2015-01-01

This work describes several synthetic approaches to append organic functional groups to gold and silver N-heterocyclic carbene (NHC) complexes suitable for applications in biomolecule conjugation. Carboxylate appended NHC ligands (3) lead to unstable AuI complexes that convert into bis-NHC species (4). A benzyl protected carboxylate NHC-AuI complex 2 was synthesized but deprotection to produce the carboxylic acid functionality could not be achieved. A small library of new alkyne functionalized NHC proligands were synthesized and used for subsequent silver and gold metalation reactions. The alkyne appended NHC gold complex 13 readily react with benzyl azide in a copper catalyzed azide-alkyne cycloaddition reaction to form the triazole appended NHC gold complex 14. Cell cytotoxicity studies were performed on DLD-1 (colorectal adenocarcinoma), Hep-G2 (hepatocellular carcinoma), MCF-7 (breast adenocarcinoma), CCRF-CEM (human T-Cell leukemia), and HEK (human embryonic kidney). Complete spectroscopic characterization of the ligands and complexes was achieved using 1H and 13C NMR, gHMBC, ESI-MS, and combustion analysis. PMID:25490699

Integrative analysis workflow for the structural and functional classification of C-type lectins

PubMed Central

2011-01-01

Background It is important to understand the roles of C-type lectins in the immune system due to their ubiquity and diverse range of functions in animal cells. It has been observed that currently confirmed C-type lectins share a highly conserved domain known as the C-type carbohydrate recognition domain (CRD). Using the sequence profile of the CRD, an increasing number of putative C-type lectins have been identified. Hence, it is highly needed to develop a systematic framework that enables us to elucidate their carbohydrate (glycan) recognition function, and discover their physiological and pathological roles. Results Presented herein is an integrated workflow for characterizing the sequence and structural features of novel C-type lectins. Our workflow utilizes web-based queries and available software suites to annotate features that can be found on the C-type lectin, given its amino acid sequence. At the same time, it incorporates modeling and analysis of glycans - a major class of ligands that interact with C-type lectins. Thereafter, the results are analyzed together with context-specific knowledge to filter off unlikely predictions. This allows researchers to design their subsequent experiments to confirm the functions of the C-type lectins in a systematic manner. Conclusions The efficacy and usefulness of our proposed immunoinformatics workflow was demonstrated by applying our integrated workflow to a novel C-type lectin -CLEC17A - and we report some of its possible functions that warrants further validation through wet-lab experiments. PMID:22372988

Subtle changes in daily functioning predict conversion from normal to mild cognitive impairment or dementia: an analysis of the NACC database

PubMed Central

Nowrangi, Milap A.; Rosenberg, Paul B.; Leoutsakos, Jeannie-Marie S.

2017-01-01

Background There are relatively small but observable changes in functional ability in those without Mild cognitive impairment (MCI) or dementia. The present study seeks to understand whether these individuals go on to develop MCI or dementia by assessing the association between baseline Functional Activities Questionnaire (FAQ) and conversion independent and after adjustment for cognitive tests. Methods The NACC database was used to conduct the analysis of which 7,625 participants were initially identified as having more than one visit and who were cognitively normal at their first visit. Cox proportional hazards were used to fit three models that controlled for executive and non-executive cognitive domains. A similar model was used to assess the effect of FAQ subcategories on conversion. Results Of these individuals, 1,328 converted to either MCI or dementia by visit 10. Converters had a total visit 1 FAQ score significantly higher than non-converters indicating more functional impairment at baseline. After adjustment for cognitive tests, the association between visit 1 FAQ and subsequent conversion was not attenuated. Doing taxes, remembering dates, and traveling were individually identified as significant predictors of conversion. Conclusions The FAQ can be used as an indirect measure of functional ability and is associated with conversion to MCI or dementia. There is a selective and significant association between changes in financial ability and conversion that is in accordance with other research of financial capacity. PMID:27585497

Impaired executive function can predict recurrent falls in Parkinson's disease.

PubMed

Mak, Margaret K; Wong, Adrian; Pang, Marco Y

2014-12-01

To examine whether impairment in executive function independently predicts recurrent falls in people with Parkinson's disease (PD). Prospective cohort study. University motor control research laboratory. A convenience sample of community-dwelling people with PD (N=144) was recruited from a patient self-help group and movement disorders clinics. Not applicable. Executive function was assessed with the Mattis Dementia Rating Scale Initiation/Perseveration (MDRS-IP) subtest, and fear of falling (FoF) with the Activities-specific Balance Confidence (ABC) Scale. All participants were followed up for 12 months to record the number of monthly fall events. Forty-two people with PD had at least 2 falls during the follow-up period and were classified as recurrent fallers. After accounting for demographic variables and fall history (P=.001), multiple logistic regression analysis showed that the ABC scores (P=.014) and MDRS-IP scores (P=.006) were significantly associated with future recurrent falls among people with PD. The overall accuracy of the prediction was 85.9%. With the use of the significant predictors identified in multiple logistic regression analysis, a prediction model determined by the logistic function was generated: Z = 1.544 + .378 (fall history) - .045 (ABC) - .145 (MDRS-IP). Impaired executive function is a significant predictor of future recurrent falls in people with PD. Participants with executive dysfunction and greater FoF at baseline had a significantly greater risk of sustaining a recurrent fall within the subsequent 12 months. Copyright © 2014 American Congress of Rehabilitation Medicine. Published by Elsevier Inc. All rights reserved.

Influence of speckle image reconstruction on photometric precision for large solar telescopes

NASA Astrophysics Data System (ADS)

Peck, C. L.; Wöger, F.; Marino, J.

2017-11-01

Context. High-resolution observations from large solar telescopes require adaptive optics (AO) systems to overcome image degradation caused by Earth's turbulent atmosphere. AO corrections are, however, only partial. Achieving near-diffraction limited resolution over a large field of view typically requires post-facto image reconstruction techniques to reconstruct the source image. Aims: This study aims to examine the expected photometric precision of amplitude reconstructed solar images calibrated using models for the on-axis speckle transfer functions and input parameters derived from AO control data. We perform a sensitivity analysis of the photometric precision under variations in the model input parameters for high-resolution solar images consistent with four-meter class solar telescopes. Methods: Using simulations of both atmospheric turbulence and partial compensation by an AO system, we computed the speckle transfer function under variations in the input parameters. We then convolved high-resolution numerical simulations of the solar photosphere with the simulated atmospheric transfer function, and subsequently deconvolved them with the model speckle transfer function to obtain a reconstructed image. To compute the resulting photometric precision, we compared the intensity of the original image with the reconstructed image. Results: The analysis demonstrates that high photometric precision can be obtained for speckle amplitude reconstruction using speckle transfer function models combined with AO-derived input parameters. Additionally, it shows that the reconstruction is most sensitive to the input parameter that characterizes the atmospheric distortion, and sub-2% photometric precision is readily obtained when it is well estimated.

Clustering of Midlife Lifestyle Behaviors and Subsequent Cognitive Function: A Longitudinal Study

PubMed Central

Andreeva, Valentina A.; Lassale, Camille; Hercberg, Serge; Galan, Pilar

2014-01-01

Objectives. We examined the association between individual and clustered lifestyle behaviors in middle age and later in cognitive functioning. Methods. Middle-aged participants (n = 2430) in the Supplémentation en Vitamines et Minéraux Antioxydant study self-reported their low physical activity, sedentary behavior, alcohol use, smoking, low fruit and vegetable consumption, and low fish consumption. We assessed cognition 13 years later via 6 neuropsychological tests. After standardization, we summed the scores for a composite cognitive measure. We estimated executive functioning and verbal memory scores using principal component analysis. We estimated the mean differences (95% confidence intervals [CIs]) in cognitive performance by the number of unhealthy behaviors using analysis of covariance. We identified latent unhealthy behavior factor via structural equation modeling. Results. Global cognitive function and verbal memory were linearly, negatively associated with the number of unhealthy behaviors: adjusted mean differences = −0.36 (95% CI = −0.69, −0.03) and −0.46 (95% CI = −0.80, −0.11), respectively, per unit increase in the number of unhealthy behaviors. The latent unhealthy behavior factor with low fruit and vegetable consumption and low physical activity as main contributors was associated with reduced verbal memory (RMSEA = 0.02; CFI = 0.96; P = .004). No association was found with executive functioning. Conclusions. Comprehensive public health strategies promoting healthy lifestyles might help deter cognitive aging. PMID:25211733

NATbox: a network analysis toolbox in R.

PubMed

Chavan, Shweta S; Bauer, Michael A; Scutari, Marco; Nagarajan, Radhakrishnan

2009-10-08

There has been recent interest in capturing the functional relationships (FRs) from high-throughput assays using suitable computational techniques. FRs elucidate the working of genes in concert as a system as opposed to independent entities hence may provide preliminary insights into biological pathways and signalling mechanisms. Bayesian structure learning (BSL) techniques and its extensions have been used successfully for modelling FRs from expression profiles. Such techniques are especially useful in discovering undocumented FRs, investigating non-canonical signalling mechanisms and cross-talk between pathways. The objective of the present study is to develop a graphical user interface (GUI), NATbox: Network Analysis Toolbox in the language R that houses a battery of BSL algorithms in conjunction with suitable statistical tools for modelling FRs in the form of acyclic networks from gene expression profiles and their subsequent analysis. NATbox is a menu-driven open-source GUI implemented in the R statistical language for modelling and analysis of FRs from gene expression profiles. It provides options to (i) impute missing observations in the given data (ii) model FRs and network structure from gene expression profiles using a battery of BSL algorithms and identify robust dependencies using a bootstrap procedure, (iii) present the FRs in the form of acyclic graphs for visualization and investigate its topological properties using network analysis metrics, (iv) retrieve FRs of interest from published literature. Subsequently, use these FRs as structural priors in BSL (v) enhance scalability of BSL across high-dimensional data by parallelizing the bootstrap routines. NATbox provides a menu-driven GUI for modelling and analysis of FRs from gene expression profiles. By incorporating readily available functions from existing R-packages, it minimizes redundancy and improves reproducibility, transparency and sustainability, characteristic of open-source environments. NATbox is especially suited for interdisciplinary researchers and biologists with minimal programming experience and would like to use systems biology approaches without delving into the algorithmic aspects. The GUI provides appropriate parameter recommendations for the various menu options including default parameter choices for the user. NATbox can also prove to be a useful demonstration and teaching tool in graduate and undergraduate course in systems biology. It has been tested successfully under Windows and Linux operating systems. The source code along with installation instructions and accompanying tutorial can be found at http://bioinformatics.ualr.edu/natboxWiki/index.php/Main_Page.

Prediction of rhythmic and periodic EEG patterns and seizures on continuous EEG with early epileptiform discharges.

PubMed

Koren, J; Herta, J; Draschtak, S; Pötzl, G; Pirker, S; Fürbass, F; Hartmann, M; Kluge, T; Baumgartner, C

2015-08-01

Continuous EEG (cEEG) is necessary to document nonconvulsive seizures (NCS), nonconvulsive status epilepticus (NCSE), as well as rhythmic and periodic EEG patterns of 'ictal-interictal uncertainty' (RPPIIU) including periodic discharges, rhythmic delta activity, and spike-and-wave complexes in neurological intensive care patients. However, cEEG is associated with significant recording and analysis efforts. Therefore, predictors from short-term routine EEG with a reasonably high yield are urgently needed in order to select patients for evaluation with cEEG. The aim of this study was to assess the prognostic significance of early epileptiform discharges (i.e., within the first 30 min of EEG recording) on the following: (1) incidence of ictal EEG patterns and RPPIIU on subsequent cEEG, (2) occurrence of acute convulsive seizures during the ICU stay, and (3) functional outcome after 6 months of follow-up. We conducted a separate analysis of the first 30 min and the remaining segments of prospective cEEG recordings according to the ACNS Standardized Critical Care EEG Terminology as well as NCS criteria and review of clinical data of 32 neurological critical care patients. In 17 patients with epileptiform discharges within the first 30 min of EEG (group 1), electrographic seizures were observed in 23.5% (n = 4), rhythmic or periodic EEG patterns of 'ictal-interictal uncertainty' in 64.7% (n = 11), and neither electrographic seizures nor RPPIIU in 11.8% (n = 2). In 15 patients with no epileptiform discharges in the first 30 min of EEG (group 2), no electrographic seizures were recorded on subsequent cEEG, RPPIIU were seen in 26.7% (n = 4), and neither electrographic seizures nor RPPIIU in 73.3% (n = 11). The incidence of EEG patterns on cEEG was significantly different between the two groups (p = 0.008). Patients with early epileptiform discharges developed acute seizures more frequently than patients without early epileptiform discharges (p = 0.009). Finally, functional outcome six months after discharge was significantly worse in patients with early epileptiform discharges (p=0.01). Epileptiform discharges within the first 30 min of EEG recording are predictive for the occurrence of ictal EEG patterns and for RPPIIU on subsequent cEEG, for acute convulsive seizures during the ICU stay, and for a worse functional outcome after 6 months of follow-up. This article is part of a Special Issue entitled Status Epilepticus. Copyright © 2015 Elsevier Inc. All rights reserved.

3D fluid-structure modelling and vibration analysis for fault diagnosis of Francis turbine using multiple ANN and multiple ANFIS

NASA Astrophysics Data System (ADS)

Saeed, R. A.; Galybin, A. N.; Popov, V.

2013-01-01

This paper discusses condition monitoring and fault diagnosis in Francis turbine based on integration of numerical modelling with several different artificial intelligence (AI) techniques. In this study, a numerical approach for fluid-structure (turbine runner) analysis is presented. The results of numerical analysis provide frequency response functions (FRFs) data sets along x-, y- and z-directions under different operating load and different position and size of faults in the structure. To extract features and reduce the dimensionality of the obtained FRF data, the principal component analysis (PCA) has been applied. Subsequently, the extracted features are formulated and fed into multiple artificial neural networks (ANN) and multiple adaptive neuro-fuzzy inference systems (ANFIS) in order to identify the size and position of the damage in the runner and estimate the turbine operating conditions. The results demonstrated the effectiveness of this approach and provide satisfactory accuracy even when the input data are corrupted with certain level of noise.

An investigation about the structures, thermodynamics and kinetics of the formic acid involved molecular clusters

NASA Astrophysics Data System (ADS)

Zhang, Rui; Jiang, Shuai; Liu, Yi-Rong; Wen, Hui; Feng, Ya-Juan; Huang, Teng; Huang, Wei

2018-05-01

Despite the very important role of atmospheric aerosol nucleation in climate change and air quality, the detailed aerosol nucleation mechanism is still unclear. Here we investigated the formic acid (FA) involved multicomponent nucleation molecular clusters including sulfuric acid (SA), dimethylamine (DMA) and water (W) through a quantum chemical method. The thermodynamics and kinetics analysis was based on the global minima given by Basin-Hopping (BH) algorithm coupled with Density Functional Theory (DFT) and subsequent benchmarked calculations. Then the interaction analysis based on ElectroStatic Potential (ESP), Topological and Atomic Charges analysis was made to characterize the binding features of the clusters. The results show that FA binds weakly with the other molecules in the cluster while W binds more weakly. Further kinetic analysis about the time evolution of the clusters show that even though the formic acid's weak interaction with other nucleation precursors, its effect on sulfuric acid dimer steady state concentration cannot be neglected due to its high concentration in the atmosphere.

Prospective Cohort Study of Work Functioning Impairment and Subsequent Absenteeism Among Japanese Workers.

PubMed

Fujino, Yoshihisa; Shazuki, Shuichiro; Izumi, Hiroyuki; Uehara, Masamichi; Muramatsu, Keiji; Kubo, Tatsuhiko; Oyama, Ichiro; Matsuda, Shinya

2016-07-01

This study examined the association of work functioning impairment as measured by work functioning impairment scale (WFun) and subsequent sick leave. A prospective cohort study was conducted at a manufacturer in Japan, and 1263 employees participated. Information on sick leave was gathered during an 18-month follow-up period. The hazard ratios (HRs) of long-term sick leave were substantially increased for those with a WFun score greater than 25 (HR = 3.99, P = 0.003). The incidence rate ratios (IRRs) of days of short-term absence gradually increased as scores of WFun increased (IRR = 1.18, P < 0.001 in the subjects with WFun of over 25 comparing with those with WFun of 14 or less). Assessing work functioning impairment is a useful way of classifying risk for future sick leave among employees.

Simulating Vibrations in a Complex Loaded Structure

NASA Technical Reports Server (NTRS)

Cao, Tim T.

2005-01-01

The Dynamic Response Computation (DIRECT) computer program simulates vibrations induced in a complex structure by applied dynamic loads. Developed to enable rapid analysis of launch- and landing- induced vibrations and stresses in a space shuttle, DIRECT also can be used to analyze dynamic responses of other structures - for example, the response of a building to an earthquake, or the response of an oil-drilling platform and attached tanks to large ocean waves. For a space-shuttle simulation, the required input to DIRECT includes mathematical models of the space shuttle and its payloads, and a set of forcing functions that simulates launch and landing loads. DIRECT can accommodate multiple levels of payload attachment and substructure as well as nonlinear dynamic responses of structural interfaces. DIRECT combines the shuttle and payload models into a single structural model, to which the forcing functions are then applied. The resulting equations of motion are reduced to an optimum set and decoupled into a unique format for simulating dynamics. During the simulation, maximum vibrations, loads, and stresses are monitored and recorded for subsequent analysis to identify structural deficiencies in the shuttle and/or payloads.

Habituation as an adaptive shift in response strategy mediated by neuropeptides

NASA Astrophysics Data System (ADS)

Ardiel, Evan L.; Yu, Alex J.; Giles, Andrew C.; Rankin, Catharine H.

2017-08-01

Habituation is a non-associative form of learning characterized by a decremented response to repeated stimulation. It is typically framed as a process of selective attention, allowing animals to ignore irrelevant stimuli in order to free up limited cognitive resources. However, habituation can also occur to threatening and toxic stimuli, suggesting that habituation may serve other functions. Here we took advantage of a high-throughput Caenorhabditis elegans learning assay to investigate habituation to noxious stimuli. Using real-time computer vision software for automated behavioral tracking and optogenetics for controlled activation of a polymodal nociceptor, ASH, we found that neuropeptides mediated habituation and performed an RNAi screen to identify candidate receptors. Through subsequent mutant analysis and cell-type-specific gene expression, we found that pigment-dispersing factor (PDF) neuropeptides function redundantly to promote habituation via PDFR-1-mediated cAMP signaling in both neurons and muscles. Behavioral analysis during learning acquisition suggests that response habituation and sensitization of locomotion are parts of a shifting behavioral strategy orchestrated by pigment dispersing factor signaling to promote dispersal away from repeated aversive stimuli.

