Magnetic-Activated Cell Sorting for the Fast and Efficient Separation of Human and Rodent Schwann Cells from Mixed Cell Populations.

PubMed

Ravelo, Kristine M; Andersen, Natalia D; Monje, Paula V

2018-01-01

To date, magnetic-activated cell sorting (MACS) remains a powerful method to isolate distinct cell populations based on differential cell surface labeling. Optimized direct and indirect MACS protocols for cell immunolabeling are presented here as methods to divest Schwann cell (SC) cultures of contaminating cells (specifically, fibroblast cells) and isolate SC populations at different stages of differentiation. This chapter describes (1) the preparation of single-cell suspensions from established human and rat SC cultures, (2) the design and application of cell selection strategies using SC-specific (p75 NGFR , O4, and O1) and fibroblast-specific (Thy-1) markers, and (3) the characterization of both the pre- and post-sorting cell populations. A simple protocol for the growth of hybridoma cell cultures as a source of monoclonal antibodies for cell surface immunolabeling of SCs and fibroblasts is provided as a cost-effective alternative for commercially available products. These steps allow for the timely and efficient recovery of purified SC populations without compromising the viability and biological activity of the cells.

IAP-Based Cell Sorting Results in Homogeneous Transplantable Dopaminergic Precursor Cells Derived from Human Pluripotent Stem Cells.

PubMed

Lehnen, Daniela; Barral, Serena; Cardoso, Tiago; Grealish, Shane; Heuer, Andreas; Smiyakin, Andrej; Kirkeby, Agnete; Kollet, Jutta; Cremer, Harold; Parmar, Malin; Bosio, Andreas; Knöbel, Sebastian

2017-10-10

Human pluripotent stem cell (hPSC)-derived mesencephalic dopaminergic (mesDA) neurons can relieve motor deficits in animal models of Parkinson's disease (PD). Clinical translation of differentiation protocols requires standardization of production procedures, and surface-marker-based cell sorting is considered instrumental for reproducible generation of defined cell products. Here, we demonstrate that integrin-associated protein (IAP) is a cell surface marker suitable for enrichment of hPSC-derived mesDA progenitor cells. Immunomagnetically sorted IAP + mesDA progenitors showed increased expression of ventral midbrain floor plate markers, lacked expression of pluripotency markers, and differentiated into mature dopaminergic (DA) neurons in vitro. Intrastriatal transplantation of IAP + cells sorted at day 16 of differentiation in a rat model of PD resulted in functional recovery. Grafts from sorted IAP + mesDA progenitors were more homogeneous in size and DA neuron density. Thus, we suggest IAP-based sorting for reproducible prospective enrichment of mesDA progenitor cells in clinical cell replacement strategies. Copyright © 2017 Miltenyi Biotec GmbH. Published by Elsevier Inc. All rights reserved.

Denni Algorithm An Enhanced Of SMS (Scan, Move and Sort) Algorithm

NASA Astrophysics Data System (ADS)

Aprilsyah Lubis, Denni; Salim Sitompul, Opim; Marwan; Tulus; Andri Budiman, M.

2017-12-01

Sorting has been a profound area for the algorithmic researchers, and many resources are invested to suggest a more working sorting algorithm. For this purpose many existing sorting algorithms were observed in terms of the efficiency of the algorithmic complexity. Efficient sorting is important to optimize the use of other algorithms that require sorted lists to work correctly. Sorting has been considered as a fundamental problem in the study of algorithms that due to many reasons namely, the necessary to sort information is inherent in many applications, algorithms often use sorting as a key subroutine, in algorithm design there are many essential techniques represented in the body of sorting algorithms, and many engineering issues come to the fore when implementing sorting algorithms., Many algorithms are very well known for sorting the unordered lists, and one of the well-known algorithms that make the process of sorting to be more economical and efficient is SMS (Scan, Move and Sort) algorithm, an enhancement of Quicksort invented Rami Mansi in 2010. This paper presents a new sorting algorithm called Denni-algorithm. The Denni algorithm is considered as an enhancement on the SMS algorithm in average, and worst cases. The Denni algorithm is compared with the SMS algorithm and the results were promising.

Card sorting to evaluate the robustness of the information architecture of a protocol website.

PubMed

Wentzel, J; Müller, F; Beerlage-de Jong, N; van Gemert-Pijnen, J

2016-02-01

A website on Methicillin-Resistant Staphylococcus Aureus, MRSA-net, was developed for Health Care Workers (HCWs) and the general public, in German and in Dutch. The website's content was based on existing protocols and its structure was based on a card sort study. A Human Centered Design approach was applied to ensure a match between user and technology. In the current study we assess whether the website's structure still matches user needs, again via a card sort study. An open card sort study was conducted. Randomly drawn samples of 100 on-site search queries as they were entered on the MRSA-net website (during one year of use) were used as card input. In individual sessions, the cards were sorted by each participant (18 German and 10 Dutch HCWs, and 10 German and 10 Dutch members of the general public) into piles that were meaningful to them. Each participant provided a label for every pile of cards they created. Cluster analysis was performed on the resulting sorts, creating an overview of clusters of items placed together in one pile most frequently. In addition, pile labels were qualitatively analyzed to identify the participants' mental models. Cluster analysis confirmed existing categories and revealed new themes emerging from the search query samples, such as financial issues and consequences for the patient. Even though MRSA-net addresses these topics, they are not prominently covered in the menu structure. The label analysis shows that 7 of a total of 44 MRSA-net categories were not reproduced by the participants. Additional themes such as information on other pathogens and categories such as legal issues emerged. This study shows that the card sort performed to create MRSA-net resulted in overall long-lasting structure and categories. New categories were identified, indicating that additional information needs emerged. Therefore, evaluating website structure should be a recurrent activity. Card sorting with ecological data as input for the cards is useful to identify changes in needs and mental models. By combining qualitative and quantitative analysis we gained insight into additional information needed by the target group, including their view on the domain and related themes. The results show differences between the four user groups in their sorts, which can mostly be explained by the groups' background. These findings confirm that HCD is a valuable approach to tailor information to the target group. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

LIS Professionals as Knowledge Engineers.

ERIC Educational Resources Information Center

Poulter, Alan; And Others

1994-01-01

Considers the role of library and information science professionals as knowledge engineers. Highlights include knowledge acquisition, including personal experience, interviews, protocol analysis, observation, multidimensional sorting, printed sources, and machine learning; knowledge representation, including production rules and semantic nets;…

Millon Clinical Multiaxial Inventory–III Subtypes of Opioid Dependence: Validity and Matching to Behavioral Therapies

PubMed Central

Ball, Samuel A.; Nich, Charla; Rounsaville, Bruce J.; Eagan, Dorothy; Carroll, Kathleen M.

2013-01-01

The concurrent and predictive validity of 2 different methods of Millon Clinical Multiaxial Inventory–III subtyping (protocol sorting, cluster analysis) was evaluated in 125 recently detoxified opioid-dependent outpatients in a 12-week randomized clinical trial. Participants received naltrexone and relapse prevention group counseling and were assigned to 1 of 3 intervention conditions: (a) no-incentive vouchers, (b) incentive vouchers alone, or (c) incentive vouchers plus relationship counseling. Affective disturbance was the most common Axis I protocol-sorted subtype (66%), antisocial–narcissistic was the most common Axis II subtype (46%), and cluster analysis suggested that a 2-cluster solution (high vs. low psychiatric severity) was optimal. Predictive validity analyses indicated less symptom improvement for the higher problem subtypes, and patient treatment matching analyses indicated that some subtypes had better outcomes in the no-incentive voucher conditions. PMID:15301655

Encapsulation of sex sorted boar semen: sperm membrane status and oocyte penetration parameters.

PubMed

Spinaci, Marcella; Chlapanidas, Theodora; Bucci, Diego; Vallorani, Claudia; Perteghella, Sara; Lucconi, Giulia; Communod, Ricardo; Vigo, Daniele; Galeati, Giovanna; Faustini, Massimo; Torre, Maria Luisa

2013-03-01

Although sorted semen is experimentally used for artificial, intrauterine, and intratubal insemination and in vitro fertilization, its commercial application in swine species is still far from a reality. This is because of the low sort rate and the large number of sperm required for routine artificial insemination in the pig, compared with other production animals, and the greater susceptibility of porcine spermatozoa to stress induced by the different sex sorting steps and the postsorting handling protocols. The encapsulation technology could overcome this limitation in vivo, protecting and allowing the slow release of low-dose sorted semen. The aim of this work was to evaluate the impact of the encapsulation process on viability, acrosome integrity, and on the in vitro fertilizing potential of sorted boar semen. Our results indicate that the encapsulation technique does not damage boar sorted semen; in fact, during a 72-hour storage, no differences were observed between liquid-stored sorted semen and encapsulated sorted semen in terms of plasma membrane (39.98 ± 14.38% vs. 44.32 ± 11.72%, respectively) and acrosome integrity (74.32 ± 12.17% vs. 66.07 ± 10.83%, respectively). Encapsulated sorted spermatozoa presented a lower penetration potential than nonencapsulated ones (47.02% vs. 24.57%, respectively, P < 0.0001), and a significant reduction of polyspermic fertilization (60.76% vs. 36.43%, respectively, polyspermic ova/total ova; P < 0.0001). However, no difference (P > 0.05) was observed in terms of total efficiency of fertilization expressed as normospermic oocytes/total oocytes (18.45% vs. 15.43% for sorted diluted and sorted encapsulated semen, respectively). The encapsulation could be an alternative method of storing of pig sex sorted spermatozoa and is potentially a promising technique in order to optimize the use of low dose of sexed spermatozoa in vivo. Copyright © 2013 Elsevier Inc. All rights reserved.