Study of the Low Temperature Oxidation of Propane

PubMed Central

Cord, Maximilien; Husson, Benoit; Huerta, Juan Carlos Lizardo; Herbinet, Olivier; Glaude, Pierre-Alexandre; Fournet, René; Sirjean, Baptiste; Battin-Leclerc, Frédérique; Ruiz-Lopez, Manuel; Wang, Zhandong; Xie, Mingfeng; Cheng, Zhanjun; Qi, Fei

2013-01-01

The low-temperature oxidation of propane was investigated using a jet-stirred reactor at atmospheric pressure and two methods of analysis: gas chromatography and synchrotron vacuum ultraviolet photoionization mass spectrometry (SVUV-PIMS) with direct sampling through a molecular jet. The second method allowed the identification of products, such as molecules with hydroperoxy functions, which are not stable enough to be detected by gas chromatography. Mole fractions of the reactants and reaction products were measured as a function of the temperature (530-730 K), with a particular attention to reaction products involved in the low temperature oxidation, such as cyclic ethers, aldehydes, alcohols, ketones, and hydroperoxides. A new model has been obtained from an automatically generated one, which was used as a starting point, with a large number of re-estimated thermochemical and kinetic data. The kinetic data of the most sensitive reactions, i.e., isomerizations of alkylperoxy radicals and the subsequent decompositions, have been calculated at the CBS-QB3 level of theory. The model allows a satisfactory prediction of the experimental data. A flow rate analysis has allowed highlighting the important reaction channels. PMID:23181456

Computational studies of novel chymase inhibitors against cardiovascular and allergic diseases: mechanism and inhibition.

PubMed

Arooj, Mahreen; Thangapandian, Sundarapandian; John, Shalini; Hwang, Swan; Park, Jong K; Lee, Keun W

2012-12-01

To provide a new idea for drug design, a computational investigation is performed on chymase and its novel 1,4-diazepane-2,5-diones inhibitors that explores the crucial molecular features contributing to binding specificity. Molecular docking studies of inhibitors within the active site of chymase were carried out to rationalize the inhibitory properties of these compounds and understand their inhibition mechanism. The density functional theory method was used to optimize molecular structures with the subsequent analysis of highest occupied molecular orbital, lowest unoccupied molecular orbital, and molecular electrostatic potential maps, which revealed that negative potentials near 1,4-diazepane-2,5-diones ring are essential for effective binding of inhibitors at active site of enzyme. The Bayesian model with receiver operating curve statistic of 0.82 also identified arylsulfonyl and aminocarbonyl as the molecular features favoring and not favoring inhibition of chymase, respectively. Moreover, genetic function approximation was applied to construct 3D quantitative structure-activity relationships models. Two models (genetic function approximation model 1 r(2) = 0.812 and genetic function approximation model 2 r(2) = 0.783) performed better in terms of correlation coefficients and cross-validation analysis. In general, this study is used as example to illustrate how combinational use of 2D/3D quantitative structure-activity relationships modeling techniques, molecular docking, frontier molecular orbital density fields (highest occupied molecular orbital and lowest unoccupied molecular orbital), and molecular electrostatic potential analysis may be useful to gain an insight into the binding mechanism between enzyme and its inhibitors. © 2012 John Wiley & Sons A/S.

High-throughput fabrication and screening improves gold nanoparticle chemiresistor sensor performance.

PubMed

Hubble, Lee J; Cooper, James S; Sosa-Pintos, Andrea; Kiiveri, Harri; Chow, Edith; Webster, Melissa S; Wieczorek, Lech; Raguse, Burkhard

2015-02-09

Chemiresistor sensor arrays are a promising technology to replace current laboratory-based analysis instrumentation, with the advantage of facile integration into portable, low-cost devices for in-field use. To increase the performance of chemiresistor sensor arrays a high-throughput fabrication and screening methodology was developed to assess different organothiol-functionalized gold nanoparticle chemiresistors. This high-throughput fabrication and testing methodology was implemented to screen a library consisting of 132 different organothiol compounds as capping agents for functionalized gold nanoparticle chemiresistor sensors. The methodology utilized an automated liquid handling workstation for the in situ functionalization of gold nanoparticle films and subsequent automated analyte testing of sensor arrays using a flow-injection analysis system. To test the methodology we focused on the discrimination and quantitation of benzene, toluene, ethylbenzene, p-xylene, and naphthalene (BTEXN) mixtures in water at low microgram per liter concentration levels. The high-throughput methodology identified a sensor array configuration consisting of a subset of organothiol-functionalized chemiresistors which in combination with random forests analysis was able to predict individual analyte concentrations with overall root-mean-square errors ranging between 8-17 μg/L for mixtures of BTEXN in water at the 100 μg/L concentration. The ability to use a simple sensor array system to quantitate BTEXN mixtures in water at the low μg/L concentration range has direct and significant implications to future environmental monitoring and reporting strategies. In addition, these results demonstrate the advantages of high-throughput screening to improve the performance of gold nanoparticle based chemiresistors for both new and existing applications.

Application of the International Classification of Functioning, Disability and Health (ICF) to people with dysphagia following non-surgical head and neck cancer management.

PubMed

Nund, Rebecca L; Scarinci, Nerina A; Cartmill, Bena; Ward, Elizabeth C; Kuipers, Pim; Porceddu, Sandro V

2014-12-01

The International Classification of Functioning, Disability, and Health (ICF) is an internationally recognized framework which allows its user to describe the consequences of a health condition on an individual in the context of their environment. With growing recognition that dysphagia can have broad ranging physical and psychosocial impacts, the aim of this paper was to identify the ICF domains and categories that describe the full functional impact of dysphagia following non-surgical head and neck cancer (HNC) management, from the perspective of the person with dysphagia. A secondary analysis was conducted on previously published qualitative study data which explored the lived experiences of dysphagia of 24 individuals with self-reported swallowing difficulties following HNC management. Categories and sub-categories identified by the qualitative analysis were subsequently mapped to the ICF using the established linking rules to develop a set of ICF codes relevant to the impact of dysphagia following HNC management. The 69 categories and sub-categories that had emerged from the qualitative analysis were successfully linked to 52 ICF codes. The distribution of these codes across the ICF framework revealed that the components of Body Functions, Activities and Participation, and Environmental Factors were almost equally represented. The findings confirm that the ICF is a valuable framework for representing the complexity and multifaceted impact of dysphagia following HNC. This list of ICF codes, which reflect the diverse impact of dysphagia associated with HNC on the individual, can be used to guide more holistic assessment and management for this population.

Two general models that generate long range correlation

NASA Astrophysics Data System (ADS)

Gan, Xiaocong; Han, Zhangang

2012-06-01

In this paper we study two models that generate sequences with LRC (long range correlation). For the IFT (inverse Fourier transform) model, our conclusion is the low frequency part leads to LRC, while the high frequency part tends to eliminate it. Therefore, a typical method to generate a sequence with LRC is multiplying the spectrum of a white noise sequence by a decaying function. A special case is analyzed: the linear combination of a smooth curve and a white noise sequence, in which the DFA plot consists of two line segments. For the patch model, our conclusion is long subsequences leads to LRC, while short subsequences tend to eliminate it. Therefore, we can generate a sequence with LRC by using a fat-tailed PDF (probability distribution function) of the length of the subsequences. A special case is also analyzed: if a patch model with long subsequences is mixed with a white noise sequence, the DFA plot will consist of two line segments. We have checked known models and actual data, and found they are all consistent with this study.

Predicting relapse in major depressive disorder using patient-reported outcomes of depressive symptom severity, functioning, and quality of life in the Individual Burden of Illness Index for Depression (IBI-D).

PubMed

Ishak, Waguih William; Greenberg, Jared M; Cohen, Robert M

2013-10-01

Patients with Major Depressive Disorder (MDD) often experience unexpected relapses, despite achieving remission. This study examines the utility of a single multidimensional measure that captures variance in patient-reported Depressive Symptom Severity, Functioning, and Quality of Life (QOL), in predicting MDD relapse. Complete data from remitted patients at the completion of 12 weeks of citalopram in the STAR*D study were used to calculate the Individual Burden of Illness index for Depression (IBI-D), and predict subsequent relapse at six (n=956), nine (n=778), and twelve months (n=479) using generalized linear models. Depressive Symptom Severity, Functioning, and QOL were all predictors of subsequent relapse. Using Akaike information criteria (AIC), the IBI-D provided a good model for relapse even when Depressive Symptom Severity, Functioning, and QOL were combined in a single model. Specifically, an increase of one in the IBI-D increased the odds ratio of relapse by 2.5 at 6 months (β=0.921 ± 0.194, z=4.76, p<2 × 10(-6)), by 2.84 at 9 months (β=1.045 ± 0.22, z=4.74, p<2.2 × 10(-6)), and by 4.1 at 12 months (β=1.41 ± 0.29, z=4.79, p<1.7 × 10(-6)). Self-report poses a risk to measurement precision. Using highly valid and reliable measures could mitigate this risk. The IBI-D requires time and effort for filling out the scales and index calculation. Technological solutions could help ease these burdens. The sample suffered from attrition. Separate analysis of dropouts would be helpful. Incorporating patient-reported outcomes of Functioning and QOL in addition to Depressive Symptom Severity in the IBI-D is useful in assessing the full burden of illness and in adequately predicting relapse, in MDD. © 2013 Elsevier B.V. All rights reserved.

Semen molecular and cellular features: these parameters can reliably predict subsequent ART outcome in a goat model

PubMed Central

Berlinguer, Fiammetta; Madeddu, Manuela; Pasciu, Valeria; Succu, Sara; Spezzigu, Antonio; Satta, Valentina; Mereu, Paolo; Leoni, Giovanni G; Naitana, Salvatore

2009-01-01

Currently, the assessment of sperm function in a raw or processed semen sample is not able to reliably predict sperm ability to withstand freezing and thawing procedures and in vivo fertility and/or assisted reproductive biotechnologies (ART) outcome. The aim of the present study was to investigate which parameters among a battery of analyses could predict subsequent spermatozoa in vitro fertilization ability and hence blastocyst output in a goat model. Ejaculates were obtained by artificial vagina from 3 adult goats (Capra hircus) aged 2 years (A, B and C). In order to assess the predictive value of viability, computer assisted sperm analyzer (CASA) motility parameters and ATP intracellular concentration before and after thawing and of DNA integrity after thawing on subsequent embryo output after an in vitro fertility test, a logistic regression analysis was used. Individual differences in semen parameters were evident for semen viability after thawing and DNA integrity. Results of IVF test showed that spermatozoa collected from A and B lead to higher cleavage rates (0 < 0.01) and blastocysts output (p < 0.05) compared with C. Logistic regression analysis model explained a deviance of 72% (p < 0.0001), directly related with the mean percentage of rapid spermatozoa in fresh semen (p < 0.01), semen viability after thawing (p < 0.01), and with two of the three comet parameters considered, i.e tail DNA percentage and comet length (p < 0.0001). DNA integrity alone had a high predictive value on IVF outcome with frozen/thawed semen (deviance explained: 57%). The model proposed here represents one of the many possible ways to explain differences found in embryo output following IVF with different semen donors and may represent a useful tool to select the most suitable donors for semen cryopreservation. PMID:19900288

Evaluation of the predictive value of a clinical worsening definition using 2-year outcomes in patients with pulmonary arterial hypertension: a REVEAL Registry analysis.

PubMed

Frost, Adaani E; Badesch, David B; Miller, Dave P; Benza, Raymond L; Meltzer, Leslie A; McGoon, Michael D

2013-11-01

Time to clinical worsening has been proposed as a primary end point in clinical trials of pulmonary arterial hypertension (PAH); however, neither standardized nor validated definitions of clinical worsening across PAH trials exist. This study aims to evaluate a proposed definition of clinical worsening within a large prospective, observational registry of patients with PAH with respect to its value as a predictor of proximate (within 1 year) risk for subsequent major events (ie, death, transplantation, or atrial septostomy). We assessed overall 2-year survival and survival free from major events to determine the relationship between clinical worsening and major events among adults with hemodynamically defined PAH (N = 3,001). Freedom from clinical worsening was defined as freedom from worsening functional class (FC), a ≥ 15% reduction in 6-min walk distance (6MWD), all-cause hospitalization, or the introduction of parenteral prostacyclin analog therapy. In the 2 years of follow-up, 583 patients died. Four hundred twenty-six died after a documented clinical worsening event, including FC worsening (n = 128), a ≥ 15% reduction in 6MWD (n = 118), all-cause hospitalization (n = 370), or introduction of a prostacyclin analog (n = 91). Patients who experienced clinical worsening had significantly poorer subsequent 1-year survival postworsening than patients who did not worsen (P < .001). Clinical worsening was highly predictive of subsequent proximate mortality in this analysis from an observational study. These results validate the use of clinical worsening as a meaningful prognostic tool in clinical practice and as a primary end point in clinical trial design. ClinicalTrials.gov; No.: NCT00370214; URL: www.clinicaltrials.gov.

Exploratory double-blind, parallel-group, placebo-controlled extension study of edaravone (MCI-186) in amyotrophic lateral sclerosis.

PubMed

2017-10-01

Following the first phase III study of edaravone for amyotrophic lateral sclerosis (ALS), this extension study was performed to evaluate longer-term efficacy and safety. Patients given edaravone in the first 24-week phase III study (Cycles 1-6) were randomised to edaravone (E-E) or placebo (E-P) in the subsequent 24-week double-blind period (Cycles 7-12). Patients given placebo in phase III were switched to edaravone (P-E). Subsequently, all patients received edaravone for 12 weeks (Cycles 13-15). Efficacy endpoints included revised ALS Functional Rating Scale (ALSFRS-R) score. Analysis populations were the full analysis set (FAS) and the efficacy-expected subpopulation (EESP) defined by post-hoc analysis of the first phase III study. The least-squares mean and standard error of the intergroup difference (E-E vs. E-P) of change in the ALSFRS-R score from Cycles 7-12 was 1.16 ± 0.93 (p = 0.2176) in the FAS, and 1.85 ± 1.14 (p = 0.1127) in the EESP. The ALSFRS-R score changed almost linearly in the E-E group throughout Cycles 1-15 (60 weeks). The incidence of serious adverse events associated with ALS progression was higher in E-E than in E-P. Edaravone might have potential efficacy for up to 15 cycles when used to treat patients in the EESP with careful safety monitoring.

Modelling Comparative Efficacy of Drugs with Different Survival Profiles: Ipilimumab, Vemurafenib and Dacarbazine in Advanced Melanoma.

PubMed

Lee, D; Porter, J; Hertel, N; Hatswell, A J; Briggs, A

2016-08-01

In the absence of head-to-head data, a common method for modelling comparative survival for cost-effectiveness analysis is estimating hazard ratios from trial publications. This assumes that the hazards of mortality are proportional between treatments and that outcomes are not polluted by subsequent therapy use. Newer techniques that compare treatments where the proportional hazards assumption is violated and adjust for use of subsequent therapies often require patient-level data, which are rarely available for all treatments. The objective of this study was to provide a comparison of overall survival data for ipilimumab, vemurafenib and dacarbazine using data from three trials lacking a common comparator arm and confounded by the use of subsequent treatment. We compared three estimated overall survival curves for vemurafenib and the difference compared to ipilimumab and dacarbazine. We performed a naïve comparison and adjusted it for heterogeneity between the ipilimumab and vemurafenib trials, including differences in prognostic characteristics and subsequent therapy using a published hazard function for the impact of prognostic characteristics in melanoma and trial data on the impact of second-line use of ipilimumab. The mean incremental life-years gained for patients receiving ipilimumab compared with vemurafenib were 0.34 (95 % confidence interval [CI] -0.24 to 0.84) using the naïve comparison and 0.51 (95 % CI -0.08 to 0.99) using the covariate-adjusted survival curve. The analyses estimated the comparative efficacy of ipilimumab and vemurafenib in the absence of head-to-head patient-level data for all trials and proportional hazards in overall survival.

Are scarce metals in cars functionally recycled?

PubMed

Andersson, Magnus; Ljunggren Söderman, Maria; Sandén, Björn A

2017-02-01

Improved recycling of end-of-life vehicles (ELVs) may serve as an important strategy to address resource security risks related to increased global demand for scarce metals. However, in-depth knowledge of the magnitude and fate of such metals entering ELV recycling is lacking. This paper quantifies input of 25 scarce metals to Swedish ELV recycling, and estimates the extent to which they are recycled to material streams where their metal properties are utilised, i.e. are functionally recycled. Methodologically, scarce metals are mapped to main types of applications within newly produced Swedish car models and subsequently, material flow analysis of ELV waste streams is used as basis for identifying pathways of these applications and assessing whether contained metals are functionally recycled. Results indicate that, of the scarce metals, only platinum may be functionally recycled in its main application. Cobalt, gold, manganese, molybdenum, palladium, rhodium and silver may be functionally recycled depending on application and pathways taken. For remaining 17 metals, functional recycling is absent. Consequently, despite high overall ELV recycling rates of materials in general, there is considerable risk of losing ELV scarce metals to carrier metals, construction materials, backfilling materials and landfills. Given differences in the application of metals and identified pathways, prospects for increasing functional recycling are discussed. Copyright © 2016 Elsevier Ltd. All rights reserved.

Peripheral natural killer cytotoxicity and CD56(pos)CD16(pos) cells increase during early pregnancy in women with a history of recurrent spontaneous abortion.

PubMed

Emmer, P M; Nelen, W L; Steegers, E A; Hendriks, J C; Veerhoek, M; Joosten, I

2000-05-01

For diagnostic purposes we assessed peripheral natural killer (NK) cell cytotoxicity and NK and T cell numbers to assess their putative predictive value in recurrent spontaneous abortion (RSA). A total of 43 women with subsequent pregnancy, 37 healthy controls and 39 women successfully partaking in an in-vitro fertilization (IVF) procedure, were included in the study. We show that before pregnancy, levels of NK cytotoxicity and numbers of both single CD56(pos) and double CD56(pos)CD16(pos) cells were similar between RSA women and controls. But notably, within the RSA group, NK cell numbers of <12% were strongly associated with a subsequent pregnancy carried to term. Supplementation of folic acid led to an increase of single CD56(pos) cells, but cytotoxic function appeared unaffected. The expression pattern of killer inhibitory receptors on CD56(pos) cells was not different between patients and controls. A longitudinal study revealed that, compared with controls, in RSA women higher numbers of double CD56(pos)CD16(pos) cells were present during early pregnancy, paralleled by an increase in cytotoxic NK cell reactivity. The single CD56(pos) population decreased in number. In conclusion, the analysis of peripheral NK cell characteristics appears a suitable diagnostic tool in RSA. Immunomodulation aimed at NK cell function appears a promising therapeutic measure.

Discovery of Colorectal Cancer Biomarker Candidates by Membrane Proteomic Analysis and Subsequent Verification using Selected Reaction Monitoring (SRM) and Tissue Microarray (TMA) Analysis*

PubMed Central

Kume, Hideaki; Muraoka, Satoshi; Kuga, Takahisa; Adachi, Jun; Narumi, Ryohei; Watanabe, Shio; Kuwano, Masayoshi; Kodera, Yoshio; Matsushita, Kazuyuki; Fukuoka, Junya; Masuda, Takeshi; Ishihama, Yasushi; Matsubara, Hisahiro; Nomura, Fumio; Tomonaga, Takeshi

2014-01-01

Recent advances in quantitative proteomic technology have enabled the large-scale validation of biomarkers. We here performed a quantitative proteomic analysis of membrane fractions from colorectal cancer tissue to discover biomarker candidates, and then extensively validated the candidate proteins identified. A total of 5566 proteins were identified in six tissue samples, each of which was obtained from polyps and cancer with and without metastasis. GO cellular component analysis predicted that 3087 of these proteins were membrane proteins, whereas TMHMM algorithm predicted that 1567 proteins had a transmembrane domain. Differences were observed in the expression of 159 membrane proteins and 55 extracellular proteins between polyps and cancer without metastasis, while the expression of 32 membrane proteins and 17 extracellular proteins differed between cancer with and without metastasis. A total of 105 of these biomarker candidates were quantitated using selected (or multiple) reaction monitoring (SRM/MRM) with stable synthetic isotope-labeled peptides as an internal control. The results obtained revealed differences in the expression of 69 of these proteins, and this was subsequently verified in an independent set of patient samples (polyps (n = 10), cancer without metastasis (n = 10), cancer with metastasis (n = 10)). Significant differences were observed in the expression of 44 of these proteins, including ITGA5, GPRC5A, PDGFRB, and TFRC, which have already been shown to be overexpressed in colorectal cancer, as well as proteins with unknown function, such as C8orf55. The expression of C8orf55 was also shown to be high not only in colorectal cancer, but also in several cancer tissues using a multicancer tissue microarray, which included 1150 cores from 14 cancer tissues. This is the largest verification study of biomarker candidate membrane proteins to date; our methods for biomarker discovery and subsequent validation using SRM/MRM will contribute to the identification of useful biomarker candidates for various cancers. Data are available via ProteomeXchange with identifier PXD000851. PMID:24687888

Discovery of colorectal cancer biomarker candidates by membrane proteomic analysis and subsequent verification using selected reaction monitoring (SRM) and tissue microarray (TMA) analysis.

PubMed

Kume, Hideaki; Muraoka, Satoshi; Kuga, Takahisa; Adachi, Jun; Narumi, Ryohei; Watanabe, Shio; Kuwano, Masayoshi; Kodera, Yoshio; Matsushita, Kazuyuki; Fukuoka, Junya; Masuda, Takeshi; Ishihama, Yasushi; Matsubara, Hisahiro; Nomura, Fumio; Tomonaga, Takeshi

2014-06-01

Recent advances in quantitative proteomic technology have enabled the large-scale validation of biomarkers. We here performed a quantitative proteomic analysis of membrane fractions from colorectal cancer tissue to discover biomarker candidates, and then extensively validated the candidate proteins identified. A total of 5566 proteins were identified in six tissue samples, each of which was obtained from polyps and cancer with and without metastasis. GO cellular component analysis predicted that 3087 of these proteins were membrane proteins, whereas TMHMM algorithm predicted that 1567 proteins had a transmembrane domain. Differences were observed in the expression of 159 membrane proteins and 55 extracellular proteins between polyps and cancer without metastasis, while the expression of 32 membrane proteins and 17 extracellular proteins differed between cancer with and without metastasis. A total of 105 of these biomarker candidates were quantitated using selected (or multiple) reaction monitoring (SRM/MRM) with stable synthetic isotope-labeled peptides as an internal control. The results obtained revealed differences in the expression of 69 of these proteins, and this was subsequently verified in an independent set of patient samples (polyps (n = 10), cancer without metastasis (n = 10), cancer with metastasis (n = 10)). Significant differences were observed in the expression of 44 of these proteins, including ITGA5, GPRC5A, PDGFRB, and TFRC, which have already been shown to be overexpressed in colorectal cancer, as well as proteins with unknown function, such as C8orf55. The expression of C8orf55 was also shown to be high not only in colorectal cancer, but also in several cancer tissues using a multicancer tissue microarray, which included 1150 cores from 14 cancer tissues. This is the largest verification study of biomarker candidate membrane proteins to date; our methods for biomarker discovery and subsequent validation using SRM/MRM will contribute to the identification of useful biomarker candidates for various cancers. Data are available via ProteomeXchange with identifier PXD000851. © 2014 by The American Society for Biochemistry and Molecular Biology, Inc.

Post-discharge kidney function is associated with subsequent ten-year renal progression risk among survivors of acute kidney injury.

PubMed

Sawhney, Simon; Marks, Angharad; Fluck, Nick; Levin, Adeera; McLernon, David; Prescott, Gordon; Black, Corri

2017-08-01

The extent to which renal progression after acute kidney injury (AKI) arises from an initial step drop in kidney function (incomplete recovery), or from a long-term trajectory of subsequent decline, is unclear. This makes it challenging to plan or time post-discharge follow-up. This study of 14651 hospital survivors in 2003 (1966 with AKI, 12685 no AKI) separates incomplete recovery from subsequent renal decline by using the post-discharge estimated glomerular filtration rate (eGFR) rather than the pre-admission as a new reference point for determining subsequent renal outcomes. Outcomes were sustained 30% renal decline and de novo CKD stage 4, followed from 2003-2013. Death was a competing risk. Overall, death was more common than subsequent renal decline (37.5% vs 11.3%) and CKD stage 4 (4.5%). Overall, 25.7% of AKI patients had non-recovery. Subsequent renal decline was greater after AKI (vs no AKI) (14.8% vs 10.8%). Renal decline after AKI (vs no AKI) was greatest among those with higher post-discharge eGFRs with multivariable hazard ratios of 2.29 (1.88-2.78); 1.50 (1.13-2.00); 0.94 (0.68-1.32) and 0.95 (0.64-1.41) at eGFRs of 60 or more; 45-59; 30-44 and under 30, respectively. The excess risk after AKI persisted over ten years of study, irrespective of AKI severity, or post-episode proteinuria. Thus, even if post-discharge kidney function returns to normal, hospital admission with AKI is associated with increased renal progression that persists for up to ten years. Follow-up plans should avoid false reassurance when eGFR after AKI returns to normal. Copyright © 2017 International Society of Nephrology. Published by Elsevier Inc. All rights reserved.

78 FR 54387 - Airworthiness Directives; The Boeing Company Airplanes

Federal Register 2010, 2011, 2012, 2013, 2014

2013-09-04

... at S-6L and S-6R on several airplanes, and subsequent analysis results that indicated that the... reach a critical length. We are issuing this AD to detect and correct cracking at the upper row of... and S-6R on several airplanes, and subsequent analysis results that indicated that the protruding head...

Space Flight and Manual Control: Implications for Sensorimotor Function on Future Missions

NASA Technical Reports Server (NTRS)

Reschke, Millard F.; Kornilova, Ludmila; Tomilovskaya, Elena; Parker, Donald E.; Leigh, R. John; Kozlovskaya, Inessa

2009-01-01

Control of vehicles, and other complex mechanical motion systems, is a high-level integrative function of the central nervous system (CNS) that requires good visual acuity, eye-hand coordination, spatial (and, in some cases, geographic) orientation perception, and cognitive function. Existing evidence from space flight research (Paloski et.al., 2008, Clement and Reschke 2008, Reschke et al., 2007) demonstrates that the function of each of these systems is altered by removing (and subsequently by reintroducing) a gravitational field that can be sensed by vestibular, proprioceptive, and haptic receptors and used by the CNS for spatial orientation, navigation, and coordination of movements. Furthermore, much of the operational performance data collected as a function of space flight has not been available for independent analysis, and those data that have been reviewed are equivocal owing to uncontrolled environmental and/or engineering factors. Thus, our current understanding, when it comes to manual control, is limited primarily to a review of those situations where manual control has been a factor. One of the simplest approaches to the manual control problem is to review shuttle landing data. See the Figure below for those landing for which we have Shuttle velocities over the runway threshold.

Phylogenetic and Functional Structure of Wintering Waterbird Communities Associated with Ecological Differences.

PubMed

Che, Xianli; Zhang, Min; Zhao, Yanyan; Zhang, Qiang; Quan, Qing; Møller, Anders; Zou, Fasheng

2018-01-19

Ecological differences may be related to community component divisions between Oriental (west) and Sino-Japanese (east) realms, and such differences may result in weak geographical breaks in migratory species that are highly mobile. Here, we conducted comparative phylogenetic and functional structure analyses of wintering waterbird communities in southern China across two realms and subsequently examined possible climate drivers of the observed patterns. An analysis based on such highly migratory species is particularly telling because migration is bound to reduce or completely eliminate any divergence between communities. Phylogenetic and functional structure of eastern communities showed over-dispersion while western communities were clustered. Basal phylogenetic and functional turnover of western communities was significant lower than that of eastern communities. The break between eastern and western communities was masked by these two realms. Geographic patterns were related to mean temperature changes and temperature fluctuations, suggesting that temperature may filter waterbird lineages and traits, thus underlying geographical community divisions. These results suggest phylogenetic and functional divisions in southern China, coinciding with biogeography. This study shows that temperature fluctuations constitute an essential mechanism shaping geographical divisions that have largely gone undetected previously, even under climate change.

[Telemonitoring of swallowing function: technologies in speech therapy practice.

PubMed

Tedesco, Angela; Lavermicocca, Valentina; Notarnicola, Marilina; De Francesco, Luca; Dellomonaco, Anna Rita

2018-02-01

The process of medical-healthcare technological revolution represents an advantage for the patient and for the care provider, in terms of costs and distances reduction. The telehomecare approach could be useful for monitoring the swallowing disorder in neurodegenerative diseases, preventing complications. In this study the applicability of telemedicine techniques for the monitoring of swallowing function, in patients affected by Huntington's disease (HD), was evaluated through the acquisition and analysis of the sound of swallowing. Two patients with HD were outpatient screened for dysphagia through the Bedside Swallowing Assessment Scale (BSAS) sensitized with pulse oximetry and cervical auscultation. Subsequently, the swallowing functionality was telemonitored for three months with Skype. The swallowing sounds were acquired with a detection microphone attached to the lateral edge of the trachea during fluid intake. The sounds were instantly processed and graphically represented through the Praat software. The analysis of the acoustic signal acquired remotely has made it possible to identify the situations that required immediate speech therapy intervention, suggesting to the patients further modifications of food consistencies, and saving frequent moving to the hospital even in the absence of critical situations. Remote assistance applied to speech therapy could represent a benefit for patients and their carers and a more efficient use of medical and health resources.

A genetic screen for vascular mutants in zebrafish reveals dynamic roles for Vegf/Plcg1 signaling during artery development.

PubMed

Covassin, L D; Siekmann, A F; Kacergis, M C; Laver, E; Moore, J C; Villefranc, J A; Weinstein, B M; Lawson, N D

2009-05-15

In this work we describe a forward genetic approach to identify mutations that affect blood vessel development in the zebrafish. By applying a haploid screening strategy in a transgenic background that allows direct visualization of blood vessels, it was possible to identify several classes of mutant vascular phenotypes. Subsequent characterization of mutant lines revealed that defects in Vascular endothelial growth factor (Vegf) signaling specifically affected artery development. Comparison of phenotypes associated with different mutations within a functional zebrafish Vegf receptor-2 ortholog (referred to as kdr-like, kdrl) revealed surprisingly varied effects on vascular development. In parallel, we identified an allelic series of mutations in phospholipase c gamma 1 (plcg1). Together with in vivo structure-function analysis, our results suggest a requirement for Plcg1 catalytic activity downstream of receptor tyrosine kinases. We further find that embryos lacking both maternal and zygotic plcg1 display more severe defects in artery differentiation but are otherwise similar to zygotic mutants. Finally, we demonstrate through mosaic analysis that plcg1 functions autonomously in endothelial cells. Together our genetic analyses suggest that Vegf/Plcg1 signaling acts at multiple time points and in different signaling contexts to mediate distinct aspects of artery development.

Determining Protease Activity In Vivo by Fluorescence Cross-Correlation Analysis

PubMed Central

Kohl, Tobias; Haustein, Elke; Schwille, Petra

2005-01-01

To date, most biochemical approaches to unravel protein function have focused on purified proteins in vitro. Whereas they analyze enzyme performance under assay conditions, they do not necessarily tell us what is relevant within a living cell. Ideally, cellular functions should be examined in situ. In particular, association/dissociation reactions are ubiquitous, but so far there is no standard technique permitting online analysis of these processes in vivo. Featuring single-molecule sensitivity combined with intrinsic averaging, fluorescence correlation spectroscopy is a minimally invasive technique ideally suited to monitor proteins. Moreover, endogenous fluorescence-based assays can be established by genetically encoding fusions of autofluorescent proteins and cellular proteins, thus avoiding the disadvantages of in vitro protein labeling and subsequent delivery to cells. Here, we present an in vivo protease assay as a model system: Green and red autofluorescent proteins were connected by Caspase-3- sensitive and insensitive protein linkers to create double-labeled protease substrates. Then, dual-color fluorescence cross-correlation spectroscopy was employed to study the protease reaction in situ. Allowing assessment of multiple dynamic parameters simultaneously, this method provided internal calibration and improved experimental resolution for quantifying protein stability. This approach, which is easily extended to reversible protein-protein interactions, seems very promising for elucidating intracellular protein functions. PMID:16055538

A genetic screen for vascular mutants in zebrafish reveals dynamic roles for Vegf/Plcg1 signaling during artery development

PubMed Central

Covassin, L. D.; Siekmann, A. F.; Kacergis, M. C.; Laver, E.; Moore, J. C.; Villefranc, J. A.; Weinstein, B. M.; Lawson, N. D.

2009-01-01

In this work we describe a forward genetic approach to identify mutations that affect blood vessel development in the zebrafish. By applying a haploid screening strategy in a transgenic background that allows direct visualization of blood vessels, it was possible to identify several classes of mutant vascular phenotypes. Subsequent characterization of mutant lines revealed that defects in Vascular endothelial growth factor (Vegf) signaling specifically affected artery development. Comparison of phenotypes associated with different mutations within a functional zebrafish Vegf receptor-2 ortholog (referred to as kdr-like, kdrl) revealed surprisingly varied effects on vascular development. In parallel, we identified an allelic series of mutations in phospholipase c gamma 1 (plcg1). Together with in vivo structure-function analysis, our results suggest a requirement for Plcg1 catalytic activity downstream of receptor tyrosine kinases. We further find that embryos lacking both maternal and zygotic plcg1 display more severe defects in artery differentiation but are otherwise similar to zygotic mutants. Finally, we demonstrate through mosaic analysis that plcg1 functions autonomously in endothelial cells. Together our genetic analyses suggest that Vegf/Plcg1 signaling acts at multiple time points and in different signaling contexts to mediate distinct aspects of artery development. PMID:19269286

FMRI connectivity analysis of acupuncture effects on an amygdala-associated brain network

PubMed Central

Qin, Wei; Tian, Jie; Bai, Lijun; Pan, Xiaohong; Yang, Lin; Chen, Peng; Dai, Jianping; Ai, Lin; Zhao, Baixiao; Gong, Qiyong; Wang, Wei; von Deneen, Karen M; Liu, Yijun

2008-01-01

Background Recently, increasing evidence has indicated that the primary acupuncture effects are mediated by the central nervous system. However, specific brain networks underpinning these effects remain unclear. Results In the present study using fMRI, we employed a within-condition interregional covariance analysis method to investigate functional connectivity of brain networks involved in acupuncture. The fMRI experiment was performed before, during and after acupuncture manipulations on healthy volunteers at an acupuncture point, which was previously implicated in a neural pathway for pain modulation. We first identified significant fMRI signal changes during acupuncture stimulation in the left amygdala, which was subsequently selected as a functional reference for connectivity analyses. Our results have demonstrated that there is a brain network associated with the amygdala during a resting condition. This network encompasses the brain structures that are implicated in both pain sensation and pain modulation. We also found that such a pain-related network could be modulated by both verum acupuncture and sham acupuncture. Furthermore, compared with a sham acupuncture, the verum acupuncture induced a higher level of correlations among the amygdala-associated network. Conclusion Our findings indicate that acupuncture may change this amygdala-specific brain network into a functional state that underlies pain perception and pain modulation. PMID:19014532

A Bayesian Framework for Reliability Analysis of Spacecraft Deployments

NASA Technical Reports Server (NTRS)

Evans, John W.; Gallo, Luis; Kaminsky, Mark

2012-01-01

Deployable subsystems are essential to mission success of most spacecraft. These subsystems enable critical functions including power, communications and thermal control. The loss of any of these functions will generally result in loss of the mission. These subsystems and their components often consist of unique designs and applications for which various standardized data sources are not applicable for estimating reliability and for assessing risks. In this study, a two stage sequential Bayesian framework for reliability estimation of spacecraft deployment was developed for this purpose. This process was then applied to the James Webb Space Telescope (JWST) Sunshield subsystem, a unique design intended for thermal control of the Optical Telescope Element. Initially, detailed studies of NASA deployment history, "heritage information", were conducted, extending over 45 years of spacecraft launches. This information was then coupled to a non-informative prior and a binomial likelihood function to create a posterior distribution for deployments of various subsystems uSing Monte Carlo Markov Chain sampling. Select distributions were then coupled to a subsequent analysis, using test data and anomaly occurrences on successive ground test deployments of scale model test articles of JWST hardware, to update the NASA heritage data. This allowed for a realistic prediction for the reliability of the complex Sunshield deployment, with credibility limits, within this two stage Bayesian framework.

Prp43p Is a DEAH-Box Spliceosome Disassembly Factor Essential for Ribosome Biogenesis

PubMed Central

Combs, D. Joshua; Nagel, Roland J.; Ares, Manuel; Stevens, Scott W.

2006-01-01

The known function of the DEXH/D-box protein Prp43p is the removal of the U2, U5, and U6 snRNPs from the postsplicing lariat-intron ribonucleoprotein complex. We demonstrate that affinity-purified Prp43p-associated material includes the expected spliceosomal components; however, we also identify several preribosomal complexes that are specifically purified with Prp43p. Conditional prp43 mutant alleles confer a 35S pre-rRNA processing defect, with subsequent depletion of 27S and 20S precursors. Upon a shift to a nonpermissive temperature, both large and small-ribosomal-subunit proteins accumulate in the nucleolus of prp43 mutants. Pulse-chase analysis demonstrates delayed kinetics of 35S, 27S, and 20S pre-rRNA processing with turnover of these intermediates. Microarray analysis of pre-mRNA splicing defects in prp43 mutants shows a very mild effect, similar to that of nonessential pre-mRNA splicing factors. Prp43p is the first DEXH/D-box protein shown to function in both RNA polymerase I and polymerase II transcript metabolism. Its essential function is in its newly characterized role in ribosome biogenesis of both ribosomal subunits, positioning Prp43p to regulate both pre-mRNA splicing and ribosome biogenesis. PMID:16382144

Human Lymphatic Mesenteric Vessels: Morphology and Possible Function of Aminergic and NPY-ergic Nerve Fibers.

PubMed

D'Andrea, Vito; Panarese, Alessandra; Taurone, Samanta; Coppola, Luigi; Cavallotti, Carlo; Artico, Marco

2015-09-01

The lymphatic vessels have been studied in different organs from a morphological to a clinical point of view. Nevertheless, the knowledge of the catecholaminergic control of the lymphatic circulation is still incomplete. The aim of this work is to study the presence and distribution of the catecholaminergic and NPY-ergic nerve fibers in the whole wall of the human mesenteric lymphatic vessels in order to obtain knowledge about their morphology and functional significance. The following experimental procedures were performed: 1) drawing of tissue containing lymphatic vessels; 2) cutting of tissue; 3) staining of tissue; 4) staining of nerve fibers; 5) histofluorescence microscopy for the staining of catecholaminergic nerve fibers; 6) staining of neuropeptide Y like-immune reactivity; 7) biochemical assay of proteins; 8) measurement of noradrenaline; 9) quantitative analysis of images; 10) statistical analysis of data. Numerous nerve fibers run in the wall of lymphatic vessels. Many of them are catecholaminergic in nature. Some nerve fibers are NPY-positive. The biochemical results on noradrenaline amounts are in agreement with morphological results on catecholaminergic nerve fibers. Moreover, the morphometric results, obtained by the quantitative analysis of images and the subsequent statistical analysis of data, confirm all our morphological and biochemical data. The knowledge of the physiological or pathological mechanism regulating the functions of the lymphatic system is incomplete. Nevertheless the catecholaminergic nerve fibers of the human mesenteric lymphatic vessels come from the adrenergic periarterial plexuses of the mesenterial arterial bed. NPY-ergic nerve fibers may modulate the microcirculatory mesenterial bed in different pathological conditions.