Reducing 4D CT artifacts using optimized sorting based on anatomic similarity.

PubMed

Johnston, Eric; Diehn, Maximilian; Murphy, James D; Loo, Billy W; Maxim, Peter G

2011-05-01

Four-dimensional (4D) computed tomography (CT) has been widely used as a tool to characterize respiratory motion in radiotherapy. The two most commonly used 4D CT algorithms sort images by the associated respiratory phase or displacement into a predefined number of bins, and are prone to image artifacts at transitions between bed positions. The purpose of this work is to demonstrate a method of reducing motion artifacts in 4D CT by incorporating anatomic similarity into phase or displacement based sorting protocols. Ten patient datasets were retrospectively sorted using both the displacement and phase based sorting algorithms. Conventional sorting methods allow selection of only the nearest-neighbor image in time or displacement within each bin. In our method, for each bed position either the displacement or the phase defines the center of a bin range about which several candidate images are selected. The two dimensional correlation coefficients between slices bordering the interface between adjacent couch positions are then calculated for all candidate pairings. Two slices have a high correlation if they are anatomically similar. Candidates from each bin are then selected to maximize the slice correlation over the entire data set using the Dijkstra's shortest path algorithm. To assess the reduction of artifacts, two thoracic radiation oncologists independently compared the resorted 4D datasets pairwise with conventionally sorted datasets, blinded to the sorting method, to choose which had the least motion artifacts. Agreement between reviewers was evaluated using the weighted kappa score. Anatomically based image selection resulted in 4D CT datasets with significantly reduced motion artifacts with both displacement (P = 0.0063) and phase sorting (P = 0.00022). There was good agreement between the two reviewers, with complete agreement 34 times and complete disagreement 6 times. Optimized sorting using anatomic similarity significantly reduces 4D CT motion artifacts compared to conventional phase or displacement based sorting. This improved sorting algorithm is a straightforward extension of the two most common 4D CT sorting algorithms.

Efficient generation of monoclonal antibodies from single rhesus macaque antibody secreting cells.

PubMed

Meng, Weixu; Li, Leike; Xiong, Wei; Fan, Xuejun; Deng, Hui; Bett, Andrew J; Chen, Zhifeng; Tang, Aimin; Cox, Kara S; Joyce, Joseph G; Freed, Daniel C; Thoryk, Elizabeth; Fu, Tong-Ming; Casimiro, Danilo R; Zhang, Ningyan; A Vora, Kalpit; An, Zhiqiang

2015-01-01

Nonhuman primates (NHPs) are used as a preclinical model for vaccine development, and the antibody profiles to experimental vaccines in NHPs can provide critical information for both vaccine design and translation to clinical efficacy. However, an efficient protocol for generating monoclonal antibodies from single antibody secreting cells of NHPs is currently lacking. In this study we established a robust protocol for cloning immunoglobulin (IG) variable domain genes from single rhesus macaque (Macaca mulatta) antibody secreting cells. A sorting strategy was developed using a panel of molecular markers (CD3, CD19, CD20, surface IgG, intracellular IgG, CD27, Ki67 and CD38) to identify the kinetics of B cell response after vaccination. Specific primers for the rhesus macaque IG genes were designed and validated using cDNA isolated from macaque peripheral blood mononuclear cells. Cloning efficiency was averaged at 90% for variable heavy (VH) and light (VL) domains, and 78.5% of the clones (n = 335) were matched VH and VL pairs. Sequence analysis revealed that diverse IGHV subgroups (for VH) and IGKV and IGLV subgroups (for VL) were represented in the cloned antibodies. The protocol was tested in a study using an experimental dengue vaccine candidate. About 26.6% of the monoclonal antibodies cloned from the vaccinated rhesus macaques react with the dengue vaccine antigens. These results validate the protocol for cloning monoclonal antibodies in response to vaccination from single macaque antibody secreting cells, which have general applicability for determining monoclonal antibody profiles in response to other immunogens or vaccine studies of interest in NHPs.

The Container Problem in Bubble-Sort Graphs

NASA Astrophysics Data System (ADS)

Suzuki, Yasuto; Kaneko, Keiichi

Bubble-sort graphs are variants of Cayley graphs. A bubble-sort graph is suitable as a topology for massively parallel systems because of its simple and regular structure. Therefore, in this study, we focus on n-bubble-sort graphs and propose an algorithm to obtain n-1 disjoint paths between two arbitrary nodes in time bounded by a polynomial in n, the degree of the graph plus one. We estimate the time complexity of the algorithm and the sum of the path lengths after proving the correctness of the algorithm. In addition, we report the results of computer experiments evaluating the average performance of the algorithm.

Design of mechanical arm for an automatic sorting system of recyclable cans

NASA Astrophysics Data System (ADS)

Resti, Y.; Mohruni, A. S.; Burlian, F.; Yani, I.; Amran, A.

2018-04-01

The use of a mechanical arm for an automatic sorting system of used cans should be designed carefully. The right design will result in a high precision sorting rate and a short sorting time. The design includes first; design manipulator,second; determine link and joint specifications, and third; build mechanical systems and control systems. This study aims to design the mechanical arm as a hardware system for automatic cans sorting system. The material used for the manipulator is the aluminum plate. The manipulator is designed using 6 links and 6 join where the 6th link is the end effectorand the 6th join is the gripper. As a driving motor used servo motor, while as a microcontroller used Arduino Uno which is connected with Matlab programming language. Based on testing, a mechanical arm designed for this recyclable canned recycling system has a precision sorting rate at 93%, where the average total time required for sorting is 10.82 seconds.

Isolation of CD4+CD25+ regulatory T cells for clinical trials.

PubMed

Hoffmann, Petra; Boeld, Tina J; Eder, Ruediger; Albrecht, Julia; Doser, Kristina; Piseshka, Biserka; Dada, Ashraf; Niemand, Claudia; Assenmacher, Mario; Orsó, Evelyn; Andreesen, Reinhard; Holler, Ernst; Edinger, Matthias

2006-03-01

The adoptive transfer of donor CD4+CD25+ regulatory T cells has been shown to protect from lethal graft-versus-host disease after allogeneic bone marrow transplantation in murine disease models. Efficient isolation strategies that comply with good manufacturing practice (GMP) guidelines are prerequisites for the clinical application of human CD4+CD25+ regulatory T cells. Here we describe the isolation of CD4+CD25+ T cells with regulatory function from standard leukapheresis products by using a 2-step magnetic cell-separation protocol performed under GMP conditions. The generated cell products contained on average 49.5% CD4+CD25high T cells that phenotypically and functionally represented natural CD4+CD25+ regulatory T cells and showed a suppressive activity comparable to that of CD4+CD25+ regulatory T-cell preparations purified by non-GMP-approved fluorescence-activated cell sorting.

Purifying, Separating, and Concentrating Cells From a Sample Low in Biomass

NASA Technical Reports Server (NTRS)

Benardini, James N.; LaDuc, Myron T.; Diamond, Rochelle

2012-01-01

Frequently there is an inability to process and analyze samples of low biomass due to limiting amounts of relevant biomaterial in the sample. Furthermore, molecular biological protocols geared towards increasing the density of recovered cells and biomolecules of interest, by their very nature, also concentrate unwanted inhibitory humic acids and other particulates that have an adversarial effect on downstream analysis. A novel and robust fluorescence-activated cell-sorting (FACS)-based technology has been developed for purifying (removing cells from sampling matrices), separating (based on size, density, morphology), and concentrating cells (spores, prokaryotic, eukaryotic) from a sample low in biomass. The technology capitalizes on fluorescent cell-sorting technologies to purify and concentrate bacterial cells from a low-biomass, high-volume sample. Over the past decade, cell-sorting detection systems have undergone enhancements and increased sensitivity, making bacterial cell sorting a feasible concept. Although there are many unknown limitations with regard to the applicability of this technology to environmental samples (smaller cells, few cells, mixed populations), dogmatic principles support the theoretical effectiveness of this technique upon thorough testing and proper optimization. Furthermore, the pilot study from which this report is based proved effective and demonstrated this technology capable of sorting and concentrating bacterial endospore and bacterial cells of varying size and morphology. Two commercial off-the-shelf bacterial counting kits were used to optimize a bacterial stain/dye FACS protocol. A LIVE/DEAD BacLight Viability and Counting Kit was used to distinguish between the live and dead cells. A Bacterial Counting Kit comprising SYTO BC (mixture of SYTO dyes) was employed as a broad-spectrum bacterial counting agent. Optimization using epifluorescence microscopy was performed with these two dye/stains. This refined protocol was further validated using varying ratios and mixtures of cells to ensure homogenous staining compared to that of individual cells, and were utilized for flow analyzer and FACS labeling. This technology focuses on the purification and concentration of cells from low-biomass spacecraft assembly facility samples. Currently, purification and concentration of low-biomass samples plague planetary protection downstream analyses. Having a capability to use flow cytometry to concentrate cells out of low-biomass, high-volume spacecraft/ facility sample extracts will be of extreme benefit to the fields of planetary protection and astrobiology. Successful research and development of this novel methodology will significantly increase the knowledge base for designing more effective cleaning protocols, and ultimately lead to a more empirical and true account of the microbial diversity present on spacecraft surfaces. Refined cleaning and an enhanced ability to resolve microbial diversity may decrease the overall cost of spacecraft assembly and/or provide a means to begin to assess challenging planetary protection missions.