Enrichment and proteomic analysis of plasma membrane from rat dorsal root ganglions

PubMed Central

2009-01-01

Background Dorsal root ganglion (DRG) neurons are primary sensory neurons that conduct neuronal impulses related to pain, touch and temperature senses. Plasma membrane (PM) of DRG cells plays important roles in their functions. PM proteins are main performers of the functions. However, mainly due to the very low amount of DRG that leads to the difficulties in PM sample collection, few proteomic analyses on the PM have been reported and it is a subject that demands further investigation. Results By using aqueous polymer two-phase partition in combination with high salt and high pH washing, PMs were efficiently enriched, demonstrated by western blot analysis. A total of 954 non-redundant proteins were identified from the plasma membrane-enriched preparation with CapLC-MS/MS analysis subsequent to protein separation by sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) or shotgun digestion. 205 (21.5%) of the identified proteins were unambiguously assigned as PM proteins, including a large number of signal proteins, receptors, ion channel and transporters. Conclusion The aqueous polymer two-phase partition is a simple, rapid and relatively inexpensive method. It is well suitable for the purification of PMs from small amount of tissues. Therefore, it is reasonable for the DRG PM to be enriched by using aqueous two-phase partition as a preferred method. Proteomic analysis showed that DRG PM was rich in proteins involved in the fundamental biological processes including material exchange, energy transformation and information transmission, etc. These data would help to our further understanding of the fundamental DRG functions. PMID:19889238

Structural damage identification using piezoelectric impedance measurement with sparse inverse analysis

NASA Astrophysics Data System (ADS)

Cao, Pei; Qi, Shuai; Tang, J.

2018-03-01

The impedance/admittance measurements of a piezoelectric transducer bonded to or embedded in a host structure can be used as damage indicator. When a credible model of the healthy structure, such as the finite element model, is available, using the impedance/admittance change information as input, it is possible to identify both the location and severity of damage. The inverse analysis, however, may be under-determined as the number of unknowns in high-frequency analysis is usually large while available input information is limited. The fundamental challenge thus is how to find a small set of solutions that cover the true damage scenario. In this research we cast the damage identification problem into a multi-objective optimization framework to tackle this challenge. With damage locations and severities as unknown variables, one of the objective functions is the difference between impedance-based model prediction in the parametric space and the actual measurements. Considering that damage occurrence generally affects only a small number of elements, we choose the sparsity of the unknown variables as another objective function, deliberately, the l 0 norm. Subsequently, a multi-objective Dividing RECTangles (DIRECT) algorithm is developed to facilitate the inverse analysis where the sparsity is further emphasized by sigmoid transformation. As a deterministic technique, this approach yields results that are repeatable and conclusive. In addition, only one algorithmic parameter, the number of function evaluations, is needed. Numerical and experimental case studies demonstrate that the proposed framework is capable of obtaining high-quality damage identification solutions with limited measurement information.

SIENA Customer Problem Statement and Requirements

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

L. Sauer; R. Clay; C. Adams

2000-08-01

This document describes the problem domain and functional requirements of the SIENA framework. The software requirements and system architecture of SIENA are specified in separate documents (called SIENA Software Requirement Specification and SIENA Software Architecture, respectively). While currently this version of the document describes the problems and captures the requirements within the Analysis domain (concentrating on finite element models), it is our intention to subsequent y expand this document to describe problems and capture requirements from the Design and Manufacturing domains. In addition, SIENA is designed to be extendible to support and integrate elements from the other domains (see SIENAmore » Software Architecture document).« less

Single scattering solution for radiative transfer through Rayleigh and aerosol atmosphere

NASA Technical Reports Server (NTRS)

Otterman, J.

1977-01-01

A solution is presented to the radiative transfer of the solar irradiation through a turbid atmosphere, based on the single-scattering approximation, i.e., an assumption that a photon that underwent scattering either leaves the top of the atmosphere or strikes the surface. The solution depends on a special idealization of the scattering phase function of the aerosols. The equations developed are subsequently applied to analyze quantitatively the enhancement of the surface irradiation and the enhancement of the scattered radiant emittance as seen from above the atmosphere, caused by the surface reflectance and atmospheric back scattering. An order of magnitude error analysis is presented.

Use of focused ultrasonication in activity-based profiling of deubiquitinating enzymes in tissue.

PubMed

Nanduri, Bindu; Shack, Leslie A; Rai, Aswathy N; Epperson, William B; Baumgartner, Wes; Schmidt, Ty B; Edelmann, Mariola J

2016-12-15

To develop a reproducible tissue lysis method that retains enzyme function for activity-based protein profiling, we compared four different methods to obtain protein extracts from bovine lung tissue: focused ultrasonication, standard sonication, mortar & pestle method, and homogenization combined with standard sonication. Focused ultrasonication and mortar & pestle methods were sufficiently effective for activity-based profiling of deubiquitinases in tissue, and focused ultrasonication also had the fastest processing time. We used focused-ultrasonicator for subsequent activity-based proteomic analysis of deubiquitinases to test the compatibility of this method in sample preparation for activity-based chemical proteomics. Copyright © 2016 Elsevier Inc. All rights reserved.

Revealing the spatial region of a future fracture nucleation in heterogeneous materials at the initial deformation stage

NASA Astrophysics Data System (ADS)

Damaskinskaya, Ekaterina; Hilarov, Vladimir; Frolov, Dmitriy

2016-11-01

The energy distributions of acoustic emission (AE) signals have been analyzed on two scaling levels corresponding to deformation of granite samples and processes on a commercial mining enterprise. It is established that, in cases of localized fracture, the energy distribution of AE signals has shape described by a power law, while a dispersed fracture is characterized by an exponential energy distribution of the AE signals. Analysis of the functional form of the energy distribution performed at the initial stage of loading allows one to recognize a spatial region in the sample where localization of the defect formation will subsequently take place.

Swarm intelligence metaheuristics for enhanced data analysis and optimization.

PubMed

Hanrahan, Grady

2011-09-21

The swarm intelligence (SI) computing paradigm has proven itself as a comprehensive means of solving complicated analytical chemistry problems by emulating biologically-inspired processes. As global optimum search metaheuristics, associated algorithms have been widely used in training neural networks, function optimization, prediction and classification, and in a variety of process-based analytical applications. The goal of this review is to provide readers with critical insight into the utility of swarm intelligence tools as methods for solving complex chemical problems. Consideration will be given to algorithm development, ease of implementation and model performance, detailing subsequent influences on a number of application areas in the analytical, bioanalytical and detection sciences.

Distribution of oxygen in silicon and its effects on electronic characteristics on a microscale

NASA Technical Reports Server (NTRS)

Gatos, H. C.; Rava, P.; Lagowski, J. J.

1980-01-01

The microdistribution of oxygen in silicon was obtained by scanning IR absorption in as grown Czochralski crystals. The crystals were subsequently submitted to various heat treatments. The profiles of the generated thermal donors were determined by spreading resistance measurements. Contrary to the prevailing views, it was found that the concentration of the activated thermal donors is not strictly a function of the oxygen concentration, but depends strongly on an additional factor, which was shown to be associated with vacancy concentration. These conclusions could only be reached on the basis of microscale characterization. In fact, commonly employed macroscale analysis has led to erroneous conclusions.

Matrix-assisted laser desorption ionization time-of-flight mass spectrometric analysis of degradation products after treatment of methylene blue aqueous solution with three-dimensionally integrated microsolution plasma

NASA Astrophysics Data System (ADS)

Shirafuji, Tatsuru; Nomura, Ayano; Hayashi, Yui; Tanaka, Kenji; Goto, Motonobu

2016-01-01

Methylene blue can be degraded in three-dimensionally integrated microsolution plasma. The degradation products have been analyzed by matrix-assisted laser desorption ionization time-of-flight (MALDI TOF) mass spectrometry to understand the degradation mechanisms. The results of MALDI TOF mass spectrometry have shown that sulfoxide is formed at the first stage of the oxidation. Then, partial oxidation proceeds on the methyl groups left on the sulfoxide. The sulfoxide is subsequently separated to two benzene derivatives. Finally, weak functional groups are removed from the benzene derivatives.

Academic Functioning and Mental Health in Adolescence: Patterns, Progressions, and Routes from Childhood.

ERIC Educational Resources Information Center

Roeser, Robert W.; Eccles, Jacquelynne S.; Freedman-Doan, Carol

1999-01-01

Examined patterns of academic functioning and mental health in middle school students and the relation of such patterns to their prior and subsequent functioning. Found variegated patterns of academic and emotional functioning at eighth grade and stability in these patterns across the high school transition. Found some long-term stability among…

Uniform Atomic Layer Deposition of Al2O3 on Graphene by Reversible Hydrogen Plasma Functionalization

PubMed Central

2017-01-01

A novel method to form ultrathin, uniform Al2O3 layers on graphene using reversible hydrogen plasma functionalization followed by atomic layer deposition (ALD) is presented. ALD on pristine graphene is known to be a challenge due to the absence of dangling bonds, leading to nonuniform film coverage. We show that hydrogen plasma functionalization of graphene leads to uniform ALD of closed Al2O3 films down to 8 nm in thickness. Hall measurements and Raman spectroscopy reveal that the hydrogen plasma functionalization is reversible upon Al2O3 ALD and subsequent annealing at 400 °C and in this way does not deteriorate the graphene’s charge carrier mobility. This is in contrast with oxygen plasma functionalization, which can lead to a uniform 5 nm thick closed film, but which is not reversible and leads to a reduction of the charge carrier mobility. Density functional theory (DFT) calculations attribute the uniform growth on both H2 and O2 plasma functionalized graphene to the enhanced adsorption of trimethylaluminum (TMA) on these surfaces. A DFT analysis of the possible reaction pathways for TMA precursor adsorption on hydrogenated graphene predicts a binding mechanism that cleans off the hydrogen functionalities from the surface, which explains the observed reversibility of the hydrogen plasma functionalization upon Al2O3 ALD. PMID:28405059

Cognitive-Behavioral Therapy for Depression Using Mind Over Mood: CBT Skill Use and Differential Symptom Alleviation.

PubMed

Hawley, Lance L; Padesky, Christine A; Hollon, Steven D; Mancuso, Enza; Laposa, Judith M; Brozina, Karen; Segal, Zindel V

2017-01-01

Cognitive-behavioral therapy (CBT) for depression is highly effective. An essential element of this therapy involves acquiring and utilizing CBT skills; however, it is unclear whether the type of CBT skill used is associated with differential symptom alleviation. Outpatients (N = 356) diagnosed with a primary mood disorder received 14 two-hour group sessions of CBT for depression, using the Mind Over Mood protocol. In each session, patients completed the Beck Depression Inventory and throughout the week they reported on their use of CBT skills: behavioral activation (BA), cognitive restructuring (CR), and core belief (CB) strategies. Bivariate latent difference score (LDS) longitudinal analyses were used to examine patterns of differential skill use and subsequent symptom change, and multigroup LDS analyses were used to determine whether longitudinal associations differed as a function of initial depression severity. Higher levels of BA use were associated with a greater subsequent decrease in depressive symptoms for patients with mild to moderate initial depression symptoms relative to those with severe symptoms. Higher levels of CR use were associated with a greater subsequent decrease in depressive symptoms, whereas higher levels of CB use were followed by a subsequent increase in depressive symptoms, regardless of initial severity. Results indicated that the type of CBT skill used is associated with differential patterns of subsequent symptom change. BA use was associated with differential subsequent change as a function of initial severity (patients with less severe depression symptoms demonstrated greater symptom improvement), whereas CR use was associated with symptom alleviation and CB use with an increase in subsequent symptoms as related to initial severity. Copyright © 2016. Published by Elsevier Ltd.

21 CFR 1316.57 - Submission of documentary evidence and affidavits and identification of witnesses subsequent to...

Code of Federal Regulations, 2014 CFR

2014-04-01

... 21 Food and Drugs 9 2014-04-01 2014-04-01 false Submission of documentary evidence and affidavits and identification of witnesses subsequent to prehearing conference. 1316.57 Section 1316.57 Food and Drugs DRUG ENFORCEMENT ADMINISTRATION, DEPARTMENT OF JUSTICE ADMINISTRATIVE FUNCTIONS, PRACTICES, AND PROCEDURES Administrative Hearings § 1316.57...

21 CFR 1316.57 - Submission of documentary evidence and affidavits and identification of witnesses subsequent to...

Code of Federal Regulations, 2012 CFR

2012-04-01

... 21 Food and Drugs 9 2012-04-01 2012-04-01 false Submission of documentary evidence and affidavits and identification of witnesses subsequent to prehearing conference. 1316.57 Section 1316.57 Food and Drugs DRUG ENFORCEMENT ADMINISTRATION, DEPARTMENT OF JUSTICE ADMINISTRATIVE FUNCTIONS, PRACTICES, AND PROCEDURES Administrative Hearings § 1316.57...

21 CFR 1316.57 - Submission of documentary evidence and affidavits and identification of witnesses subsequent to...

Code of Federal Regulations, 2013 CFR

2013-04-01

... 21 Food and Drugs 9 2013-04-01 2013-04-01 false Submission of documentary evidence and affidavits and identification of witnesses subsequent to prehearing conference. 1316.57 Section 1316.57 Food and Drugs DRUG ENFORCEMENT ADMINISTRATION, DEPARTMENT OF JUSTICE ADMINISTRATIVE FUNCTIONS, PRACTICES, AND PROCEDURES Administrative Hearings § 1316.57...

21 CFR 1316.57 - Submission of documentary evidence and affidavits and identification of witnesses subsequent to...

Code of Federal Regulations, 2011 CFR

2011-04-01

... 21 Food and Drugs 9 2011-04-01 2011-04-01 false Submission of documentary evidence and affidavits and identification of witnesses subsequent to prehearing conference. 1316.57 Section 1316.57 Food and Drugs DRUG ENFORCEMENT ADMINISTRATION, DEPARTMENT OF JUSTICE ADMINISTRATIVE FUNCTIONS, PRACTICES, AND PROCEDURES Administrative Hearings § 1316.57...

The Effect of Repetitive Saccade Execution on the Attention Network Test: Enhancing Executive Function with a Flick of the Eyes

ERIC Educational Resources Information Center

Edlin, James M.; Lyle, Keith B.

2013-01-01

The simple act of repeatedly looking left and right can enhance subsequent cognition, including divergent thinking, detection of matching letters from visual arrays, and memory retrieval. One hypothesis is that saccade execution enhances subsequent cognition by altering attentional control. To test this hypothesis, we compared performance…

Traditional measures of normal anal sphincter function using high-resolution anorectal manometry (HRAM) in 115 healthy volunteers.

PubMed

Carrington, E V; Brokjaer, A; Craven, H; Zarate, N; Horrocks, E J; Palit, S; Jackson, W; Duthie, G S; Knowles, C H; Lunniss, P J; Scott, S M

2014-05-01

High-resolution anorectal manometry (HRAM) is a relatively new method for collection and interpretation of data relevant to sphincteric function, and for the first time allows a global appreciation of the anorectum as a functional unit. Historically, traditional anal manometry has been plagued by lack of standardization and healthy volunteer data of variable quality. The aims of this study were: (i) to obtain normative data sets for traditional measures of anorectal function using HRAM in healthy subjects and; (ii) to qualitatively describe novel physiological phenomena, which may be of future relevance when this method is applied to patients. 115 healthy subjects (96 female) underwent HRAM using a 10 channel, 12F solid-state catheter. Measurements were performed during rest, squeeze, cough, and simulated defecation (push). Data were displayed as color contour plots and analysed using a commercially available manometric system (Solar GI HRM v9.1, Medical Measurement Systems). Associations between age, gender and parity were subsequently explored. HRAM color contour plots provided clear delineation of the high-pressure zone within the anal canal and showed recruitment during maneuvers that altered intra-anal pressures. Automated analysis produced quantitative data, which have been presented on the basis of gender and parity due to the effect of these covariates on some sphincter functions. In line with traditional manometry, some age and gender differences were seen. Males had a greater functional anal canal length and anal pressures during the cough maneuver. Parity in females was associated with reduced squeeze increments. The study provides a large healthy volunteer dataset and parameters of traditional measures of anorectal function. A number of novel phenomena are appreciated, the significance of which will require further analysis and comparisons with patient populations. © 2014 John Wiley & Sons Ltd.

The short Synacthen (corticotropin) test can be used to predict recovery of hypothalamo-pituitary-adrenal axis function.

PubMed

Pofi, Riccardo; Feliciano, Chona; Sbardella, Emilia; Argese, Nicola; Woods, Conor P; Grossman, Ashley B; Jafar-Mohammadi, Bahram; Gleeson, Helena; Lenzi, Andrea; Isidori, Andrea M; Tomlinson, Jeremy W

2018-05-25

The 250μg Short Synacthen (corticotropin) Test (SST) is the most commonly used tool to assess hypothalamo-pituitary-adrenal (HPA) axis function. There are many potentially reversible causes of adrenal insufficiency (AI), but currently no data to guide clinicians as to the frequency of repeat testing or likelihood of HPA axis recovery. To use the SST results to predict recovery of adrenal function. A retrospective analysis of data from 1912 SSTs. 776 patients with reversible causes of AI were identified who had at least two SSTs performed. A subgroup analysis was performed on individuals previously treated with suppressive doses of glucocorticoids (n=110). Recovery of HPA axis function. SST 30-minute cortisol levels above or below 350nmol/L (12.7μg/dL) best predicted HPA axis recovery (AUC ROC=0.85; median recovery time 334 vs. 1368 days, p=8.5x10-13): 99% of patients with a 30-minute cortisol >350nmol/L recovered adrenal function within 4-years, compared with 49% in those with cortisol levels <350nmol/L. In patients exposed to suppressive doses of glucocorticoids, delta cortisol (30-minute - basal) was the best predictor of recovery (AUC ROC = 0.77; median recovery time 262 vs. 974 days, p=7.0x10-6). No patient with a delta cortisol <100nmol (3.6μg/dL) and a subsequent random cortisol <200nmol/L (7.3μg/dL) measured approximately 1-year later recovered HPA axis function. Cortisol levels across an SST can be used to predict recovery of AI and may guide the frequency of repeat testing and inform both clinicians and patients as to the likelihood of restoration of HPA axis function.

Striatal functional connectivity changes following specific balance training in elderly people: MRI results of a randomized controlled pilot study.

PubMed

Magon, Stefano; Donath, Lars; Gaetano, Laura; Thoeni, Alain; Radue, Ernst-Wilhelm; Faude, Oliver; Sprenger, Till

2016-09-01

Practice-induced effects of specific balance training on brain structure and activity in elderly people are largely unknown. In the present study, we investigated morphological and functional brain changes following slacking training (balancing over nylon ribbons) in a group of elderly people. Twenty-eight healthy volunteers were recruited and randomly assigned to the intervention (mean age: 62.3±5.4years) or control group (mean age: 61.8±5.3years). The intervention group completed six-weeks of slackline training. Brain morphological changes were investigated using voxel-based morphometry and functional connectivity changes were computed via independent component analysis and seed-based analyses. All analyses were applied to the whole sample and to a subgroup of participants who improved in slackline performance. The repeated measures analysis of variance showed a significant interaction effect between groups and sessions. Specifically, the Tukey post-hoc analysis revealed a significantly improved slackline standing performance after training for the left leg stance time (pre: 4.5±3.6s vs. 26.0±30.0s, p<0.038) as well as for tandem stance time (pre: 1.4±0.6s vs. post: 4.5±4.0s, p=0.003) in the intervention group. No significant changes in balance performance were observed in the control group. The MRI analysis did not reveal morphological or functional connectivity differences before or after the training between the intervention and control groups (whole sample). However, subsequent analysis in subjects with improved slackline performance showed a decrease of connectivity between the striatum and other brain areas during the training period. These preliminary results suggest that improved balance performance with slackline training goes along with an increased efficiency of the striatal network. Copyright © 2016 Elsevier B.V. All rights reserved.

Successful ageing: A study of the literature using citation network analysis.

PubMed

Kusumastuti, Sasmita; Derks, Marloes G M; Tellier, Siri; Di Nucci, Ezio; Lund, Rikke; Mortensen, Erik Lykke; Westendorp, Rudi G J

2016-11-01

Ageing is accompanied by an increased risk of disease and a loss of functioning on several bodily and mental domains and some argue that maintaining health and functioning is essential for a successful old age. Paradoxically, studies have shown that overall wellbeing follows a curvilinear pattern with the lowest point at middle age but increases thereafter up to very old age. To shed further light on this paradox, we reviewed the existing literature on how scholars define successful ageing and how they weigh the contribution of health and functioning to define success. We performed a novel, hypothesis-free and quantitative analysis of citation networks exploring the literature on successful ageing that exists in the Web of Science Core Collection Database using the CitNetExplorer software. Outcomes were visualized using timeline-based citation patterns. The clusters and sub-clusters of citation networks identified were starting points for in-depth qualitative analysis. Within the literature from 1902 through 2015, two distinct citation networks were identified. The first cluster had 1146 publications and 3946 citation links. It focused on successful ageing from the perspective of older persons themselves. Analysis of the various sub-clusters emphasized the importance of coping strategies, psycho-social engagement, and cultural differences. The second cluster had 609 publications and 1682 citation links and viewed successful ageing based on the objective measurements as determined by researchers. Subsequent sub-clustering analysis pointed to different domains of functioning and various ways of assessment. In the current literature two mutually exclusive concepts of successful ageing are circulating that depend on whether the individual himself or an outsider judges the situation. These different points of view help to explain the disability paradox, as successful ageing lies in the eyes of the beholder. Copyright © 2016 The Authors. Published by Elsevier Ireland Ltd.. All rights reserved.

Effect of roughage on rumen microbiota composition in the efficient feed converter and sturdy Indian Jaffrabadi buffalo (Bubalus bubalis).

PubMed

Nathani, Neelam M; Patel, Amrutlal K; Mootapally, Chandra Shekar; Reddy, Bhaskar; Shah, Shailesh V; Lunagaria, Pravin M; Kothari, Ramesh K; Joshi, Chaitanya G

2015-12-29

The rumen microbiota functions as an effective system for conversion of dietary feed to microbial proteins and volatile fatty acids. In the present study, metagenomic approach was applied to elucidate the buffalo rumen microbiome of Jaffrabadi buffalo adapted to varied dietary treatments with the hypothesis that the microbial diversity and subsequent in the functional capacity will alter with diet change and enhance our knowledge of effect of microbe on host physiology. Eight adult animals were gradually adapted to an increasing roughage diet (4 animals each with green and dry roughage) containing 50:50 (J1), 75:25 (J2) and 100:0 (J3) roughage to concentrate proportion for 6 weeks. Metagenomic sequences of solid (fiber adherent microbiota) and liquid (fiber free microbiota) fractions obtained using Ion Torrent PGM platform were analyzed using MG-RAST server and CAZymes approach. Taxonomic analysis revealed that Bacteroidetes was the most abundant phylum followed by Firmicutes, Fibrobacter and Proteobacteria. Functional analysis revealed protein (25-30 %) and carbohydrate (15-20 %) metabolism as the dominant categories. Principal component analysis demonstrated that roughage proportion, fraction of rumen and type of forage affected rumen microbiome at taxonomic as well as functional level. Rumen metabolite study revealed that rumen fluid nitrogen content reduced in high roughage diet fed animals and pathway analysis showed reduction in the genes coding enzymes involved in methanogenesis pathway. CAZyme annotation revealed the abundance of genes encoding glycoside hydrolases (GH), with the GH3 family most abundant followed by GH2 and GH13 in all samples. Results reveals that high roughage diet feed improved microbial protein synthesis and reduces methane emission. CAZyme analysis indicated the importance of microbiome in feed component digestion for fulfilling energy requirements of the host. The findings help determine the role of rumen microbes in plant polysaccharide breakdown and in developing strategies to maximize productivity in ruminants.

Sequential Linker Installation: Precise Placement of Functional Groups in Multivariate Metal-Organic Frameworks

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

Yuan, S; Lu, WG; Chen, YP

2015-03-11

A unique strategy, sequential linker installation (SLI), has been developed to construct multivariate MOFs with functional groups precisely positioned. PCN-700, a Zr-MOF with eight-connected Zr6O4(OH)(8)(H2O)(4) clusters, has been judiciously designed; the Zr-6 clusters in this MOF are arranged in such a fashion that, by replacement of terminal OH-/H2O ligands, subsequent insertion of linear dicarboxylate linkers is achieved. We demonstrate that linkers with distinct lengths and functionalities can be sequentially installed into PCN-700. Single-crystal to single-crystal transformation is realized so that the positions of the subsequently installed linkers are pinpointed via single-crystal X-ray diffraction analyses. This methodology provides a powerful toolmore » to construct multivariate MOFs with precisely positioned functionalities in the desired proximity, which would otherwise be difficult to achieve.« less

Do Children's Executive Functions Account for Associations Between Early Autonomy-Supportive Parenting and Achievement Through High School?

PubMed Central

Bindman, Samantha W.; Pomerantz, Eva M.; Roisman, Glenn I.

2015-01-01

This study evaluated whether the positive association between early autonomy-supportive parenting and children's subsequent achievement is mediated by children's executive functions. Using observations of mothers’ parenting from the NICHD Study of Early Child Care and Youth Development (N = 1,306), analyses revealed that mothers’ autonomy support over the first 3 years of life predicted enhanced executive functions (i.e., inhibition, delay of gratification, and sustained attention) during the year prior to kindergarten and academic achievement in elementary and high school even when mothers’ warmth and cognitive stimulation, as well as other factors (e.g., children's early general cognitive skills and mothers’ educational attainment) were covaried. Mediation analyses demonstrated that over and above other attributes (e.g., temperament), children's executive functions partially accounted for the association between early autonomy-supportive parenting and children's subsequent achievement. PMID:26366009

Do Children's Executive Functions Account for Associations Between Early Autonomy-Supportive Parenting and Achievement Through High School?

PubMed

Bindman, Samantha W; Pomerantz, Eva M; Roisman, Glenn I

2015-08-01

This study evaluated whether the positive association between early autonomy-supportive parenting and children's subsequent achievement is mediated by children's executive functions. Using observations of mothers' parenting from the NICHD Study of Early Child Care and Youth Development ( N = 1,306), analyses revealed that mothers' autonomy support over the first 3 years of life predicted enhanced executive functions (i.e., inhibition, delay of gratification, and sustained attention) during the year prior to kindergarten and academic achievement in elementary and high school even when mothers' warmth and cognitive stimulation, as well as other factors (e.g., children's early general cognitive skills and mothers' educational attainment) were covaried. Mediation analyses demonstrated that over and above other attributes (e.g., temperament), children's executive functions partially accounted for the association between early autonomy-supportive parenting and children's subsequent achievement.

Marital Status as a Moderating Factor in the Process of Disablement.

PubMed

Kail, Ben Lennox

2016-02-01

To test current marital status as a moderator on the influence of depressive symptoms and chronic conditions on subsequent functional limitations. Data come from the Health and Retirement Study (HRS; 1998-2010). Hierarchal linear modeling models tested differences in functional limitations among a sample of 20,215 people. At baseline, married people suffered from fewer subsequent functional limitations than the unmarried. Moreover, limited evidence suggests the influence of depressive symptoms was greater for the married than the unmarried; however, the influence of chronic conditions was consistently attenuated for married people. Accounting for differences in prior health, work, socioeconomic status, and health behaviors did not explain the moderating influence of marital status on the associations between symptoms of depression and chronic conditions with functional limitations. This research highlights the need to identify potential modifiers that may help disrupt the process of disablement among both the married and the unmarried alike. © The Author(s) 2015.

Microbial functional diversity plays an important role in the degradation of polyhydroxybutyrate (PHB) in soil.

PubMed

Dey, Samrat; Tribedi, Prosun

2018-03-01

Towards bioremediation of recalcitrant materials like synthetic polymer, soil has been recognized as a traditional site for disposal and subsequent degradation as some microorganisms in soil can degrade the polymer in a non-toxic, cost-effective, and environment friendly way. Microbial functional diversity is a constituent of biodiversity that includes wide range of metabolic activities that can influence numerous aspects of ecosystem functioning like ecosystem stability, nutrient availability, ecosystem dynamics, etc. Thus, in the current study, we assumed that microbial functional diversity could play an important role in polymer degradation in soil. To verify this hypothesis, we isolated soil from five different sites of landfill and examined several microbiological parameters wherein we observed a significant variation in heterotrophic microbial count as well as microbial activities among the soil microcosms tested. Multivariate analysis (principle component analysis) based on the carbon sources utilization pattern revealed that soil microcosms showed different metabolic patterns suggesting the variable distribution of microorganisms among the soil microcosms tested. Since microbial functional diversity depends on both microbial richness and evenness, Shannon diversity index was determined to measure microbial richness and Gini coefficient was determined to measure microbial evenness. The tested soil microcosms exhibited variation in both microbial richness and evenness suggesting the considerable difference in microbial functional diversity among the tested microcosms. We then measured polyhydroxybutyrate (PHB) degradation in soil microcosms after desired period of incubation of PHB in soil wherein we found that soil microcosms having higher functional diversity showed enhanced PHB degradation and soil microcosms having lower functional diversity showed reduced PHB degradation. We also noticed that all the tested soil microcosms showed similar pattern in both microbial functional diversity and PHB degradation suggesting a strong positive correlation ( r  = 0.95) between microbial functional diversity and PHB degradation. Thus, the results demonstrate that microbial functional diversity plays an important role in PHB degradation in soil by exhibiting versatile microbial metabolic potentials that lead to the enhanced degradation of PHB.

SLUDGE TREATMENT PROJECT KOP CONCEPTUAL DESIGN CONTROL DECISION REPORT

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

CARRO CA

2010-03-09

This control decision addresses the Knock-Out Pot (KOP) Disposition KOP Processing System (KPS) conceptual design. The KPS functions to (1) retrieve KOP material from canisters, (2) remove particles less than 600 {micro}m in size and low density materials from the KOP material, (3) load the KOP material into Multi-Canister Overpack (MCO) baskets, and (4) stage the MCO baskets for subsequent loading into MCOs. Hazard and accident analyses of the KPS conceptual design have been performed to incorporate safety into the design process. The hazard analysis is documented in PRC-STP-00098, Knock-Out Pot Disposition Project Conceptual Design Hazard Analysis. The accident analysismore » is documented in PRC-STP-CN-N-00167, Knock-Out Pot Disposition Sub-Project Canister Over Lift Accident Analysis. Based on the results of these analyses, and analyses performed in support of MCO transportation and MCO processing and storage activities at the Cold Vacuum Drying Facility (CVDF) and Canister Storage Building (CSB), control decision meetings were held to determine the controls required to protect onsite and offsite receptors and facility workers. At the conceptual design stage, these controls are primarily defined by their safety functions. Safety significant structures, systems, and components (SSCs) that could provide the identified safety functions have been selected for the conceptual design. It is anticipated that some safety SSCs identified herein will be reclassified based on hazard and accident analyses performed in support of preliminary and detailed design.« less

A multi-tissue type genome-scale metabolic network for analysis of whole-body systems physiology

PubMed Central

2011-01-01

Background Genome-scale metabolic reconstructions provide a biologically meaningful mechanistic basis for the genotype-phenotype relationship. The global human metabolic network, termed Recon 1, has recently been reconstructed allowing the systems analysis of human metabolic physiology and pathology. Utilizing high-throughput data, Recon 1 has recently been tailored to different cells and tissues, including the liver, kidney, brain, and alveolar macrophage. These models have shown utility in the study of systems medicine. However, no integrated analysis between human tissues has been done. Results To describe tissue-specific functions, Recon 1 was tailored to describe metabolism in three human cells: adipocytes, hepatocytes, and myocytes. These cell-specific networks were manually curated and validated based on known cellular metabolic functions. To study intercellular interactions, a novel multi-tissue type modeling approach was developed to integrate the metabolic functions for the three cell types, and subsequently used to simulate known integrated metabolic cycles. In addition, the multi-tissue model was used to study diabetes: a pathology with systemic properties. High-throughput data was integrated with the network to determine differential metabolic activity between obese and type II obese gastric bypass patients in a whole-body context. Conclusion The multi-tissue type modeling approach presented provides a platform to study integrated metabolic states. As more cell and tissue-specific models are released, it is critical to develop a framework in which to study their interdependencies. PMID:22041191

Multi-Parametric Analysis and Modeling of Relationships between Mitochondrial Morphology and Apoptosis

PubMed Central

Reis, Yara; Wolf, Thomas; Brors, Benedikt; Hamacher-Brady, Anne; Eils, Roland; Brady, Nathan R.

2012-01-01

Mitochondria exist as a network of interconnected organelles undergoing constant fission and fusion. Current approaches to study mitochondrial morphology are limited by low data sampling coupled with manual identification and classification of complex morphological phenotypes. Here we propose an integrated mechanistic and data-driven modeling approach to analyze heterogeneous, quantified datasets and infer relations between mitochondrial morphology and apoptotic events. We initially performed high-content, multi-parametric measurements of mitochondrial morphological, apoptotic, and energetic states by high-resolution imaging of human breast carcinoma MCF-7 cells. Subsequently, decision tree-based analysis was used to automatically classify networked, fragmented, and swollen mitochondrial subpopulations, at the single-cell level and within cell populations. Our results revealed subtle but significant differences in morphology class distributions in response to various apoptotic stimuli. Furthermore, key mitochondrial functional parameters including mitochondrial membrane potential and Bax activation, were measured under matched conditions. Data-driven fuzzy logic modeling was used to explore the non-linear relationships between mitochondrial morphology and apoptotic signaling, combining morphological and functional data as a single model. Modeling results are in accordance with previous studies, where Bax regulates mitochondrial fragmentation, and mitochondrial morphology influences mitochondrial membrane potential. In summary, we established and validated a platform for mitochondrial morphological and functional analysis that can be readily extended with additional datasets. We further discuss the benefits of a flexible systematic approach for elucidating specific and general relationships between mitochondrial morphology and apoptosis. PMID:22272225

Non-Pharmacologic Interventions for Older Adults with Subjective Cognitive Decline: Systematic Review, Meta-Analysis, and Preliminary Recommendations.

PubMed

Smart, Colette M; Karr, Justin E; Areshenkoff, Corson N; Rabin, Laura A; Hudon, Carol; Gates, Nicola; Ali, Jordan I; Arenaza-Urquijo, Eider M; Buckley, Rachel F; Chetelat, Gael; Hampel, Harald; Jessen, Frank; Marchant, Natalie L; Sikkes, Sietske A M; Tales, Andrea; van der Flier, Wiesje M; Wesselman, Linda

2017-09-01

In subjective cognitive decline (SCD), older adults present with concerns about self-perceived cognitive decline but are found to have clinically normal function. However, a significant proportion of those adults are subsequently found to develop mild cognitive impairment, Alzheimer's dementia or other neurocognitive disorder. In other cases, SCD may be associated with mood, personality, and physical health concerns. Regardless of etiology, adults with SCD may benefit from interventions that could enhance current function or slow incipient cognitive decline. The objective of this systematic review and meta-analysis, conducted in accordance with the PRISMA guidelines, is to examine the benefits of non-pharmacologic intervention (NPI) in persons with SCD. Inclusion criteria were studies of adults aged 55 + with SCD defined using published criteria, receiving NPI or any control condition, with cognitive, behavioural, or psychological outcomes in controlled trails. Published empirical studies were obtained through a standardized search of CINAHL Complete, Cochrane Central Register of Controlled Trials, MEDLINE with Full Text, PsycINFO, and PsycARTICLES, supplemented by a manual retrieval of relevant articles. Study quality and bias was determined using PEDro. Nine studies were included in the review and meta-analysis. A wide range of study quality was observed. Overall, a small effect size was found on cognitive outcomes, greater for cognitive versus other intervention types. The available evidence suggests that NPI may benefit current cognitive function in persons with SCD. Recommendations are provided to improve future trials of NPI in SCD.

Identifying arsenic trioxide (ATO) functions in leukemia cells by using time series gene expression profiles.

PubMed

Yang, Hong; Lin, Shan; Cui, Jingru

2014-02-10

Arsenic trioxide (ATO) is presently the most active single agent in the treatment of acute promyelocytic leukemia (APL). In order to explore the molecular mechanism of ATO in leukemia cells with time series, we adopted bioinformatics strategy to analyze expression changing patterns and changes in transcription regulation modules of time series genes filtered from Gene Expression Omnibus database (GSE24946). We totally screened out 1847 time series genes for subsequent analysis. The KEGG (Kyoto encyclopedia of genes and genomes) pathways enrichment analysis of these genes showed that oxidative phosphorylation and ribosome were the top 2 significantly enriched pathways. STEM software was employed to compare changing patterns of gene expression with assigned 50 expression patterns. We screened out 7 significantly enriched patterns and 4 tendency charts of time series genes. The result of Gene Ontology showed that functions of times series genes mainly distributed in profiles 41, 40, 39 and 38. Seven genes with positive regulation of cell adhesion function were enriched in profile 40, and presented the same first increased model then decreased model as profile 40. The transcription module analysis showed that they mainly involved in oxidative phosphorylation pathway and ribosome pathway. Overall, our data summarized the gene expression changes in ATO treated K562-r cell lines with time and suggested that time series genes mainly regulated cell adhesive. Furthermore, our result may provide theoretical basis of molecular biology in treating acute promyelocytic leukemia. Copyright © 2013 Elsevier B.V. All rights reserved.

Whole-Genome Analysis of a Novel Fish Reovirus (MsReV) Discloses Aquareovirus Genomic Structure Relationship with Host in Saline Environments.

PubMed

Chen, Zhong-Yuan; Gao, Xiao-Chan; Zhang, Qi-Ya

2015-08-03

Aquareoviruses are serious pathogens of aquatic animals. Here, genome characterization and functional gene analysis of a novel aquareovirus, largemouth bass Micropterus salmoides reovirus (MsReV), was described. It comprises 11 dsRNA segments (S1-S11) covering 24,024 bp, and encodes 12 putative proteins including the inclusion forming-related protein NS87 and the fusion-associated small transmembrane (FAST) protein NS22. The function of NS22 was confirmed by expression in fish cells. Subsequently, MsReV was compared with two representative aquareoviruses, saltwater fish turbot Scophthalmus maximus reovirus (SMReV) and freshwater fish grass carp reovirus strain 109 (GCReV-109). MsReV NS87 and NS22 genes have the same structure and function with those of SMReV, whereas GCReV-109 is either missing the coiled-coil region in NS79 or the gene-encoding NS22. Significant similarities are also revealed among equivalent genome segments between MsReV and SMReV, but a difference is found between MsReV and GCReV-109. Furthermore, phylogenetic analysis showed that 13 aquareoviruses could be divided into freshwater and saline environments subgroups, and MsReV was closely related to SMReV in saline environments. Consequently, these viruses from hosts in saline environments have more genomic structural similarities than the viruses from hosts in freshwater. This is the first study of the relationships between aquareovirus genomic structure and their host environments.