Flow cytometric sorting of fecal bacteria after in situ hybridization with polynucleotide probes.

PubMed

Bruder, Lena M; Dörkes, Marcel; Fuchs, Bernhard M; Ludwig, Wolfgang; Liebl, Wolfgang

2016-10-01

The gut microbiome represents a key contributor to human physiology, metabolism, immune function, and nutrition. Elucidating the composition and genetics of the gut microbiota under various conditions is essential to understand how microbes function individually and as a community. Metagenomic analyses are increasingly used to study intestinal microbiota. However, for certain scientific questions it is sufficient to examine taxon-specific submetagenomes, covering selected bacterial genera in a targeted manner. Here we established a new variant of fluorescence in situ hybridization (FISH) combined with fluorescence-activated cell sorting (FACS), providing access to the genomes of specific taxa belonging to the complex community of the intestinal microbiota. In contrast to standard oligonucleotide probes, the RNA polynucleotide probe used here, which targets domain III of the 23S rRNA gene, extends the resolution power in environmental samples by increasing signal intensity. Furthermore, cells hybridized with the polynucleotide probe are not subjected to harsh pretreatments, and their genetic information remains intact. The protocol described here was tested on genus-specifically labeled cells in various samples, including complex fecal samples from different laboratory mouse types that harbor diverse intestinal microbiota. Specifically, as an example for the protocol described here, RNA polynucleotide probes could be used to label Enterococcus cells for subsequent sorting by flow cytometry. To detect and quantify enterococci in fecal samples prior to enrichment, taxon-specific PCR and qPCR detection systems have been developed. The accessibility of the genomes from taxon-specifically sorted cells for subsequent molecular analyses was demonstrated by amplification of functional genes. Copyright © 2016 Elsevier GmbH. All rights reserved.

Handling of boar spermatozoa during and after flow cytometric sex-sorting process to improve their in vitro fertilizing ability.

PubMed

del Olmo, D; Parrilla, I; Gil, M A; Maside, C; Tarantini, T; Angel, M A; Roca, J; Martinez, E A; Vazquez, J M

2013-09-01

The objective of this study was to develop an adequate sperm handling protocol in order to obtain a sex-sorted sperm population with an optimal fertilizing ability. For this purpose, different aspects of the sorting procedure were examined. The effects of the high dilution rates (experiment 1), type of collection medium used (experiment 2), and sheath fluid composition (experiment 3) on sorted boar sperm quality and function were evaluated. Sperm quality was assessed by motility and viability tests, whereas sperm function was evaluated by an in vitro fertilization assay which determined the penetration and polyspermy rates as well as the mean number of sperm penetrating each oocyte. In experiment 1, the results obtained indicated that the high dilution rates did not cause a decrease either in the sperm quality parameters evaluated or the in vitro fertilization ability of spermatozoa. In experiment 2, although sperm quality was not affected, fertilizing ability was compromised after sorting, regardless of the collection medium that was used. In the experiment 3, all groups displayed adequate sperm quality values, but higher in vitro fertility parameters were obtained for spermatozoa sorted in presence of EDTA in the sheath fluid and egg yolk (EY) in the collection media when compared with those sorted in absence of these protective agents. No differences in penetration rates between unsorted highly diluted (control) and sorted sperm in the presence of EDTA and EY were observed. In conclusion, fertilizing ability was compromised in sex-sorted sperm. The addition of EDTA to sheath fluid and EY to collection medium improved boar sperm fertilizing ability, and both agents should be included as essential media components in future studies. Copyright © 2013 Elsevier Inc. All rights reserved.

Microenvironments and Signaling Pathways Regulating Early Dissemination, Dormancy, and Metastasis

DTIC Science & Technology

2015-09-01

late disseminated tumor cells. Progress has also been made in devising a sorting protocol to isolate CFP+/HER2+ DTCs from lungs and CTCs in the MMTV...early dissemination of pre- malignant MECs. We further hypothesize that after extravasation at S-TMEM, in order to exit dormancy a stable S-TMEM...mentioned in section SA1.2, and the optimization of these protocols is underway. Aim 2.1 requires that we validate the components of the TMEM in the

An Unsupervised Online Spike-Sorting Framework.

PubMed

Knieling, Simeon; Sridharan, Kousik S; Belardinelli, Paolo; Naros, Georgios; Weiss, Daniel; Mormann, Florian; Gharabaghi, Alireza

2016-08-01

Extracellular neuronal microelectrode recordings can include action potentials from multiple neurons. To separate spikes from different neurons, they can be sorted according to their shape, a procedure referred to as spike-sorting. Several algorithms have been reported to solve this task. However, when clustering outcomes are unsatisfactory, most of them are difficult to adjust to achieve the desired results. We present an online spike-sorting framework that uses feature normalization and weighting to maximize the distinctiveness between different spike shapes. Furthermore, multiple criteria are applied to either facilitate or prevent cluster fusion, thereby enabling experimenters to fine-tune the sorting process. We compare our method to established unsupervised offline (Wave_Clus (WC)) and online (OSort (OS)) algorithms by examining their performance in sorting various test datasets using two different scoring systems (AMI and the Adamos metric). Furthermore, we evaluate sorting capabilities on intra-operative recordings using established quality metrics. Compared to WC and OS, our algorithm achieved comparable or higher scores on average and produced more convincing sorting results for intra-operative datasets. Thus, the presented framework is suitable for both online and offline analysis and could substantially improve the quality of microelectrode-based data evaluation for research and clinical application.

Microfluidic, marker-free isolation of circulating tumor cells from blood samples

PubMed Central

Karabacak, Nezihi Murat; Spuhler, Philipp S; Fachin, Fabio; Lim, Eugene J; Pai, Vincent; Ozkumur, Emre; Martel, Joseph M; Kojic, Nikola; Smith, Kyle; Chen, Pin-i; Yang, Jennifer; Hwang, Henry; Morgan, Bailey; Trautwein, Julie; Barber, Thomas A; Stott, Shannon L; Maheswaran, Shyamala; Kapur, Ravi; Haber, Daniel A; Toner, Mehmet

2014-01-01

The ability to isolate and analyze rare circulating tumor cells (CTCs) has the potential to further our understanding of cancer metastasis and enhance the care of cancer patients. In this protocol, we describe the procedure for isolating rare CTCs from blood samples by using tumor antigen–independent microfluidic CTC-iChip technology. The CTC-iChip uses deterministic lateral displacement, inertial focusing and magnetophoresis to sort up to 107 cells/s. By using two-stage magnetophoresis and depletion antibodies against leukocytes, we achieve 3.8-log depletion of white blood cells and a 97% yield of rare cells with a sample processing rate of 8 ml of whole blood/h. The CTC-iChip is compatible with standard cytopathological and RNA-based characterization methods. This protocol describes device production, assembly, blood sample preparation, system setup and the CTC isolation process. Sorting 8 ml of blood sample requires 2 h including setup time, and chip production requires 2–5 d. PMID:24577360

DNA flow cytometry of human spermatozoa: consistent stoichiometric staining of sperm DNA using a novel decondensation protocol.

PubMed

Kovács, Tamás; Békési, Gyöngyi; Fábián, Akos; Rákosy, Zsuzsa; Horváth, Gábor; Mátyus, László; Balázs, Margit; Jenei, Attila

2008-10-01

Rapid flow cytometric measurement of the frequency of aneuploid human sperms is in increasing demand but development of an exploitable method is hindered by difficulties of stoichiometric staining of sperm DNA. An aggressive decondensation protocol is needed after which cell integrity still remains intact. We used flow cytometry to examine the effect of lithium diiodosalicylate (LIS, chaotropic agent) on fluorescence intensity of propidium iodide-treated human spermatozoa from 10 normozoospermic men. When flow cytometric identification of diploid spermatozoa was achieved, validation was performed after sorting by three-color FISH. In contrast with the extremely variable histograms of nondecondensed sperms, consistent identification of haploid and diploid spermatozoa was possible if samples were decondensed with LIS prior to flow cytometry. A 76-fold enrichment of diploid sperms was observed in the sorted fractions by FISH. A significant correlation was found between the proportion of sorted cells and of diploid sperms by FISH. Application of LIS during the preparation of sperm for flow cytometry appears to ensure the stoichiometric staining of sperm DNA, making quantification of aneuploid sperm percentage possible. To our knowledge this is the first report in terms of separating spermatozoa with confirmedly abnormal chromosomal content. High correlation between the proportion of cells identified as having double DNA content by flow cytometry and diploid sperm by FISH allows rapid calculation of diploidy rate. Copyright 2008 International Society for Advancement of Cytometry.

Non-invasive sex assessment in bovine semen by Raman spectroscopy

NASA Astrophysics Data System (ADS)

De Luca, A. C.; Managó, S.; Ferrara, M. A.; Rendina, I.; Sirleto, L.; Puglisi, R.; Balduzzi, D.; Galli, A.; Ferraro, P.; Coppola, G.

2014-05-01

X- and Y-chromosome-bearing sperm cell sorting is of great interest, especially for animal production management systems and genetic improvement programs. Here, we demonstrate an optical method based on Raman spectroscopy to separate X- and Y-chromosome-bearing sperm cells, overcoming many of the limitations associated with current sex-sorting protocols. A priori Raman imaging of bull spermatozoa was utilized to select the sampling points (head-neck region), which were then used to discriminate cells based on a spectral classification model. Main variations of Raman peaks associated with the DNA content were observed together with a variation due to the sex membrane proteins. Next, we used principal component analysis to determine the efficiency of our device as a cell sorting method. The results (>90% accuracy) demonstrated that Raman spectroscopy is a powerful candidate for the development of a highly efficient, non-invasive, and non-destructive tool for sperm sexing.

A study of the asymmetrical distribution of solar activity features on solar and plasma parameters (1967-2016)

NASA Astrophysics Data System (ADS)

El-Borie, M. A.; El-Taher, A. M.; Aly, N. E.; Bishara, A. A.

2018-04-01

The impact of asymmetrical distribution of hemispheric sunspot areas (SSAs) on the interplanetary magnetic field, plasma, and solar parameters from 1967 to 2016 has been studied. The N-S asymmetry of solar-plasma activities based on SSAs has a northern dominance during solar cycles 20 and 24. However, it has a tendency to shift to the southern hemisphere in cycles 21, 22, and 23. The solar cycle 23 showed that the sorted southern SSAs days predominated over the northern days by ˜17%. Through the solar cycles 21-24, the SSAs of the southern hemisphere were more active. In contrast, the northern SSAs predominate over the southern one by 9% throughout solar cycle 20. On the other hand, the average differences of field magnitude for the sorted northern and southern groups during solar cycles 20-24 are statistically insignificant. Clearly, twenty years showed that the solar plasma ion density from the sorted northern group was denser than that of southern group and a highest northern dominant peak occurred in 1971. In contrast, seventeen out of fifty years showed the reverse. In addition, there are fifteen clear asymmetries of solar wind speed (SWS), with SWS (N) > SWS (S), and during the years 1972, 2002, and 2008, the SWS from the sorted northern group was faster than that of southern activity group by 6.16 ± 0.65 km/s, 5.70 ± 0.86 km/s, and 5.76 ± 1.35 km/s, respectively. For the solar cycles 20-24, the grand-averages of P from the sorted solar northern and southern have nearly the same parameter values. The solar plasma was hotter for the sorted northern activity group than the southern ones for 17 years out of 50. Most significant northern prevalent asymmetries were found in 1972 (5.76 ± 0.66 × 103 K) and 1996 (4.7 ± 0.8 × 103 K), while two significant equivalent dominant southern asymmetries (˜3.8 ± 0.3 × 103 K) occurred in 1978 and 1993. The grand averages of sunspot numbers have symmetric activity for the two sorted northern and southern hemispheres through the solar cycles 20 and 21. The sunspots tend to be the southern dominance during the solar cycles 22 and 23, and it shifted during solar cycle 24 to symmetric distribution on both solar hemispheres.

Feature extraction using extrema sampling of discrete derivatives for spike sorting in implantable upper-limb neural prostheses.

PubMed

Zamani, Majid; Demosthenous, Andreas

2014-07-01

Next generation neural interfaces for upper-limb (and other) prostheses aim to develop implantable interfaces for one or more nerves, each interface having many neural signal channels that work reliably in the stump without harming the nerves. To achieve real-time multi-channel processing it is important to integrate spike sorting on-chip to overcome limitations in transmission bandwidth. This requires computationally efficient algorithms for feature extraction and clustering suitable for low-power hardware implementation. This paper describes a new feature extraction method for real-time spike sorting based on extrema analysis (namely positive peaks and negative peaks) of spike shapes and their discrete derivatives at different frequency bands. Employing simulation across different datasets, the accuracy and computational complexity of the proposed method are assessed and compared with other methods. The average classification accuracy of the proposed method in conjunction with online sorting (O-Sort) is 91.6%, outperforming all the other methods tested with the O-Sort clustering algorithm. The proposed method offers a better tradeoff between classification error and computational complexity, making it a particularly strong choice for on-chip spike sorting.

Design of MPPT Controller Monitoring Software Based on QT Framework

NASA Astrophysics Data System (ADS)

Meng, X. Z.; Lu, P. G.

2017-10-01

The MPPT controller was a hardware device for tracking the maximum power point of solar photovoltaic array. Multiple controllers could be working as networking mode by specific communicating protocol. In this article, based on C++ GUI programming with Qt frame, we designed one sort of desktop application for monitoring and analyzing operational parameter of MPPT controller. The type of communicating protocol for building network was Modbus protocol which using Remote Terminal Unit mode and The desktop application of host computer was connected with all the controllers in the network through RS485 communication or ZigBee wireless communication. Using this application, user could monitor the parameter of controller wherever they were by internet.

Development of procedures for sex-sorting frozen-thawed bovine spermatozoa.

PubMed

Underwood, S L; Bathgate, R; Maxwell, W M C; Evans, G

2009-06-01

Dairy bull sperm may be sex-sorted, frozen and used to artificially inseminate heifers with acceptable fertility if the herd is well-managed. One drawback to the technology is that donor bulls must be located within a short distance of the sorting facility in order to collect semen, which limits the number of bulls from which sorted sperm are available. A successful method used to overcome this limitation in sheep is sex-sorting from frozen-thawed semen and refreezing for artificial insemination. This technique is attractive to the dairy industry, and therefore a series of three experiments was designed to investigate the optimal methods to prepare, sex-sort and re-freeze frozen-thawed bovine sperm. Sperm were prepared for sorting by density gradient separation in either PureSperm or BoviPure, followed by staining in one of three diluents (Androhep, Bovine Sheath Fluid + 0.3% BSA or TALP buffer). Sperm were sorted and collected into Test yolk buffer, and frozen in an extender containing 0, 0.25, 0.375 or 0.5% Equex STM Paste. Frozen-thawed sperm were better orientated (p = 0.006) and had fewer damaged membranes (8.7 +/- 0.6% vs 19.5 +/- 2.4%; p = 0.003) after centrifugation in PureSperm rather than BoviPure gradients. Sperm orientation (p < 0.05) and motility (69.9 +/- 3.0 vs 55.6 +/- 4.0; p < 0.001) were highest after staining in Androhep rather than in TALP buffer. Sperm were more motile (58.2 +/- 4.7 vs 38.7 +/- 3.5; p < 0.001) and had better acrosome integrity (74.3 +/- 2.9 vs 66.8 +/- 2.0; p < 0.001) after freezing in an extender containing 0.375% Equex STM Paste than in extender without Equex. Hence, a protocol has been developed to allow frozen-thawed bull sperm to be sex-sorted with high resolution between the sexes, then re-frozen and thawed with retention of motility and acrosome integrity.

Sorting signed permutations by inversions in O(nlogn) time.

PubMed

Swenson, Krister M; Rajan, Vaibhav; Lin, Yu; Moret, Bernard M E

2010-03-01

The study of genomic inversions (or reversals) has been a mainstay of computational genomics for nearly 20 years. After the initial breakthrough of Hannenhalli and Pevzner, who gave the first polynomial-time algorithm for sorting signed permutations by inversions, improved algorithms have been designed, culminating with an optimal linear-time algorithm for computing the inversion distance and a subquadratic algorithm for providing a shortest sequence of inversions--also known as sorting by inversions. Remaining open was the question of whether sorting by inversions could be done in O(nlogn) time. In this article, we present a qualified answer to this question, by providing two new sorting algorithms, a simple and fast randomized algorithm and a deterministic refinement. The deterministic algorithm runs in time O(nlogn + kn), where k is a data-dependent parameter. We provide the results of extensive experiments showing that both the average and the standard deviation for k are small constants, independent of the size of the permutation. We conclude (but do not prove) that almost all signed permutations can be sorted by inversions in O(nlogn) time.