Wronski's Foundations of Mathematics.

PubMed

Wagner, Roi

2016-09-01

Argument This paper reconstructs Wronski's philosophical foundations of mathematics. It uses his critique of Lagrange's algebraic analysis as a vignette to introduce the problems that he raised, and argues that these problems have not been properly appreciated by his contemporaries and subsequent commentators. The paper goes on to reconstruct Wronski's mathematical law of creation and his notions of theory and techne, in order to put his objections to Lagrange in their philosophical context. Finally, Wronski's proof of his universal law (the expansion of a given function by any series of functions) is reviewed in terms of the above reconstruction. I argue that Wronski's philosophical approach poses an alternative to the views of his contemporary mainstream mathematicians, which brings up the contingency of their choices, and bridges the foundational concerns of early modernity with those of the twentieth-century foundations crisis. I also argue that Wronski's views may be useful to contemporary philosophy of mathematical practice, if they are read against their metaphysical grain.

Reproductive capability in dogs with canine leukocyte adhesion deficiency treated with nonmyeloablative conditioning prior to allogeneic hematopoietic stem cell transplantation

PubMed Central

Burkholder, Tanya H.; Colenda, Lyn; Tuschong, Laura M.; Starost, Matthew F.; Bauer, Thomas R.; Hickstein, Dennis D.

2006-01-01

Nonmyeloablative conditioning regimens are increasingly replacing myeolablative conditioning prior to allogeneic hematopoietic stem cell transplantation (SCT). The recent advent of these conditioning regimens has limited the assessment of the long-term effects of this treatment, including analysis of reproductive function. To address the question of reproductive function after nonmyeloablative transplantation, we analyzed a cohort of young dogs with the genetic disease canine leukocyte adhesion deficiency that were treated with a nonmyeloablative dose of 200 cGy total body irradiation followed by matched-littermate SCT. Five males and 5 females entered puberty; all 5 males and 4 females subsequently sired or delivered litters following transplantation. We demonstrate that fertility is intact and dogs have uncomplicated parturitions following nonmyeloablative conditioning for SCT. These results are encouraging for children and adults of childbearing age who receive similar conditioning regimens prior to allogeneic transplantation. PMID:16645166

Prospect evaluation as a function of numeracy and probability denominator.

PubMed

Millroth, Philip; Juslin, Peter

2015-05-01

This study examines how numeracy and probability denominator (a direct-ratio probability, a relative frequency with denominator 100, a relative frequency with denominator 10,000) affect the evaluation of prospects in an expected-value based pricing task. We expected that numeracy would affect the results due to differences in the linearity of number perception and the susceptibility to denominator neglect with different probability formats. An analysis with functional measurement verified that participants integrated value and probability into an expected value. However, a significant interaction between numeracy and probability format and subsequent analyses of the parameters of cumulative prospect theory showed that the manipulation of probability denominator changed participants' psychophysical response to probability and value. Standard methods in decision research may thus confound people's genuine risk attitude with their numerical capacities and the probability format used. Copyright © 2015 Elsevier B.V. All rights reserved.

Functional Fe3O4@ZnO magnetic nanoparticle-assisted enrichment and enzymatic digestion of phosphoproteins from saliva.

PubMed

Chen, Wei-Yu; Chen, Yu-Chie

2010-11-01

Saliva contains various proteins, particularly abundant are phosphoproteins, that may be related to disease occurrences and that play significant roles in a biological system. Thus, medical diagnostics will benefit tremendously if disease-related protein biomarkers are discovered from saliva. In this paper, we propose and demonstrate an approach using functional zinc oxide coated iron oxide magnetic nanoparticles (Fe(3)O(4)@ZnO MNPs) as affinity probes to selectively enrich phosphoproteins from complex saliva samples and as microwave absorbers to assist the enrichment and subsequent tryptic digestion of trapped proteins under microwave heating. The target species trapped by MNPs were characterized by matrix-assisted laser desorption/ionization mass spectrometry (MALDI MS) combined with protein database search. Entire analysis time was shortened to less than 20 min. The detection limit of this approach for a monophosphopeptide was as low as 250 pM (10 μL).

The difference between two random mixed quantum states: exact and asymptotic spectral analysis

NASA Astrophysics Data System (ADS)

Mejía, José; Zapata, Camilo; Botero, Alonso

2017-01-01

We investigate the spectral statistics of the difference of two density matrices, each of which is independently obtained by partially tracing a random bipartite pure quantum state. We first show how a closed-form expression for the exact joint eigenvalue probability density function for arbitrary dimensions can be obtained from the joint probability density function of the diagonal elements of the difference matrix, which is straightforward to compute. Subsequently, we use standard results from free probability theory to derive a relatively simple analytic expression for the asymptotic eigenvalue density (AED) of the difference matrix ensemble, and using Carlson’s theorem, we obtain an expression for its absolute moments. These results allow us to quantify the typical asymptotic distance between the two random mixed states using various distance measures; in particular, we obtain the almost sure asymptotic behavior of the operator norm distance and the trace distance.

From random microstructures to representative volume elements

NASA Astrophysics Data System (ADS)

Zeman, J.; Šejnoha, M.

2007-06-01

A unified treatment of random microstructures proposed in this contribution opens the way to efficient solutions of large-scale real world problems. The paper introduces a notion of statistically equivalent periodic unit cell (SEPUC) that replaces in a computational step the actual complex geometries on an arbitrary scale. A SEPUC is constructed such that its morphology conforms with images of real microstructures. Here, the appreciated two-point probability function and the lineal path function are employed to classify, from the statistical point of view, the geometrical arrangement of various material systems. Examples of statistically equivalent unit cells constructed for a unidirectional fibre tow, a plain weave textile composite and an irregular-coursed masonry wall are given. A specific result promoting the applicability of the SEPUC as a tool for the derivation of homogenized effective properties that are subsequently used in an independent macroscopic analysis is also presented.

Missing data exploration: highlighting graphical presentation of missing pattern

PubMed Central

2015-01-01

Functions shipped with R base can fulfill many tasks of missing data handling. However, because the data volume of electronic medical record (EMR) system is always very large, more sophisticated methods may be helpful in data management. The article focuses on missing data handling by using advanced techniques. There are three types of missing data, that is, missing completely at random (MCAR), missing at random (MAR) and not missing at random (NMAR). This classification system depends on how missing values are generated. Two packages, Multivariate Imputation by Chained Equations (MICE) and Visualization and Imputation of Missing Values (VIM), provide sophisticated functions to explore missing data pattern. In particular, the VIM package is especially helpful in visual inspection of missing data. Finally, correlation analysis provides information on the dependence of missing data on other variables. Such information is useful in subsequent imputations. PMID:26807411

The Multi-Step CADIS method for shutdown dose rate calculations and uncertainty propagation

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

Ibrahim, Ahmad M.; Peplow, Douglas E.; Grove, Robert E.

2015-12-01

Shutdown dose rate (SDDR) analysis requires (a) a neutron transport calculation to estimate neutron flux fields, (b) an activation calculation to compute radionuclide inventories and associated photon sources, and (c) a photon transport calculation to estimate final SDDR. In some applications, accurate full-scale Monte Carlo (MC) SDDR simulations are needed for very large systems with massive amounts of shielding materials. However, these simulations are impractical because calculation of space- and energy-dependent neutron fluxes throughout the structural materials is needed to estimate distribution of radioisotopes causing the SDDR. Biasing the neutron MC calculation using an importance function is not simple becausemore » it is difficult to explicitly express the response function, which depends on subsequent computational steps. Furthermore, the typical SDDR calculations do not consider how uncertainties in MC neutron calculation impact SDDR uncertainty, even though MC neutron calculation uncertainties usually dominate SDDR uncertainty.« less

Biomechanical Analysis of the Efficacy of Locking Plates during Cyclic Loading in Metacarpal Fractures

PubMed Central

Meffert, Rainer H.; Raschke, Michael J.; Blunk, Torsten; Ochman, Sabine

2014-01-01

Purpose. To analyse the biomechanical characteristics of locking plates under cyclic loading compared to a nonlocking plate in a diaphyseal metacarpal fracture. Methods. Oblique diaphyseal shaft fractures in porcine metacarpal bones were created in a biomechanical fracture model. An anatomical reduction and stabilization with a nonlocking and a comparable locking plate in mono- or bicortical screw fixation followed. Under cyclic loading, the displacement, and in subsequent load-to-failure tests, the maximum load and stiffness were measured. Results. For the monocortical screw fixation of the locking plate, a similar displacement, maximum load, and stiffness could be demonstrated compared to the bicortical screw fixation of the nonlocking plate. Conclusions. Locking plates in monocortical configuration may function as a useful alternative to the currently common treatment with bicortical fixations. Thereby, irritation of the flexor tendons would be avoided without compromising the stability, thus enabling the necessary early functional rehabilitation. PMID:24757429

Decoupled ARX and RBF Neural Network Modeling Using PCA and GA Optimization for Nonlinear Distributed Parameter Systems.

PubMed

Zhang, Ridong; Tao, Jili; Lu, Renquan; Jin, Qibing

2018-02-01

Modeling of distributed parameter systems is difficult because of their nonlinearity and infinite-dimensional characteristics. Based on principal component analysis (PCA), a hybrid modeling strategy that consists of a decoupled linear autoregressive exogenous (ARX) model and a nonlinear radial basis function (RBF) neural network model are proposed. The spatial-temporal output is first divided into a few dominant spatial basis functions and finite-dimensional temporal series by PCA. Then, a decoupled ARX model is designed to model the linear dynamics of the dominant modes of the time series. The nonlinear residual part is subsequently parameterized by RBFs, where genetic algorithm is utilized to optimize their hidden layer structure and the parameters. Finally, the nonlinear spatial-temporal dynamic system is obtained after the time/space reconstruction. Simulation results of a catalytic rod and a heat conduction equation demonstrate the effectiveness of the proposed strategy compared to several other methods.

Predictive Compensator Optimization for Head Tracking Lag in Virtual Environments

NASA Technical Reports Server (NTRS)

Adelstein, Barnard D.; Jung, Jae Y.; Ellis, Stephen R.

2001-01-01

We examined the perceptual impact of plant noise parameterization for Kalman Filter predictive compensation of time delays intrinsic to head tracked virtual environments (VEs). Subjects were tested in their ability to discriminate between the VE system's minimum latency and conditions in which artificially added latency was then predictively compensated back to the system minimum. Two head tracking predictors were parameterized off-line according to cost functions that minimized prediction errors in (1) rotation, and (2) rotation projected into translational displacement with emphasis on higher frequency human operator noise. These predictors were compared with a parameterization obtained from the VE literature for cost function (1). Results from 12 subjects showed that both parameterization type and amount of compensated latency affected discrimination. Analysis of the head motion used in the parameterizations and the subsequent discriminability results suggest that higher frequency predictor artifacts are contributory cues for discriminating the presence of predictive compensation.

What is the role of impression management in adolescent cigarette smoking?

PubMed

O'Callaghan, F; Doyle, J

2001-01-01

This study examined the role of impression management in cigarette smoking by linking the constructs of self-monitoring, perceived success in impression management, self-esteem and social anxiety among nonsmokers (NS), occasional smokers (OS), and frequent smokers (FS). High school students (N=243) in years 8-12 completed a questionnaire assessing the above-mentioned variables. Multivariate discriminant function analysis and a priori contrasts were used to analyze the data. In comparison to OS, FS and NS had the lowest levels of self-monitoring, perceived success in impression management and self-esteem, while having the highest levels of social anxiety. Cigarette use may serve an impression management function during adolescence and subsequently influences OS' level of smoking. Intervention programs need to give greater consideration to providing adolescents with alternative strategies for both social acceptance and the acquisition and maintenance of self-esteem.

What Has Natural Variation Taught Us about Plant Development, Physiology, and Adaptation?

PubMed Central

Alonso-Blanco, Carlos; Aarts, Mark G.M.; Bentsink, Leonie; Keurentjes, Joost J.B.; Reymond, Matthieu; Vreugdenhil, Dick; Koornneef, Maarten

2009-01-01

Nearly 100 genes and functional polymorphisms underlying natural variation in plant development and physiology have been identified. In crop plants, these include genes involved in domestication traits, such as those related to plant architecture, fruit and seed structure and morphology, as well as yield and quality traits improved by subsequent crop breeding. In wild plants, comparable traits have been dissected mainly in Arabidopsis thaliana. In this review, we discuss the major contributions of the analysis of natural variation to our understanding of plant development and physiology, focusing in particular on the timing of germination and flowering, plant growth and morphology, primary metabolism, and mineral accumulation. Overall, functional polymorphisms appear in all types of genes and gene regions, and they may have multiple mutational causes. However, understanding this diversity in relation to adaptation and environmental variation is a challenge for which tools are now available. PMID:19574434

Development of an Algorithm for Automatic Analysis of the Impedance Spectrum Based on a Measurement Model

NASA Astrophysics Data System (ADS)

Kobayashi, Kiyoshi; Suzuki, Tohru S.

2018-03-01

A new algorithm for the automatic estimation of an equivalent circuit and the subsequent parameter optimization is developed by combining the data-mining concept and complex least-squares method. In this algorithm, the program generates an initial equivalent-circuit model based on the sampling data and then attempts to optimize the parameters. The basic hypothesis is that the measured impedance spectrum can be reproduced by the sum of the partial-impedance spectra presented by the resistor, inductor, resistor connected in parallel to a capacitor, and resistor connected in parallel to an inductor. The adequacy of the model is determined by using a simple artificial-intelligence function, which is applied to the output function of the Levenberg-Marquardt module. From the iteration of model modifications, the program finds an adequate equivalent-circuit model without any user input to the equivalent-circuit model.

Egg ovotransferrin-derived ACE inhibitory peptide IRW increases ACE2 but decreases proinflammatory genes expression in mesenteric artery of spontaneously hypertensive rats.

PubMed

Majumder, Kaustav; Liang, Guanxiang; Chen, Yanhong; Guan, LeLuo; Davidge, Sandra T; Wu, Jianping

2015-09-01

Egg ovotransferrin-derived angiotensin converting enzyme (ACE) inhibitory peptide IRW was previously shown to reduce blood pressure in spontaneously hypertensive rats through reduced vascular inflammation and increased nitric oxide-mediated vasorelaxation. The main objective of the present study was to investigate the molecular mechanism of this peptide through transcriptome analysis by RNAseq technique. Total RNA was extracted from kidney and mesenteric arteries; the RNAseq libraries (from untreated and IRW-treated groups) were constructed and subjected to sequence using HiSeq 2000 system (Illumina) system. A total of 12 764 and 13 352 genes were detected in kidney and mesenteric arteries, respectively. The differentially expressed (DE) genes between untreated and IRW-treated groups were identified and the functional analysis through ingenuity pathway analysis revealed a greater role of DE genes identified from mesenteric arteries than that of kidney in modulating various cardiovascular functions. Subsequent qPCR analysis further confirmed that IRW significantly increased the expression of ACE-2, ABCB-1, IRF-8, and CDH-1 while significantly decreased the expression ICAM-1 and VCAM-1 in mesenteric arteries. Our research showed for the first time that ACE inhibitory peptide IRW could contribute to its antihypertensive activity through increased ACE2 and decreased proinflammatory genes expression. © 2015 The Authors. Molecular Nutrition & Food Research published by Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Interaction of Pb(II) and biofilm associated extracellular polymeric substances of a marine bacterium Pseudomonas pseudoalcaligenes NP103

NASA Astrophysics Data System (ADS)

Kumari, Supriya; Mangwani, Neelam; Das, Surajit

2017-02-01

Three-dimensional excitation-emission matrix (3D EEM) fluorescence spectroscopy and attenuated total reflectance fourier-transformed infrared spectroscopy (ATR-FTIR) was used to evaluate the interaction of biofilm associated extracellular polymeric substances (EPS) of a marine bacterium Pseudomonas pseudoalcaligenes NP103 with lead [Pb(II)]. EEM fluorescence spectroscopic analysis revealed the presence of one protein-like fluorophore in the EPS of P. pseudoalcaligenes NP103. Stern-Volmer equation indicated the existence of only one binding site (n = 0.789) in the EPS of P. pseudoalcaligenes NP103. The interaction of Pb(II) with EPS was spontaneous at room temperature (Δ G = - 2.78 kJ/K/mol) having binding constant (Kb) of 2.59 M- 1. ATR-FTIR analysis asserted the involvement of various functional groups such as sulphydryl, phosphate and hydroxyl and amide groups of protein in Pb(II) binding. Scanning electron microscopy (SEM) and fluorescence microscopy analysis displayed reduced growth of biofilm with altered surface topology in Pb(II) supplemented medium. Energy dispersive X-ray spectroscopy (EDX) analysis revealed the entrapment of Pb in the EPS. Uronic acid, a characteristic functional group of biofilm, was observed in 1H NMR spectroscopy. The findings suggest that biofilm associated EPS are perfect organic ligands for Pb(II) complexation and may significantly augment the bioavailability of Pb(II) in the metal contaminated environment for subsequent sequestration.

Decoding the genome with an integrative analysis tool: combinatorial CRM Decoder.

PubMed

Kang, Keunsoo; Kim, Joomyeong; Chung, Jae Hoon; Lee, Daeyoup

2011-09-01

The identification of genome-wide cis-regulatory modules (CRMs) and characterization of their associated epigenetic features are fundamental steps toward the understanding of gene regulatory networks. Although integrative analysis of available genome-wide information can provide new biological insights, the lack of novel methodologies has become a major bottleneck. Here, we present a comprehensive analysis tool called combinatorial CRM decoder (CCD), which utilizes the publicly available information to identify and characterize genome-wide CRMs in a species of interest. CCD first defines a set of the epigenetic features which is significantly associated with a set of known CRMs as a code called 'trace code', and subsequently uses the trace code to pinpoint putative CRMs throughout the genome. Using 61 genome-wide data sets obtained from 17 independent mouse studies, CCD successfully catalogued ∼12 600 CRMs (five distinct classes) including polycomb repressive complex 2 target sites as well as imprinting control regions. Interestingly, we discovered that ∼4% of the identified CRMs belong to at least two different classes named 'multi-functional CRM', suggesting their functional importance for regulating spatiotemporal gene expression. From these examples, we show that CCD can be applied to any potential genome-wide datasets and therefore will shed light on unveiling genome-wide CRMs in various species.

The optimal algorithm for Multi-source RS image fusion.