TH-E-17A-07: Improved Cine Four-Dimensional Computed Tomography (4D CT) Acquisition and Processing Method

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

Castillo, S; Castillo, R; Castillo, E

2014-06-15

Purpose: Artifacts arising from the 4D CT acquisition and post-processing methods add systematic uncertainty to the treatment planning process. We propose an alternate cine 4D CT acquisition and post-processing method to consistently reduce artifacts, and explore patient parameters indicative of image quality. Methods: In an IRB-approved protocol, 18 patients with primary thoracic malignancies received a standard cine 4D CT acquisition followed by an oversampling 4D CT that doubled the number of images acquired. A second cohort of 10 patients received the clinical 4D CT plus 3 oversampling scans for intra-fraction reproducibility. The clinical acquisitions were processed by the standard phasemore » sorting method. The oversampling acquisitions were processed using Dijkstras algorithm to optimize an artifact metric over available image data. Image quality was evaluated with a one-way mixed ANOVA model using a correlation-based artifact metric calculated from the final 4D CT image sets. Spearman correlations and a linear mixed model tested the association between breathing parameters, patient characteristics, and image quality. Results: The oversampling 4D CT scans reduced artifact presence significantly by 27% and 28%, for the first cohort and second cohort respectively. From cohort 2, the inter-replicate deviation for the oversampling method was within approximately 13% of the cross scan average at the 0.05 significance level. Artifact presence for both clinical and oversampling methods was significantly correlated with breathing period (ρ=0.407, p-value<0.032 clinical, ρ=0.296, p-value<0.041 oversampling). Artifact presence in the oversampling method was significantly correlated with amount of data acquired, (ρ=-0.335, p-value<0.02) indicating decreased artifact presence with increased breathing cycles per scan location. Conclusion: The 4D CT oversampling acquisition with optimized sorting reduced artifact presence significantly and reproducibly compared to the phase-sorted clinical acquisition.« less

DIE-RNA: A Reproducible Strategy for the Digestion of Normal and Injured Pancreas, Isolation of Pancreatic Cells from Genetically Engineered Mouse Models and Extraction of High Quality RNA

PubMed Central

Assi, Mohamad; Dauguet, Nicolas; Jacquemin, Patrick

2018-01-01

The isolation of ribonucleic acid (RNA) suitable for gene expression studies is challenging in the pancreas, due to its high ribonuclease activity. This is even more complicated during pancreatitis, a condition associated with inflammation and fibrosis. Our aim was to implement a time-effective and reproducible protocol to isolate high quality RNA from specific pancreatic cell subtypes, in normal and inflammatory conditions. We used two genetically engineered mouse models (GEMM), Ela-CreER/YFP and Sox9-CreER/YFP, to isolate acinar and ductal cells, respectively. To induce pancreatitis, mice received a caerulein treatment (125 μg/kg) for 8 and 72 h. We alternatively used EGTA and calcium buffers that contain collagenase P (0.6 mg/mL) to rapidly digest the pancreas into individual cells. Most of the cells from normal and injured pancreas were single-dissociated, exhibited a round morphology and did not incorporate trypan blue dye. Cell suspensions from Ela- and Sox9-CreER/YFP pancreas were then sorted by flow cytometry to isolate the YFP-positive acinar and ductal cells, respectively. Sorted cells kept a round shape and emitted fluorescence detected by the 38 HE green fluorescence filter. RNA was isolated by column-based purification approach. The RNA integrity number (RIN) was high in sorted acinar cell fractions treated with or without caerulein (8.6 ± 0.17 and 8.4 ± 0.09, respectively), compared to the whole pancreas fraction (4.8 ± 1.1). Given the low number of sorted ductal cells, the RIN value was slightly lower compared to acini (7.4 ± 0.4). Quantitative-PCR experiments indicated that sorted acinar and ductal cells express the specific acinar and ductal markers, respectively. Additionally, RNA preparations from caerulein-treated acinar cells were free from significant contamination with immune cell RNA. We thus validated the DIE (Digestion, Isolation, and Extraction)-RNA tool as a reproducible and efficient protocol to isolate pure acinar and ductal cells in vivo and to extract high quality RNA from these cells. PMID:29535635

DIE-RNA: A Reproducible Strategy for the Digestion of Normal and Injured Pancreas, Isolation of Pancreatic Cells from Genetically Engineered Mouse Models and Extraction of High Quality RNA.

PubMed

Assi, Mohamad; Dauguet, Nicolas; Jacquemin, Patrick

2018-01-01

The isolation of ribonucleic acid (RNA) suitable for gene expression studies is challenging in the pancreas, due to its high ribonuclease activity. This is even more complicated during pancreatitis, a condition associated with inflammation and fibrosis. Our aim was to implement a time-effective and reproducible protocol to isolate high quality RNA from specific pancreatic cell subtypes, in normal and inflammatory conditions. We used two genetically engineered mouse models (GEMM), Ela-CreER/YFP and Sox9-CreER/YFP, to isolate acinar and ductal cells, respectively. To induce pancreatitis, mice received a caerulein treatment (125 μg/kg) for 8 and 72 h. We alternatively used EGTA and calcium buffers that contain collagenase P (0.6 mg/mL) to rapidly digest the pancreas into individual cells. Most of the cells from normal and injured pancreas were single-dissociated, exhibited a round morphology and did not incorporate trypan blue dye. Cell suspensions from Ela- and Sox9-CreER/YFP pancreas were then sorted by flow cytometry to isolate the YFP-positive acinar and ductal cells, respectively. Sorted cells kept a round shape and emitted fluorescence detected by the 38 HE green fluorescence filter. RNA was isolated by column-based purification approach. The RNA integrity number (RIN) was high in sorted acinar cell fractions treated with or without caerulein (8.6 ± 0.17 and 8.4 ± 0.09, respectively), compared to the whole pancreas fraction (4.8 ± 1.1). Given the low number of sorted ductal cells, the RIN value was slightly lower compared to acini (7.4 ± 0.4). Quantitative-PCR experiments indicated that sorted acinar and ductal cells express the specific acinar and ductal markers, respectively. Additionally, RNA preparations from caerulein-treated acinar cells were free from significant contamination with immune cell RNA. We thus validated the DIE (Digestion, Isolation, and Extraction)-RNA tool as a reproducible and efficient protocol to isolate pure acinar and ductal cells in vivo and to extract high quality RNA from these cells.

Controlled quantum secure communication protocol with single photons in both polarization and spatial-mode degrees of freedom

NASA Astrophysics Data System (ADS)

Wang, Lili; Ma, Wenping

2016-02-01

In this paper, we propose a new controlled quantum secure direct communication (CQSDC) protocol with single photons in both polarization and spatial-mode degrees of freedom. Based on the defined local collective unitary operations, the sender’s secret messages can be transmitted directly to the receiver through encoding secret messages on the particles. Only with the help of the third side, the receiver can reconstruct the secret messages. Each single photon in two degrees of freedom can carry two bits of information, so the cost of our protocol is less than others using entangled qubits. Moreover, the security of our QSDC network protocol is discussed comprehensively. It is shown that our new CQSDC protocol cannot only defend the outsider eavesdroppers’ several sorts of attacks but also the inside attacks. Besides, our protocol is feasible since the preparation and the measurement of single photon quantum states in both the polarization and the spatial-mode degrees of freedom are available with current quantum techniques.

Millon Clinical Multiaxial Inventory-III Subtypes of Opioid Dependence: Validity and Matching to Behavioral Therapies

ERIC Educational Resources Information Center

Ball, Samuel A.; Nich, Charla; Rounsaville, Bruce J.; Eagan, Dorothy; Carroll, Kathleen M.

2004-01-01

The concurrent and predictive validity of 2 different methods of Millon Clinical Multiaxial Inventory-III subtyping (protocol sorting, cluster analysis) was evaluated in 125 recently detoxified opioid-dependent outpatients in a 12-week randomized clinical trial. Participants received naltrexone and relapse prevention group counseling and were…

A MORE COST-EFFECTIVE EMAP-W BENTHIC MACROFAUNAL SAMPLE UNIT

EPA Science Inventory

The standard EPA West Coast Environmental Monitoring and Assessment Program (EMAP-W) benthic macrofaunal sampling protocol is to collect 30-50 random benthic samples per reporting unit (e.g., estuary, region) using a 0.1 m2 grab and to sort out macrofauna using a 1.0 mm mesh scre...

Isolation of skeletal muscle stem cells by fluorescence-activated cell sorting.

PubMed

Liu, Ling; Cheung, Tom H; Charville, Gregory W; Rando, Thomas A

2015-10-01

The prospective isolation of purified stem cell populations has dramatically altered the field of stem cell biology, and it has been a major focus of research across tissues in different organisms. Muscle stem cells (MuSCs) are now among the most intensely studied stem cell populations in mammalian systems, and the prospective isolation of these cells has allowed cellular and molecular characterizations that were not dreamed of a decade ago. In this protocol, we describe how to isolate MuSCs from limb muscles of adult mice by fluorescence-activated cell sorting (FACS). We provide a detailed description of the physical and enzymatic dissociation of mononucleated cells from limb muscles, a procedure that is essential in order to maximize cell yield. We also describe a FACS-based method that is used subsequently to obtain highly pure populations of either quiescent or activated MuSCs (VCAM(+)CD31(-)CD45(-)Sca1(-)). The isolation process takes ∼5-6 h to complete. The protocol also allows for the isolation of endothelial cells, hematopoietic cells and mesenchymal stem cells from muscle tissue.

Single-cell analysis and sorting using droplet-based microfluidics.

PubMed

Mazutis, Linas; Gilbert, John; Ung, W Lloyd; Weitz, David A; Griffiths, Andrew D; Heyman, John A

2013-05-01

We present a droplet-based microfluidics protocol for high-throughput analysis and sorting of single cells. Compartmentalization of single cells in droplets enables the analysis of proteins released from or secreted by cells, thereby overcoming one of the major limitations of traditional flow cytometry and fluorescence-activated cell sorting. As an example of this approach, we detail a binding assay for detecting antibodies secreted from single mouse hybridoma cells. Secreted antibodies are detected after only 15 min by co-compartmentalizing single mouse hybridoma cells, a fluorescent probe and single beads coated with anti-mouse IgG antibodies in 50-pl droplets. The beads capture the secreted antibodies and, when the captured antibodies bind to the probe, the fluorescence becomes localized on the beads, generating a clearly distinguishable fluorescence signal that enables droplet sorting at ∼200 Hz as well as cell enrichment. The microfluidic system described is easily adapted for screening other intracellular, cell-surface or secreted proteins and for quantifying catalytic or regulatory activities. In order to screen ∼1 million cells, the microfluidic operations require 2-6 h; the entire process, including preparation of microfluidic devices and mammalian cells, requires 5-7 d.

Quadrupole Magnetic Sorting of Porcine Islets of Langerhans

PubMed Central

Shenkman, Rustin M.; Chalmers, Jeffrey J.; Hering, Bernhard J.; Kirchhof, Nicole

2009-01-01

Islet transplantation is emerging as a treatment option for selected patients with type 1 diabetes. Inconsistent isolation, purification, and recovery of large numbers of high-quality islets remain substantial impediments to progress in the field. Removing islets as soon as they are liberated from the pancreas during digestion and circumventing the need for density gradient purification is likely to result in substantially increased viable islet yields by minimizing exposure to proteolytic enzymes, reactive oxygen intermediates, and mechanical stress associated with centrifugation. This study capitalized on the hypervascularity of islets compared with acinar tissue to explore their preferential enrichment with magnetic beads to enable immediate separation in a magnetic field utilizing a quadrupole magnetic sorting. The results demonstrate that (1) preferential enrichment of porcine islets is achievable, but homogeneous bead distribution within the pancreas is difficult to achieve with current protocols; (2) greater than 70% of islets in the dissociated pancreatic tissue were recovered by quadrupole magnetic sorting, but their purity was low; and (3) infused islets purified by density gradients and subsequently passed through quadrupole magnetic sorting had similar potency as uninfused islets. These results demonstrate proof of concept and define the steps for implementation of this technology in pig and human islet isolation. PMID:19505179

Single-cell analysis and sorting using droplet-based microfluidics

PubMed Central

Mazutis, Linas; Gilbert, John; Ung, W Lloyd; Weitz, David A; Griffiths, Andrew D; Heyman, John A

2014-01-01

We present a droplet-based microfluidics protocol for high-throughput analysis and sorting of single cells. compartmentalization of single cells in droplets enables the analysis of proteins released from or secreted by cells, thereby overcoming one of the major limitations of traditional flow cytometry and fluorescence-activated cell sorting. as an example of this approach, we detail a binding assay for detecting antibodies secreted from single mouse hybridoma cells. secreted antibodies are detected after only 15 min by co-compartmentalizing single mouse hybridoma cells, a fluorescent probe and single beads coated with anti-mouse IgG antibodies in 50-pl droplets. the beads capture the secreted antibodies and, when the captured antibodies bind to the probe, the fluorescence becomes localized on the beads, generating a clearly distinguishable fluorescence signal that enables droplet sorting at ~200 Hz as well as cell enrichment. the microfluidic system described is easily adapted for screening other intracellular, cell-surface or secreted proteins and for quantifying catalytic or regulatory activities. In order to screen ~1 million cells, the microfluidic operations require 2–6 h; the entire process, including preparation of microfluidic devices and mammalian cells, requires 5–7 d. PMID:23558786

An algorithm for 4D CT image sorting using spatial continuity.

PubMed

Li, Chen; Liu, Jie

2013-01-01

4D CT, which could locate the position of the movement of the tumor in the entire respiratory cycle and reduce image artifacts effectively, has been widely used in making radiation therapy of tumors. The current 4D CT methods required external surrogates of respiratory motion obtained from extra instruments. However, respiratory signals recorded by these external makers may not always accurately represent the internal tumor and organ movements, especially when irregular breathing patterns happened. In this paper we have proposed a novel automatic 4D CT sorting algorithm that performs without these external surrogates. The sorting algorithm requires collecting the image data with a cine scan protocol. Beginning with the first couch position, images from the adjacent couch position are selected out according to spatial continuity. The process is continued until images from all couch positions are sorted and the entire 3D volume is produced. The algorithm is verified by respiratory phantom image data and clinical image data. The primary test results show that the 4D CT images created by our algorithm have eliminated the motion artifacts effectively and clearly demonstrated the movement of tumor and organ in the breath period.

A probability-based multi-cycle sorting method for 4D-MRI: A simulation study.

PubMed

Liang, Xiao; Yin, Fang-Fang; Liu, Yilin; Cai, Jing

2016-12-01

To develop a novel probability-based sorting method capable of generating multiple breathing cycles of 4D-MRI images and to evaluate performance of this new method by comparing with conventional phase-based methods in terms of image quality and tumor motion measurement. Based on previous findings that breathing motion probability density function (PDF) of a single breathing cycle is dramatically different from true stabilized PDF that resulted from many breathing cycles, it is expected that a probability-based sorting method capable of generating multiple breathing cycles of 4D images may capture breathing variation information missing from conventional single-cycle sorting methods. The overall idea is to identify a few main breathing cycles (and their corresponding weightings) that can best represent the main breathing patterns of the patient and then reconstruct a set of 4D images for each of the identified main breathing cycles. This method is implemented in three steps: (1) The breathing signal is decomposed into individual breathing cycles, characterized by amplitude, and period; (2) individual breathing cycles are grouped based on amplitude and period to determine the main breathing cycles. If a group contains more than 10% of all breathing cycles in a breathing signal, it is determined as a main breathing pattern group and is represented by the average of individual breathing cycles in the group; (3) for each main breathing cycle, a set of 4D images is reconstructed using a result-driven sorting method adapted from our previous study. The probability-based sorting method was first tested on 26 patients' breathing signals to evaluate its feasibility of improving target motion PDF. The new method was subsequently tested for a sequential image acquisition scheme on the 4D digital extended cardiac torso (XCAT) phantom. Performance of the probability-based and conventional sorting methods was evaluated in terms of target volume precision and accuracy as measured by the 4D images, and also the accuracy of average intensity projection (AIP) of 4D images. Probability-based sorting showed improved similarity of breathing motion PDF from 4D images to reference PDF compared to single cycle sorting, indicated by the significant increase in Dice similarity coefficient (DSC) (probability-based sorting, DSC = 0.89 ± 0.03, and single cycle sorting, DSC = 0.83 ± 0.05, p-value <0.001). Based on the simulation study on XCAT, the probability-based method outperforms the conventional phase-based methods in qualitative evaluation on motion artifacts and quantitative evaluation on tumor volume precision and accuracy and accuracy of AIP of the 4D images. In this paper the authors demonstrated the feasibility of a novel probability-based multicycle 4D image sorting method. The authors' preliminary results showed that the new method can improve the accuracy of tumor motion PDF and the AIP of 4D images, presenting potential advantages over the conventional phase-based sorting method for radiation therapy motion management.

The use of Optical Character Recognition (OCR) in the digitisation of herbarium specimen labels.

PubMed

Drinkwater, Robyn E; Cubey, Robert W N; Haston, Elspeth M

2014-01-01

At the Royal Botanic Garden Edinburgh (RBGE) the use of Optical Character Recognition (OCR) to aid the digitisation process has been investigated. This was tested using a herbarium specimen digitisation process with two stages of data entry. Records were initially batch-processed to add data extracted from the OCR text prior to being sorted based on Collector and/or Country. Using images of the specimens, a team of six digitisers then added data to the specimen records. To investigate whether the data from OCR aid the digitisation process, they completed a series of trials which compared the efficiency of data entry between sorted and unsorted batches of specimens. A survey was carried out to explore the opinion of the digitisation staff to the different sorting options. In total 7,200 specimens were processed. When compared to an unsorted, random set of specimens, those which were sorted based on data added from the OCR were quicker to digitise. Of the methods tested here, the most successful in terms of efficiency used a protocol which required entering data into a limited set of fields and where the records were filtered by Collector and Country. The survey and subsequent discussions with the digitisation staff highlighted their preference for working with sorted specimens, in which label layout, locations and handwriting are likely to be similar, and so a familiarity with the Collector or Country is rapidly established.

Sperm sex-sorting and preservation for managing the sex ratio and genetic diversity of the southern white rhinoceros (Ceratotherium simum simum).