PubMed

Fu, Wei; Huang, Shui-Guang; Li, Zeng-Shun; Shen, Hao; Li, Jun-Shuai; Wang, Peng-Yuan

2016-01-01

In order to solve the issue which the fusion rules cannot be self-adaptively adjusted by using available fusion methods according to the subsequent processing requirements of Remote Sensing (RS) image, this paper puts forward GSDA (genetic-iterative self-organizing data analysis algorithm) by integrating the merit of genetic arithmetic together with the advantage of iterative self-organizing data analysis algorithm for multi-source RS image fusion. The proposed algorithm considers the wavelet transform of the translation invariance as the model operator, also regards the contrast pyramid conversion as the observed operator. The algorithm then designs the objective function by taking use of the weighted sum of evaluation indices, and optimizes the objective function by employing GSDA so as to get a higher resolution of RS image. As discussed above, the bullet points of the text are summarized as follows.•The contribution proposes the iterative self-organizing data analysis algorithm for multi-source RS image fusion.•This article presents GSDA algorithm for the self-adaptively adjustment of the fusion rules.•This text comes up with the model operator and the observed operator as the fusion scheme of RS image based on GSDA. The proposed algorithm opens up a novel algorithmic pathway for multi-source RS image fusion by means of GSDA.

Gauge Fields in Homogeneous and Inhomogeneous Cosmologies

NASA Astrophysics Data System (ADS)

Darian, Bahman K.

Despite its formidable appearance, the study of classical Yang-Mills (YM) fields on homogeneous cosmologies is amenable to a formal treatment. This dissertation is a report on a systematic approach to the general construction of invariant YM fields on homogeneous cosmologies undertaken for the first time in this context. This construction is subsequently followed by the investigation of the behavior of YM field variables for the most simple of self-gravitating YM fields. Particularly interesting was a dynamical system analysis and the discovery of chaotic signature in the axially symmetric Bianchi I-YM cosmology. Homogeneous YM fields are well studied and are known to have chaotic properties. The chaotic behavior of YM field variables in homogeneous cosmologies might eventually lead to an invariant definition of chaos in (general) relativistic cosmological models. By choosing the gauge fields to be Abelian, the construction and the field equations presented so far reduce to that of electromagnetic field in homogeneous cosmologies. A perturbative analysis of gravitationally interacting electromagnetic and scalar fields in inhomogeneous cosmologies is performed via the Hamilton-Jacobi formulation of general relativity. An essential feature of this analysis is the spatial gradient expansion of the generating functional (Hamilton principal function) to solve the Hamiltonian constraint. Perturbations of a spatially flat Friedman-Robertson-Walker cosmology with an exponential potential for the scalar field are presented.

Infant Formula Feeding at Birth Is Common and Inversely Associated with Subsequent Breastfeeding Behavior in Vietnam123

PubMed Central

Nguyen, Tuan T; Withers, Mellissa; Hajeebhoy, Nemat; Frongillo, Edward A

2016-01-01

Background: The association between infant formula feeding at birth and subsequent feeding patterns in a low- or middle-income context is not clear. Objective: We examined the association of infant formula feeding during the first 3 d after birth with subsequent infant formula feeding and early breastfeeding cessation in Vietnam. Methods: In a cross-sectional survey, we interviewed 10,681 mothers with children aged 0−23 mo (mean age: 8.2 mo; 52% boys) about their feeding practices during the first 3 d after birth and on the previous day. We used stratified analysis, multiple logistic regression, propensity score-matching analysis, and structural equation modeling to minimize the limitation of the cross-sectional design and to ensure the consistency of the findings. Results: Infant formula feeding during the first 3 d after birth (50%) was associated with a higher prevalence of subsequent infant formula feeding [stratified analysis: 7−28% higher (nonoverlapping 95% CIs for most comparisons); propensity score-matching analysis: 13% higher (P < 0.001); multiple logistic regression: OR: 1.47 (95% CI: 1.30, 1.67)]. This practice was also associated with a higher prevalence of early breastfeeding cessation (e.g., <24 mo) [propensity score-matching analysis: 2% (P = 0.08); OR: 1.33 (95% CI: 1.12, 1.59)]. Structural equation modeling showed that infant formula feeding during the first 3 d after birth was associated with a higher prevalence of subsequent infant formula feeding (β: 0.244; P < 0.001), which in turn was linked to early breastfeeding cessation (β: 0.285; P < 0.001). Conclusions: Infant formula feeding during the first 3 d after birth was associated with increased subsequent infant formula feeding and the early cessation of breastfeeding, which underscores the need to make early, exclusive breastfeeding normative and to create environments that support it. PMID:27605404

Sounds Activate Visual Cortex and Improve Visual Discrimination

PubMed Central

Störmer, Viola S.; Martinez, Antigona; McDonald, John J.; Hillyard, Steven A.

2014-01-01

A recent study in humans (McDonald et al., 2013) found that peripheral, task-irrelevant sounds activated contralateral visual cortex automatically as revealed by an auditory-evoked contralateral occipital positivity (ACOP) recorded from the scalp. The present study investigated the functional significance of this cross-modal activation of visual cortex, in particular whether the sound-evoked ACOP is predictive of improved perceptual processing of a subsequent visual target. A trial-by-trial analysis showed that the ACOP amplitude was markedly larger preceding correct than incorrect pattern discriminations of visual targets that were colocalized with the preceding sound. Dipole modeling of the scalp topography of the ACOP localized its neural generators to the ventrolateral extrastriate visual cortex. These results provide direct evidence that the cross-modal activation of contralateral visual cortex by a spatially nonpredictive but salient sound facilitates the discriminative processing of a subsequent visual target event at the location of the sound. Recordings of event-related potentials to the targets support the hypothesis that the ACOP is a neural consequence of the automatic orienting of visual attention to the location of the sound. PMID:25031419

The Development of Comorbid Conduct Problems in Children With ADHD: An Example of an Integrative Developmental Psychopathology Perspective.

PubMed

Danforth, Jeffrey S; Connor, Daniel F; Doerfler, Leonard A

2016-03-01

We describe interactions among factors that contribute to the development of conduct problems among children with ADHD. An integrative developmental psychopathology analysis combines various approaches and posits one model of how diverse risk factors operate together to contribute to the development of conduct problems among children with ADHD. Substantial genetic risk increases covariation between ADHD and conduct problems. Candidate genes are associated with CNS monoaminergic neurotransmission. Subsequent neurodevelopmental impairment interferes with executive function, with impaired verbal working memory playing an important role. Parent/child bi-directional influences exacerbate the risk for conduct problems when ADHD symptoms increase the likelihood of a coercive parenting style. Parent stress in reaction to child comorbid ADHD and conduct problems, and parent attribution for the child's conduct problem behavior, add to the potential for coercion and reduce constructive parent-child interaction that might otherwise enhance the development of verbal working memory. In an integrated manner, these variables increase the risk that a child with ADHD will subsequently develop conduct problems. © The Author(s) 2014.

Directionality of the relationship between social well-being and subjective well-being: evidence from a 20-year longitudinal study.

PubMed

Joshanloo, Mohsen; Sirgy, M Joseph; Park, Joonha

2018-04-30

Self-determination theory suggests that psycho-social well-being prospectively predicts subjective well-being. In contrast, the broaden-and-build theory of positive emotions suggests that subjective well-being has a positive impact on subsequent levels of psycho-social well-being. The present study sought to empirically disentangle the directionality of the relationship between subjective well-being and social well-being over time. The study used three waves of survey data, with intervals of 10 years, from the Midlife in the United States (MIDUS) project, a representative longitudinal panel study of American adults (N = 2732). Cross-lagged panel modeling was used for data analysis. The results revealed that social well-being predicted increases in subsequent subjective well-being, whereas subjective well-being did not prospectively predict social well-being. Social well-being also demonstrated more stability over time than did subjective well-being. These findings suggest that optimal social functioning is more likely to be an antecedent to subjective well-being, not the other way around. The results are consistent with predictions guided by self-determination theory.

A platform for the advanced spatial and temporal control of biomolecules

NASA Astrophysics Data System (ADS)

Hook, Andrew L.; Thissen, Helmut; Hayes, Jason P.; Voelcker, Nicolas H.

2007-01-01

Manipulating biomolecules at solid/liquid interfaces is important for the development of various biodevices including microarrays. Smart materials that enable both spatial and temporal control of biomolecules by combining switchability with patterned surface chemistry offer unprecedented levels of control of biomolecule manipulation. Such a system has been developed for the microscale spatial control over both DNA and cell growth on highly doped p-type silicon. Surface modification, involving plasma polymerisation of allylamine and poly(ethlylene glycol) grafting with subsequent laser ablation, led to the production of a patterned surface with dual biomolecule adsorption and desorption properties. On patterned surfaces, preferential electro-stimulated adsorption of DNA to the allylamine plasma polymer surface and subsequent desorption by the application of a negative bias was observed. The ability of this surface to control both DNA and cell attachment in four dimensions has been demonstrated, exemplifying its capacity to be used for complex biological studies such as gene function analysis. This system has been successfully applied to living microarray applications and is an exciting platform for any system incorporating biomolecules.

Development of an electro-responsive platform for the controlled transfection of mammalian cells

NASA Astrophysics Data System (ADS)

Hook, Andrew L.; Thissen, Helmut W.; Hayes, Jason P.; Voelcker, Nicolas H.

2005-02-01

The recent development of living microarrays as novel tools for the analysis of gene expression in an in-situ environment promises to unravel gene function within living organisms. In order to significantly enhance microarray performance, we are working towards electro-responsive DNA transfection chips. This study focuses on the control of DNA adsorption and desorption by appropriate surface modification of highly doped p++ silicon. Silicon was modified by plasma polymerisation of allylamine (ALAPP), a non-toxic surface that sustains cell growth. Subsequent high surface density grafting of poly(ethylene oxide) formed a layer resistant to biomolecule adsorption and cell attachment. Spatially controlled excimer laser ablation of the surface produced micron resolution patterns of re-exposed plasma polymer whilst the rest of the surface remained non-fouling. We observed electro-stimulated preferential adsorption of DNA to the ALAPP surface and subsequent desorption by the application of a negative bias. Cell culture experiments with HEK 293 cells demonstrated efficient and controlled transfection of cells using the expression of green fluorescent protein as a reporter. Thus, these chemically patterned surfaces are promising platforms for use as living microarrays.

The Effect of Laser Irradiation on Adipose Derived Stem Cell Proliferation and Differentiation

NASA Astrophysics Data System (ADS)

Abrahamse, H.; de Villiers, J.; Mvula, B.

2009-06-01

There are two fundamental types of stem cells: Embryonic Stem cells and Adult Stem cells. Adult Stem cells have a more restricted potential and can usually differentiate into a few different cell types. In the body these cells facilitate the replacement or repair of damaged or diseased cells in organs. Low intensity laser irradiation was shown to increase stem cell migration and stimulate proliferation and it is thought that treatment of these cells with laser irradiation may increase the stem cell harvest and have a positive effect on the viability and proliferation. Our research is aimed at determining the effect of laser irradiation on differentiation of Adipose Derived Stem Cells (ADSCs) into different cell types using a diode laser with a wavelength of 636 nm and at 5 J/cm2. Confirmation of stem cell characteristics and well as subsequent differentiation were assessed using Western blot analysis and cellular morphology supported by fluorescent live cell imaging. Functionality of subsequent differentiated cells was confirmed by measuring adenosine triphosphate (ATP) production and cell viability.

Bifunctional application of sodium cobaltate as a catalyst and captor through CO oxidation and subsequent CO 2 chemisorption processes

DOE PAGES

Vera, Elizabeth; Alcántar-Vázquez, Brenda; Duan, Yuhua; ...

2015-12-21

The potential bifunctional mechanism of sodium cobaltate (NaCoO 2) in the catalysis of CO oxidation and subsequent CO 2 chemisorption was systematically analysed. Different catalytic and gravimetric experiments were performed dynamically and isothermally at multiple temperatures. Initially, the CO oxidation process was evaluated using a catalytic reactor connected to a gas chromatograph. Once the production of CO 2 was confirmed, its chemisorption capacity with NaCoO 2 was studied gravimetrically. Catalytic and gravimetric analysis products were studied by XRD, FTIR and SEM to elucidate the double reaction mechanism. Sodium cobaltate exhibited interesting catalytic properties over a wide temperature range, although themore » NaCoO 2 crystalline structure and chemical composition changed during the CO 2 capture process. Furthermore, all the experiments were theoretically supported by first-principles density functional theory thermodynamic calculations. Finally, the calculated thermodynamic properties of the CO oxidation and CO 2 capture reactions with NaCoO 2 under different oxidation conditions were in good agreement with the experimental measurements.« less

A Study of the Impact of Thirteen Celebrity Suicides on Subsequent Suicide Rates in South Korea from 2005 to 2009

PubMed Central

Fu, King-wa; Chan, C. H.

2013-01-01

A number of ecological studies have found a pattern of increasing suicide rates after suicides of several Asian entertainment celebrities. However, the finding may be subject to positive outcome bias where cases with no perceived impact may be routinely excluded. In this study, we deploy interrupted time-series analysis using ARIMA transfer function models to investigate systematically the impact of thirteen celebrity suicides on subsequent suicide rates in South Korea. We find that three out of eleven cases were found to be followed by a significant increase in suicide rate, while controlling for seasonality, secular trends, and unemployment rates. Such significant increases could last for nine weeks. Non-significance cases may be attributable to the small amount of media coverage, the “displacement” effect of preceding case, and the negative connotation of celebrity deaths. We therefore conclude that whether or not the impacts were detected may be largely conditioned by various contextual factors. Current evidence based on ecological studies is insufficient to draw a firm conclusion. Further studies using multiple approaches should be developed. PMID:23342026

Grain boundary oxidation and an analysis of the effects of pre-oxidation on subsequent fatigue life

NASA Technical Reports Server (NTRS)

Oshida, Y.; Liu, H. W.

1986-01-01

The effects of preoxidation on subsequent fatigue life were studied. Surface oxidation and grain boundary oxidation of a nickel-base superalloy (TAZ-8A) were studied at 600 to 1000 C for 10 to 1000 hours in air. Surface oxides were identified and the kinetics of surface oxidation was discussed. Grain boundary oxide penetration and morphology were studied. Pancake type grain boundary oxide penetrates deeper and its size is larger, therefore, it is more detrimental to fatigue life than cone-type grain boundary oxide. Oxide penetration depth, a (sub m), is related to oxidation temperature, T, and exposure time, t, by an empirical relation of the Arrhenius type. Effects of T and t on statistical variation of a (sub m) were analyzed according to the Weibull distribution function. Once the oxide is cracked, it serves as a fatigue crack nucleus. Statistical variation of the remaining fatigue life, after the formation of an oxide crack of a critical length, is related directly to the statistical variation of grain boundary oxide penetration depth.

Immunomagnetic isolation of pathogen-containing phagosomes and apoptotic blebs from primary phagocytes.

PubMed

Steinhäuser, Christine; Dallenga, Tobias; Tchikov, Vladimir; Schaible, Ulrich E; Schütze, Stefan; Reiling, Norbert

2014-04-02

Macrophages and polymorphonuclear neutrophils are professional phagocytes essential in the initial host response against intracellular pathogens such as Mycobacterium tuberculosis. Phagocytosis is the first step in phagocyte-pathogen interaction, where the pathogen is engulfed into a membrane-enclosed compartment termed a phagosome. Subsequent effector functions of phagocytes result in killing and degradation of the pathogen by promoting phagosome maturation, and, terminally, phago-lysosome fusion. Intracellular pathogenic microbes use various strategies to avoid detection and elimination by phagocytes, including induction of apoptosis to escape host cells, thereby generating apoptotic blebs as shuttles to other cells for pathogens and antigens thereof. Hence, phagosomes represent compartments where host and pathogen become quite intimate, and apoptotic blebs are carrier bags of the pathogen's legacy. In order to investigate the molecular mechanisms underlying these interactions, both phagosomes and apoptotic blebs are required as purified subcellular fractions for subsequent analysis of their biochemical properties. Here, we describe a lipid-based procedure to magnetically label surfaces of either pathogenic mycobacteria or apoptotic blebs for purification by a strong magnetic field in a novel free-flow system. Copyright © 2014 John Wiley & Sons, Inc.

Hantush Well Function revisited

NASA Astrophysics Data System (ADS)

Veling, E. J. M.; Maas, C.

2010-11-01

SummaryIn this paper, we comment on some recent numerical and analytical work to evaluate the Hantush Well Function. We correct an expression found in a Comment by Nadarajah [Nadarajah, S., 2007. A comment on numerical evaluation of Theis and Hantush-Jacob well functions. Journal of Hydrology 338, 152-153] to a paper by Prodanoff et al. [Prodanoff, J.A., Mansur, W.J., Mascarenhas, F.C.B., 2006. Numerical evaluation of Theis and Hantush-Jacob well functions. Journal of Hydrology 318, 173-183]. We subsequently derived another analytic representation based on a generalized hypergeometric function in two variables and from the hydrological literature we cite an analytic representation by Hunt [Hunt, B., 1977. Calculation of the leaky aquifer function. Journal of Hydrology 33, 179-183]. We have implemented both representations and compared the results. Using a convergence accelerator Hunt's representation of Hantush Well Function is efficient and accurate. While checking our implementations we found that Bear's table of the Hantush Well Function [Bear, J., 1979. Hydraulics of Groundwater. McGraw-Hill, New York, Tables 8-6] contains a number of typographical errors that are not present in the original table published by Hantush [Hantush, M.S., 1956. Analysis of data from pumping tests in leaky aquifers. Transactions, American Geophysical Union 37, 702-714]. Finally, we offer a very fast approximation with a maximum relative error of 0.0033 for the parameter range in the table given by Bear.

Critical Analysis of Cluster Models and Exchange-Correlation Functionals for Calculating Magnetic Shielding in Molecular Solids.

PubMed

Holmes, Sean T; Iuliucci, Robbie J; Mueller, Karl T; Dybowski, Cecil

2015-11-10

Calculations of the principal components of magnetic-shielding tensors in crystalline solids require the inclusion of the effects of lattice structure on the local electronic environment to obtain significant agreement with experimental NMR measurements. We assess periodic (GIPAW) and GIAO/symmetry-adapted cluster (SAC) models for computing magnetic-shielding tensors by calculations on a test set containing 72 insulating molecular solids, with a total of 393 principal components of chemical-shift tensors from 13C, 15N, 19F, and 31P sites. When clusters are carefully designed to represent the local solid-state environment and when periodic calculations include sufficient variability, both methods predict magnetic-shielding tensors that agree well with experimental chemical-shift values, demonstrating the correspondence of the two computational techniques. At the basis-set limit, we find that the small differences in the computed values have no statistical significance for three of the four nuclides considered. Subsequently, we explore the effects of additional DFT methods available only with the GIAO/cluster approach, particularly the use of hybrid-GGA functionals, meta-GGA functionals, and hybrid meta-GGA functionals that demonstrate improved agreement in calculations on symmetry-adapted clusters. We demonstrate that meta-GGA functionals improve computed NMR parameters over those obtained by GGA functionals in all cases, and that hybrid functionals improve computed results over the respective pure DFT functional for all nuclides except 15N.

Chapter 11.18 - Neuroendocrine Control of Female Reproduction.

EPA Science Inventory

The hypothalamus and pituitary are known to play roles in reproductive function. A growing body of evidence indicates that environmental toxicants can alter female reproductive function by disrupting hypothalamic control of the pituitary and subsequently the endocrine control of ...

Individual Differences in Adolescents' Sympathetic and Parasympathetic Functioning Moderate Associations between Family Environment and Psychosocial Adjustment

ERIC Educational Resources Information Center

Diamond, Lisa M.; Fagundes, Christopher P.; Cribbet, Matthew R.