PubMed

O'Brien, J K; Roth, T L; Stoops, M A; Ball, R L; Steinman, K J; Montano, G A; Love, C C; Robeck, T R

2015-01-01

White rhinoceros ejaculates (n=9) collected by electroejaculation from four males were shipped (10°C, 12h) to develop procedures for the production of chilled and frozen-thawed sex-sorted spermatozoa of adequate quality for artificial insemination (AI). Of all electroejaculate fractions, 39.7% (31/78) exhibited high quality post-collection (≥70% total motility and membrane integrity) and of those, 54.8% (17/31) presented reduced in vitro quality after transport and were retrospectively determined to exhibit urine-contamination (≥21.0μg creatinine/ml). Of fractions analyzed for creatinine concentration, 69% (44/64) were classified as urine-contaminated. For high quality non-contaminated fractions, in vitro parameters (motility, velocity, membrane, acrosome and DNA integrity) of chilled non-sorted and sorted spermatozoa were well-maintained at 5°C up to 54h post-collection, whereby >70% of post-transport (non-sorted) or post-sort (sorted) values were retained. By 54h post-collection, some motility parameters were higher (P<0.05) for non-sorted spermatozoa (total motility, rapid velocity, average path velocity) whereas all remaining motion parameters as well as membrane, acrosome and DNA integrity were similar between sperm types. In comparison with a straw method, directional freezing resulted in enhanced (P<0.05) motility and velocity of non-sorted and sorted spermatozoa, with comparable overall post-thaw quality between sperm types. High purity enrichment of X-bearing (89±6%) or Y-bearing (86±3%) spermatozoa was achieved using moderate sorting rates (2540±498X-spermatozoa/s; 1800±557Y-spermatozoa/s). Collective in vitro characteristics of sorted-chilled or sorted-frozen-thawed spermatozoa derived from high quality electroejaculates indicate acceptable fertility potential for use in AI. Copyright © 2014 Elsevier B.V. All rights reserved.

Isolation of Primary Human Skeletal Muscle Cells

PubMed Central

Spinazzola, Janelle M.; Gussoni, Emanuela

2017-01-01

Primary myoblast culture is a valuable tool in research of muscle disease, pathophysiology, and pharmacology. This protocol describes techniques for dissociation of cells from human skeletal muscle biopsies and enrichment for a highly myogenic population by fluorescence-activated cell sorting (FACS). We also describe methods for assessing myogenicity and population expansion for subsequent in vitro study. PMID:29152538

The effects of hoechst 33342 staining and the male sample donor on the sorting efficiency of canine spermatozoa.

PubMed

Rodenas, C; Lucas, X; Tarantini, T; Del Olmo, D; Roca, J; Vazquez, J M; Martinez, E A; Parrilla, I

2014-02-01

The aim of this study was to evaluate the influence of Hoechst 33342 (H-42) concentration and of the male donor on the efficiency of sex-sorting procedure in canine spermatozoa. Semen samples from six dogs (three ejaculates/dog) were diluted to 100 × 10(6) sperm/ml, split into four aliquots, stained with increasing H-42 concentrations (5, 7.5, 10 and 12.5 μl, respectively) and sorted by flow cytometry. The rates of non-viable (FDA+), oriented (OS) and selected spermatozoa (SS), as well as the average sorting rates (SR, sorted spermatozoa/s), were used to determine the sorting efficiency. The effects of the sorting procedure on the quality of sorted spermatozoa were evaluated in terms of total motility (TM), percentage of viable spermatozoa (spermatozoa with membrane and acrosomal integrity) and percentage of spermatozoa with reacted/damaged acrosomes. X- and Y-chromosome-bearing sperm populations were identified in all of the samples stained with 7.5, 10 and 12.5 μl of H-42, while these two populations were only identified in 77.5% of samples stained with 5 μl. The values of OS, SS and SR were influenced by the male donor (p < 0.01) but not by the H-42 concentration used. The quality of sorted sperm samples immediately after sorting was similar to that of fresh samples, while centrifugation resulted in significant reduction (p < 0.05) in TM and in the percentage of viable spermatozoa and a significant increase (p < 0.01) in the percentage of spermatozoa with damage/reacted acrosomes. In conclusion, the sex-sorting of canine spermatozoa by flow cytometry can be performed successfully using H-42 concentrations between 7.5 and 12.5 μl. The efficiency of the sorting procedure varies based on the dog from which the sperm sample derives. © 2013 Blackwell Verlag GmbH.

Pregnancy rate and birth rate of calves from a large-scale IVF program using reverse-sorted semen in Bos indicus, Bos indicus-taurus, and Bos taurus cattle.

PubMed

Morotti, F; Sanches, B V; Pontes, J H F; Basso, A C; Siqueira, E R; Lisboa, L A; Seneda, M M

2014-03-15

Obtaining sexed sperm from previously frozen doses (reverse-sorted semen [RSS]) provides an important advantage because of the possibility of using the semen of bulls with desired genetic attributes that have died or have become infertile but from whom frozen semen is available. We report the efficiency of RSS on the pregnancy rate and birth rate of calves in a large-scale program using ovum pick-up and in vitro embryo production (IVEP) from Bos indicus, Bos indicus-taurus, and Bos taurus cattle. From 645 ovum pick-up procedures (Holstein, Gir, and Nelore), 9438 viable oocytes were recovered. A dose of frozen semen (Holstein, Nelore, Brahman, Gir, and Braford) was thawed, and the sperm were sex-sorted and cooled for use in IVF. Additionally, IVF with sperm from three Holstein bulls with freeze-thawed, sex-sorted (RSS) or sex-sorted, freeze-thawed (control) was tested. A total of 2729 embryos were produced, exhibiting a mean blastocyst rate of 29%. Heifers and cows selected for adequate body condition, estrus, and health received 2404 embryos, and 60 days later, a 41% average pregnancy rate was observed. A total of 966 calves were born, and 910 were of a predetermined sex, with an average of 94% accuracy in determining the sex. Despite the lower blastocyst rate with freeze-thawed, sex-sorted semen compared with sex-sorted semen, (P < 0.05), the pregnancy rate (bull I, 45% vs. 40%; II, 35% vs. 50%; and III, 47% vs. 48% for RSS and control, respectively; P > 0.05) and sex-sorted efficiency (bull I, 93% vs. 98%; II, 96% vs. 94%; and III, 96% vs. 97% for RSS and control, respectively; P > 0.05) were similar for each of the three bulls regardless of the sperm type used in the IVF. The sexing of previously frozen semen, associated with IVEP, produces viable embryos with a pregnancy rate of up to 40%, and calves of the desired sex are born even if the paternal bull has acquired some infertility, died, or is located a long distance from the sexing laboratory. Furthermore, these data show the feasibility of the process even when used in a large-scale IVEP program. Copyright © 2014 Elsevier Inc. All rights reserved.

Raman-activated cell sorting based on dielectrophoretic single-cell trap and release.

PubMed

Zhang, Peiran; Ren, Lihui; Zhang, Xu; Shan, Yufei; Wang, Yun; Ji, Yuetong; Yin, Huabing; Huang, Wei E; Xu, Jian; Ma, Bo

2015-02-17

Raman-activated cell sorting (RACS) is a promising single-cell technology that holds several significant advantages, as RACS is label-free, information-rich, and potentially in situ. To date, the ability of the technique to identify single cells in a high-speed flow has been limited by inherent weakness of the spontaneous Raman signal. Here we present an alternative pause-and-sort RACS microfluidic system that combines positive dielectrophoresis (pDEP) for single-cell trap and release with a solenoid-valve-suction-based switch for cell separation. This has allowed the integration of trapping, Raman identification, and automatic separation of individual cells in a high-speed flow. By exerting a periodical pDEP field, single cells were trapped, ordered, and positioned individually to the detection point for Raman measurement. As a proof-of-concept demonstration, a mixture of two cell strains containing carotenoid-producing yeast (9%) and non-carotenoid-producing Saccharomyces cerevisiae (91%) was sorted, which enriched the former to 73% on average and showed a fast Raman-activated cell sorting at the subsecond level.

A probability-based multi-cycle sorting method for 4D-MRI: A simulation study

PubMed Central

Liang, Xiao; Yin, Fang-Fang; Liu, Yilin; Cai, Jing

2016-01-01

Purpose: To develop a novel probability-based sorting method capable of generating multiple breathing cycles of 4D-MRI images and to evaluate performance of this new method by comparing with conventional phase-based methods in terms of image quality and tumor motion measurement. Methods: Based on previous findings that breathing motion probability density function (PDF) of a single breathing cycle is dramatically different from true stabilized PDF that resulted from many breathing cycles, it is expected that a probability-based sorting method capable of generating multiple breathing cycles of 4D images may capture breathing variation information missing from conventional single-cycle sorting methods. The overall idea is to identify a few main breathing cycles (and their corresponding weightings) that can best represent the main breathing patterns of the patient and then reconstruct a set of 4D images for each of the identified main breathing cycles. This method is implemented in three steps: (1) The breathing signal is decomposed into individual breathing cycles, characterized by amplitude, and period; (2) individual breathing cycles are grouped based on amplitude and period to determine the main breathing cycles. If a group contains more than 10% of all breathing cycles in a breathing signal, it is determined as a main breathing pattern group and is represented by the average of individual breathing cycles in the group; (3) for each main breathing cycle, a set of 4D images is reconstructed using a result-driven sorting method adapted from our previous study. The probability-based sorting method was first tested on 26 patients’ breathing signals to evaluate its feasibility of improving target motion PDF. The new method was subsequently tested for a sequential image acquisition scheme on the 4D digital extended cardiac torso (XCAT) phantom. Performance of the probability-based and conventional sorting methods was evaluated in terms of target volume precision and accuracy as measured by the 4D images, and also the accuracy of average intensity projection (AIP) of 4D images. Results: Probability-based sorting showed improved similarity of breathing motion PDF from 4D images to reference PDF compared to single cycle sorting, indicated by the significant increase in Dice similarity coefficient (DSC) (probability-based sorting, DSC = 0.89 ± 0.03, and single cycle sorting, DSC = 0.83 ± 0.05, p-value <0.001). Based on the simulation study on XCAT, the probability-based method outperforms the conventional phase-based methods in qualitative evaluation on motion artifacts and quantitative evaluation on tumor volume precision and accuracy and accuracy of AIP of the 4D images. Conclusions: In this paper the authors demonstrated the feasibility of a novel probability-based multicycle 4D image sorting method. The authors’ preliminary results showed that the new method can improve the accuracy of tumor motion PDF and the AIP of 4D images, presenting potential advantages over the conventional phase-based sorting method for radiation therapy motion management. PMID:27908178

Purification of human induced pluripotent stem cell-derived neural precursors using magnetic activated cell sorting.