2012-01-01

The present study tested whether individual differences in autonomic nervous system functioning interact with environmental risk factors to predict adolescents' psychosocial functioning. The authors assessed skin conductance and respiratory sinus arrhythmia at rest and during laboratory stressors in 110 14-year-olds. Subsequently, adolescents and…

75 FR 4982 - Redelegation of Functions; Delegation of Authority to Drug Enforcement Administration Official

Federal Register 2010, 2011, 2012, 2013, 2014

2010-02-01

... which were vested in the Attorney General by the Controlled Substances Act and subsequently delegated to...-certification (21 CFR 1314.40). Redelegation of Authority The Attorney General has delegated his functions under...(b)). The Attorney General has also authorized the Administrator to redelegate any of his functions...

Genome-wide analysis of DUF221 domain-containing gene family in Oryza species and identification of its salinity stress-responsive members in rice.

PubMed

Ganie, Showkat Ahmad; Pani, Dipti Ranjan; Mondal, Tapan Kumar

2017-01-01

DUF221 domain-containing genes (DDP genes) play important roles in developmental biology, hormone signalling transduction, and responses to abiotic stress. Therefore to understand their structural and evolutionary relationship, we did a genome-wide analysis of this important gene family in rice. Further, through comparative genomics, DDP genes from Oryza sativa subsp. (indica), nine different wild species of rice and Arabidopsis were also identified. We also found an expansion of the DDP gene families in rice and Arabidopsis which is due to the segmental duplication events in some of the gene family members. In general, a highly purifying selection was found acting on all the deduced paralogous and orthologous DDP gene pairs. The data from microarray and subsequent qRT-PCR analysis revealed that although several OsDDPs were differentially regulated under salinity stress, yet OsDDP6 was upregulated at all the developmental stages in salt tolerant rice genotype, FL478. Interestingly, OsDDP6 was found to be involved in proline metabolism pathway as indicated by protein network analysis. The diverse gene structures, varied transmembrane topologies and the differential expression patterns implied the functional diversity in DDP genes. Therefore, the comprehensive evolutionary analysis of DDP genes from different Oryza species and Arabidopsis performed in this study will provide the basis for further functional validation studies vis-à-vis DDP genes of rice and other plant species.

Genome-wide analysis of DUF221 domain-containing gene family in Oryza species and identification of its salinity stress-responsive members in rice

PubMed Central

Ganie, Showkat Ahmad; Pani, Dipti Ranjan

2017-01-01

DUF221 domain-containing genes (DDP genes) play important roles in developmental biology, hormone signalling transduction, and responses to abiotic stress. Therefore to understand their structural and evolutionary relationship, we did a genome-wide analysis of this important gene family in rice. Further, through comparative genomics, DDP genes from Oryza sativa subsp. (indica), nine different wild species of rice and Arabidopsis were also identified. We also found an expansion of the DDP gene families in rice and Arabidopsis which is due to the segmental duplication events in some of the gene family members. In general, a highly purifying selection was found acting on all the deduced paralogous and orthologous DDP gene pairs. The data from microarray and subsequent qRT-PCR analysis revealed that although several OsDDPs were differentially regulated under salinity stress, yet OsDDP6 was upregulated at all the developmental stages in salt tolerant rice genotype, FL478. Interestingly, OsDDP6 was found to be involved in proline metabolism pathway as indicated by protein network analysis. The diverse gene structures, varied transmembrane topologies and the differential expression patterns implied the functional diversity in DDP genes. Therefore, the comprehensive evolutionary analysis of DDP genes from different Oryza species and Arabidopsis performed in this study will provide the basis for further functional validation studies vis-à-vis DDP genes of rice and other plant species. PMID:28846681

Hippocampal and Cognitive Function, Exercise, and Ovarian Cancer: A Pilot Study

DTIC Science & Technology

2015-08-01

the hippocampus and subsequently offset memory decline. 15. SUBJECT TERMS 16. SECURITY CLASSIFICATION OF: 17. LIMITATION OF ABSTRACT 18. NUMBER OF... hippocampus and subsequently offset memory decline. 2 KEYWORDS: Physical activity interventions, ovarian cancer treatment, chemotherapy-induced...chemotherapy complaint in a single cancer: problems with memory in patients with ovarian cancer. We focus on this problem for three reasons: 1

Aggression is associated with greater subsequent alcohol consumption: A shared neural basis in the ventral striatum.

PubMed

Chester, David S; DeWall, C Nathan

2018-05-01

Alcohol use and abuse (e.g., binge drinking) are among the most reliable causes of aggressive behavior. Conversely, people with aggressive dispositions (e.g., intermittent explosive disorder) are at greater risk for subsequent substance abuse. Yet it remains unknown why aggression might promote subsequent alcohol use. Both aggressive acts and alcohol use are rewarding and linked to greater activity in neural reward circuitry. Through this shared instantiation of reward, aggression may then increase subsequent alcohol consumption. Supporting this mechanistic hypothesis, participants' aggressive behavior directed at someone who had recently rejected them, was associated with more subsequent beer consumption on an ad-lib drinking task. Using functional MRI, both aggressive behavior and beer consumption were associated with greater activity in the bilateral ventral striatum during acts of retaliatory aggression. These results imply that aggression is linked to subsequent alcohol abuse, and that a mechanism underlying this effect is likely to be the activation of the brain's reward circuitry during aggressive acts. © 2018 Wiley Periodicals, Inc.

"Kindergarten, can I have your eyes and ears?" politeness and teacher directive choices in inquiry-based science classrooms

NASA Astrophysics Data System (ADS)

Oliveira, Alandeom Wanderlei

2009-12-01

This study explores elementary teachers' social understandings and employment of directives and politeness while facilitating inquiry science lessons prior and subsequent to their participation in a summer institute in which they were introduced to the scholarly literature on regulative discourse (directives used by teachers to regulate student behavior). A grounded theory analysis of the institute professional development activities revealed that teachers developed an increased awareness of the authoritative functions served by impolite or direct directives (i.e., pragmatic awareness). Furthermore, a comparative microethnographic analysis of participants' inquiry-based classroom practices revealed that after the institute teachers demonstrated an increased ability to share authority with students by strategically making directive choices that were more polite, indirect, inclusive, involvement-focused and creative. Such ability led to a reduced emphasis on teacher regulation of student compliance with classroom behavioral norms and an increased focus on the discursive organization of the inquiry-based science learning/teaching process. Despite teachers' increased pragmatic awareness, teacher-student linguistic relationships did not become entirely symmetrical subsequent to their participation in the summer institute (i.e., teacher authority was not completely relinquished or lost). Based on such findings, it is argued that teachers need to develop higher levels of pragmatic awareness to become effectively prepared to engage in language-mediated teacher-student interaction in the context of inquiry-based science classroom discourse.

[Fatal poisoning in the Department of Toxicology in Poznarn in 2008-2012--preliminary analysis].

PubMed

Łukasik-Głebocka, Magdalena; Adamek, Robert

2013-01-01

This paper presents the results of a preliminary analysis of deaths from acute poisoning, which occurred in the Department of Toxicology in Poznań in 2008-2012. During this period, recorded 31 cases of fatal poisoning, representing 0.38% of all treated cases. In subsequent years the percentage of poisoning deaths ranged from 0.25 to 0.49%. Throughout the period leading cause of fatal poisoning were drugs (38.71%) and non-consumptive alcohols (methanol or ethylene glycol) (38.71%). In subsequent years, however, a decrease in the percentage of drug poisoning (from 75 to 0%) and an increase in the percentage of nonconsumptive alcohol poisoning (from 0% to 100%) were observed. In fatal cases were diagnosed among others olanzapine, carbamazepine, pseudoephedrine, tramadol, benzodiazepines, clozapine, morphine and benzodiazepines, insulin, verapamil, carbon monoxide and smoke fire, cyanide, Amanita phalloides, ethanol and a mixture of drugs with ethanol poisoning. The most common fatal poisoning occurred in people addicted (45.16%), mainly in alcohol dependence syndrome (35.48%). Suicidal poisoning was the cause of 32.26% of the deaths, while accidental of 19.35%. In nine cases, the procedure of diagnosis of death from irreversible cessation of brain stem function was performed in order to qualify donors of organs for transplantation or to terminate the therapy. One of the dead was liver and kidneys, and two were kidneys donors.

Striatal and midbrain connectivity with the hippocampus selectively boosts memory for contextual novelty

PubMed Central

Kafkas, Alexandros; Montaldi, Daniela

2015-01-01

The role of contextual expectation in processing familiar and novel stimuli was investigated in a series of experiments combining eye tracking, functional magnetic resonance imaging, and behavioral methods. An experimental paradigm emphasizing either familiarity or novelty detection at retrieval was used. The detection of unexpected familiar and novel stimuli, which were characterized by lower probability, engaged activity in midbrain and striatal structures. Specifically, detecting unexpected novel stimuli, relative to expected novel stimuli, produced greater activity in the substantia nigra/ventral tegmental area (SN/VTA), whereas the detection of unexpected familiar, relative to expected, familiar stimuli, elicited activity in the striatum/globus pallidus (GP). An effective connectivity analysis showed greater functional coupling between these two seed areas (GP and SN/VTA) and the hippocampus, for unexpected than for expected stimuli. Within this network of midbrain/striatal–hippocampal interactions two pathways are apparent; the direct SN–hippocampal pathway sensitive to unexpected novelty and the perirhinal–GP–hippocampal pathway sensitive to unexpected familiarity. In addition, increased eye fixations and pupil dilations also accompanied the detection of unexpected relative to expected familiar and novel stimuli, reflecting autonomic activity triggered by the functioning of these two pathways. Finally, subsequent memory for unexpected, relative to expected, familiar, and novel stimuli was characterized by enhanced recollection, but not familiarity, accuracy. Taken together, these findings suggest that a hippocampal–midbrain network, characterized by two distinct pathways, mediates encoding facilitation and most critically, that this facilitation is driven by contextual novelty, rather than by the absolute novelty of a stimulus. This contextually sensitive neural mechanism appears to elicit increased exploratory behavior, leading subsequently to greater recollection of the unexpected stimulus. © 2015 The Authors Hippocampus Published by Wiley Periodicals, Inc. PMID:25708843

Expression, Purification, and Structural Insights for the Human Uric Acid Transporter, GLUT9, Using the Xenopus laevis Oocytes System

PubMed Central

Clémençon, Benjamin; Lüscher, Benjamin P.; Fine, Michael; Baumann, Marc U.; Surbek, Daniel V.; Bonny, Olivier; Hediger, Matthias A.

2014-01-01

The urate transporter, GLUT9, is responsible for the basolateral transport of urate in the proximal tubule of human kidneys and in the placenta, playing a central role in uric acid homeostasis. GLUT9 shares the least homology with other members of the glucose transporter family, especially with the glucose transporting members GLUT1-4 and is the only member of the GLUT family to transport urate. The recently published high-resolution structure of XylE, a bacterial D-xylose transporting homologue, yields new insights into the structural foundation of this GLUT family of proteins. While this represents a huge milestone, it is unclear if human GLUT9 can benefit from this advancement through subsequent structural based targeting and mutagenesis. Little progress has been made toward understanding the mechanism of GLUT9 since its discovery in 2000. Before work can begin on resolving the mechanisms of urate transport we must determine methods to express, purify and analyze hGLUT9 using a model system adept in expressing human membrane proteins. Here, we describe the surface expression, purification and isolation of monomeric protein, and functional analysis of recombinant hGLUT9 using the Xenopus laevis oocyte system. In addition, we generated a new homology-based high-resolution model of hGLUT9 from the XylE crystal structure and utilized our purified protein to generate a low-resolution single particle reconstruction. Interestingly, we demonstrate that the functional protein extracted from the Xenopus system fits well with the homology-based model allowing us to generate the predicted urate-binding pocket and pave a path for subsequent mutagenesis and structure-function studies. PMID:25286413

Analysis of the liver functional reserve of patients with advanced hepatocellular carcinoma undergoing sorafenib treatment: Prospects for regorafenib therapy.

PubMed

Terashima, Takeshi; Yamashita, Tatsuya; Sunagozaka, Hajime; Arai, Kuniaki; Kawaguchi, Kazunori; Kitamura, Kazuya; Yamashita, Taro; Sakai, Yoshio; Mizukoshi, Eishiro; Honda, Masao; Kaneko, Shuichi

2018-05-29

This study aimed to investigate liver functional reserves during sorafenib treatment for advanced hepatocellular carcinoma (HCC), to identify predictive factors for maintaining them, and to analyze the proportion of candidates for regorafenib, which has been proven to improve patients' outcomes in the RESORCE trial. We retrospectively investigated Child-Pugh scores during and after sorafenib treatment and evaluated their effects on second-line treatment and outcomes of 125 patients with advanced HCC. Pretreatment Child-Pugh A was maintained in 59/90 (65.6%) patients and pretreatment Child-Pugh B was improved to Child-Pugh A in 10/35 (28.6%) patients when sorafenib ceased. A Child-Pugh score = 5 and aspartate amino transferase <40 IU/L before treatment were contributing factors; vascular invasion and cessation of sorafenib due to gastrointestinal or liver-related adverse effects were reverse predictive factors for Child-Pugh A when sorafenib treatment ceased. Significantly more patients with Child-Pugh A when sorafenib treatment ceased received subsequent therapy and achieved better outcomes compared with patients with Child-Pugh B. When sorafenib treatment failed, 45/125 patients (36.0%) fulfilled key inclusion criteria of the RESORCE trial as follows: Child-Pugh A, Eastern Cooperative Oncology Group performance status 0 or 1, tumor progression revealed by imaging, and treatment with ≥400 mg sorafenib for at least 20 of the last 28 days before treatment failure in 56.8%, 84.8%, 73.6%, and 68.0% of patients, respectively. A comprehensive understanding and management of dynamic changes in liver functional reserve during sorafenib treatment contributed to the efficacy of subsequent therapy (e.g. regorafenib) and to better outcomes for patients with advanced HCC. © 2018 The Japan Society of Hepatology.

Systematic Integration of Brain eQTL and GWAS Identifies ZNF323 as a Novel Schizophrenia Risk Gene and Suggests Recent Positive Selection Based on Compensatory Advantage on Pulmonary Function

PubMed Central

Luo, Xiong-Jian; Mattheisen, Manuel; Li, Ming; Huang, Liang; Rietschel, Marcella; Børglum, Anders D.; Als, Thomas D.; van den Oord, Edwin J.; Aberg, Karolina A.; Mors, Ole; Mortensen, Preben Bo; Luo, Zhenwu; Degenhardt, Franziska; Cichon, Sven; Schulze, Thomas G.; Nöthen, Markus M.; Su, Bing; Zhao, Zhongming; Gan, Lin; Yao, Yong-Gang

2015-01-01

Genome-wide association studies have identified multiple risk variants and loci that show robust association with schizophrenia. Nevertheless, it remains unclear how these variants confer risk to schizophrenia. In addition, the driving force that maintains the schizophrenia risk variants in human gene pool is poorly understood. To investigate whether expression-associated genetic variants contribute to schizophrenia susceptibility, we systematically integrated brain expression quantitative trait loci and genome-wide association data of schizophrenia using Sherlock, a Bayesian statistical framework. Our analyses identified ZNF323 as a schizophrenia risk gene (P = 2.22×10–6). Subsequent analyses confirmed the association of the ZNF323 and its expression-associated single nucleotide polymorphism rs1150711 in independent samples (gene-expression: P = 1.40×10–6; single-marker meta-analysis in the combined discovery and replication sample comprising 44123 individuals: P = 6.85×10−10). We found that the ZNF323 was significantly downregulated in hippocampus and frontal cortex of schizophrenia patients (P = .0038 and P = .0233, respectively). Evidence for pleiotropic effects was detected (association of rs1150711 with lung function and gene expression of ZNF323 in lung: P = 6.62×10–5 and P = 9.00×10–5, respectively) with the risk allele (T allele) for schizophrenia acting as protective allele for lung function. Subsequent population genetics analyses suggest that the risk allele (T) of rs1150711 might have undergone recent positive selection in human population. Our findings suggest that the ZNF323 is a schizophrenia susceptibility gene whose expression may influence schizophrenia risk. Our study also illustrates a possible mechanism for maintaining schizophrenia risk variants in the human gene pool. PMID:25759474

Deep learning analysis of the myocardium in coronary CT angiography for identification of patients with functionally significant coronary artery stenosis.

PubMed

Zreik, Majd; Lessmann, Nikolas; van Hamersvelt, Robbert W; Wolterink, Jelmer M; Voskuil, Michiel; Viergever, Max A; Leiner, Tim; Išgum, Ivana

2018-02-01

In patients with coronary artery stenoses of intermediate severity, the functional significance needs to be determined. Fractional flow reserve (FFR) measurement, performed during invasive coronary angiography (ICA), is most often used in clinical practice. To reduce the number of ICA procedures, we present a method for automatic identification of patients with functionally significant coronary artery stenoses, employing deep learning analysis of the left ventricle (LV) myocardium in rest coronary CT angiography (CCTA). The study includes consecutively acquired CCTA scans of 166 patients who underwent invasive FFR measurements. To identify patients with a functionally significant coronary artery stenosis, analysis is performed in several stages. First, the LV myocardium is segmented using a multiscale convolutional neural network (CNN). To characterize the segmented LV myocardium, it is subsequently encoded using unsupervised convolutional autoencoder (CAE). As ischemic changes are expected to appear locally, the LV myocardium is divided into a number of spatially connected clusters, and statistics of the encodings are computed as features. Thereafter, patients are classified according to the presence of functionally significant stenosis using an SVM classifier based on the extracted features. Quantitative evaluation of LV myocardium segmentation in 20 images resulted in an average Dice coefficient of 0.91 and an average mean absolute distance between the segmented and reference LV boundaries of 0.7 mm. Twenty CCTA images were used to train the LV myocardium encoder. Classification of patients was evaluated in the remaining 126 CCTA scans in 50 10-fold cross-validation experiments and resulted in an area under the receiver operating characteristic curve of 0.74 ± 0.02. At sensitivity levels 0.60, 0.70 and 0.80, the corresponding specificity was 0.77, 0.71 and 0.59, respectively. The results demonstrate that automatic analysis of the LV myocardium in a single CCTA scan acquired at rest, without assessment of the anatomy of the coronary arteries, can be used to identify patients with functionally significant coronary artery stenosis. This might reduce the number of patients undergoing unnecessary invasive FFR measurements. Copyright © 2017 Elsevier B.V. All rights reserved.

Serious fighting-related injuries produce a significant reduction in intelligence.

PubMed

Schwartz, Joseph A; Beaver, Kevin M

2013-10-01

Fighting-related injuries are common among adolescents within the United States, but how such injuries relate to subsequent cognitive functioning remains unclear. In particular, the long-term effect of fighting-related injuries suffered during important developmental periods, such as adolescence, on subsequent cognitive functioning has been overlooked by previous studies. The purpose of this study is to examine the association between sustaining serious fighting-related injuries and changes in verbal intelligence (IQ) over a 5- to 6-year time period. Longitudinal multivariate statistical models were used to analyze data from the National Longitudinal Study of Adolescent Health collected between 1994 and 2002 and analyzed in 2013. Even a single fighting-related injury resulted in a significant reduction in IQ over time even after controlling for age, race, sex, and changes in socioeconomic status (SES) over the study period. Additionally, females experienced a significantly greater reduction in IQ from each fighting-related injury than males. Fighting-related injuries have a significant impact on subsequent cognitive functioning and intelligence. The implications for future policies and research are discussed in more detail. Copyright © 2013 Society for Adolescent Health and Medicine. Published by Elsevier Inc. All rights reserved.