PubMed

Rodrigues, Gonçalo M C; Fernandes, Tiago G; Rodrigues, Carlos A V; Cabral, Joaquim M S; Diogo, Maria Margarida

2015-01-01

Neural precursor (NP) cells derived from human induced pluripotent stem cells (hiPSCs), and their neuronal progeny, will play an important role in disease modeling, drug screening tests, central nervous system development studies, and may even become valuable for regenerative medicine treatments. Nonetheless, it is challenging to obtain homogeneous and synchronously differentiated NP populations from hiPSCs, and after neural commitment many pluripotent stem cells remain in the differentiated cultures. Here, we describe an efficient and simple protocol to differentiate hiPSC-derived NPs in 12 days, and we include a final purification stage where Tra-1-60+ pluripotent stem cells (PSCs) are removed using magnetic activated cell sorting (MACS), leaving the NP population nearly free of PSCs.

Forest, Trees, Dynamics: Results from a Novel Wisconsin Card Sorting Test Variant Protocol for Studying Global-Local Attention and Complex Cognitive Processes

PubMed Central

Cowley, Benjamin; Lukander, Kristian

2016-01-01

Background: Recognition of objects and their context relies heavily on the integrated functioning of global and local visual processing. In a realistic setting such as work, this processing becomes a sustained activity, implying a consequent interaction with executive functions. Motivation: There have been many studies of either global-local attention or executive functions; however it is relatively novel to combine these processes to study a more ecological form of attention. We aim to explore the phenomenon of global-local processing during a task requiring sustained attention and working memory. Methods: We develop and test a novel protocol for global-local dissociation, with task structure including phases of divided (“rule search”) and selective (“rule found”) attention, based on the Wisconsin Card Sorting Task (WCST). We test it in a laboratory study with 25 participants, and report on behavior measures (physiological data was also gathered, but not reported here). We develop novel stimuli with more naturalistic levels of information and noise, based primarily on face photographs, with consequently more ecological validity. Results: We report behavioral results indicating that sustained difficulty when participants test their hypotheses impacts matching-task performance, and diminishes the global precedence effect. Results also show a dissociation between subjectively experienced difficulty and objective dimension of performance, and establish the internal validity of the protocol. Contribution: We contribute an advance in the state of the art for testing global-local attention processes in concert with complex cognition. With three results we establish a connection between global-local dissociation and aspects of complex cognition. Our protocol also improves ecological validity and opens options for testing additional interactions in future work. PMID:26941689

The use of Optical Character Recognition (OCR) in the digitisation of herbarium specimen labels

PubMed Central

Drinkwater, Robyn E.; Cubey, Robert W. N.; Haston, Elspeth M.

2014-01-01

Abstract At the Royal Botanic Garden Edinburgh (RBGE) the use of Optical Character Recognition (OCR) to aid the digitisation process has been investigated. This was tested using a herbarium specimen digitisation process with two stages of data entry. Records were initially batch-processed to add data extracted from the OCR text prior to being sorted based on Collector and/or Country. Using images of the specimens, a team of six digitisers then added data to the specimen records. To investigate whether the data from OCR aid the digitisation process, they completed a series of trials which compared the efficiency of data entry between sorted and unsorted batches of specimens. A survey was carried out to explore the opinion of the digitisation staff to the different sorting options. In total 7,200 specimens were processed. When compared to an unsorted, random set of specimens, those which were sorted based on data added from the OCR were quicker to digitise. Of the methods tested here, the most successful in terms of efficiency used a protocol which required entering data into a limited set of fields and where the records were filtered by Collector and Country. The survey and subsequent discussions with the digitisation staff highlighted their preference for working with sorted specimens, in which label layout, locations and handwriting are likely to be similar, and so a familiarity with the Collector or Country is rapidly established. PMID:25009435

Flow Sorting of Marine Bacterioplankton after Fluorescence In Situ Hybridization

PubMed Central

Sekar, Raju; Fuchs, Bernhard M.; Amann, Rudolf; Pernthaler, Jakob

2004-01-01

We describe an approach to sort cells from coastal North Sea bacterioplankton by flow cytometry after in situ hybridization with rRNA-targeted horseradish peroxidase-labeled oligonucleotide probes and catalyzed fluorescent reporter deposition (CARD-FISH). In a sample from spring 2003 >90% of the cells were detected by CARD-FISH with a bacterial probe (EUB338). Approximately 30% of the microbial assemblage was affiliated with the Cytophaga-Flavobacterium lineage of the Bacteroidetes (CFB group) (probe CF319a), and almost 10% was targeted by a probe for the β-proteobacteria (probe BET42a). A protocol was optimized to detach cells hybridized with EUB338, BET42a, and CF319a from membrane filters (recovery rate, 70%) and to sort the cells by flow cytometry. The purity of sorted cells was >95%. 16S rRNA gene clone libraries were constructed from hybridized and sorted cells (S-EUB, S-BET, and S-CF libraries) and from unhybridized and unsorted cells (UNHYB library). Sequences related to the CFB group were significantly more frequent in the S-CF library (66%) than in the UNHYB library (13%). No enrichment of β-proteobacterial sequence types was found in the S-BET library, but novel sequences related to Nitrosospira were found exclusively in this library. These bacteria, together with members of marine clade OM43, represented >90% of the β-proteobacteria in the water sample, as determined by CARD-FISH with specific probes. This illustrates that a combination of CARD-FISH and flow sorting might be a powerful approach to study the diversity and potentially the activity and the genomes of different bacterial populations in aquatic habitats. PMID:15466568

[INFLUENCE OF AZOSPIRILLUM BRASILENSE 10/1 ON ASSOCIATIVE NITROGEN FIXATION AND INTRAVARIETAL POLYMORPHISM OF SPRING TRITICALE].

PubMed

Patika, V P; Nadkernichna, O V; Shahovnina, O O

2015-01-01

It is shown, that the perspective Ukrainian sorts of spring triticale characterizes by considerable polymorphism by associative N2-fixing ability in root zone of plants. Application of active strain Azospirillum brasilense 10/1 promotes the decline of variability of this sign within the limits of sort, increase potential nitrogen activity is on the average in 3,2-4,7 times and also distributing normalizations in the selections of the inoculated plants.

Time-dependent Increase in the Network Response to the Stimulation of Neuronal Cell Cultures on Micro-electrode Arrays.

PubMed

Gertz, Monica L; Baker, Zachary; Jose, Sharon; Peixoto, Nathalia

2017-05-29

Micro-electrode arrays (MEAs) can be used to investigate drug toxicity, design paradigms for next-generation personalized medicine, and study network dynamics in neuronal cultures. In contrast with more traditional methods, such as patch-clamping, which can only record activity from a single cell, MEAs can record simultaneously from multiple sites in a network, without requiring the arduous task of placing each electrode individually. Moreover, numerous control and stimulation configurations can be easily applied within the same experimental setup, allowing for a broad range of dynamics to be explored. One of the key dynamics of interest in these in vitro studies has been the extent to which cultured networks display properties indicative of learning. Mouse neuronal cells cultured on MEAs display an increase in response following training induced by electrical stimulation. This protocol demonstrates how to culture neuronal cells on MEAs; successfully record from over 95% of the plated dishes; establish a protocol to train the networks to respond to patterns of stimulation; and sort, plot, and interpret the results from such experiments. The use of a proprietary system for stimulating and recording neuronal cultures is demonstrated. Software packages are also used to sort neuronal units. A custom-designed graphical user interface is used to visualize post-stimulus time histograms, inter-burst intervals, and burst duration, as well as to compare the cellular response to stimulation before and after a training protocol. Finally, representative results and future directions of this research effort are discussed.

Quantum Algorithms and Protocols

NASA Astrophysics Data System (ADS)

Divincenzo, David

2001-06-01

Quantum Computing is better than classical computing, but not just because it speeds up some computations. Some of the best known quantum algorithms, like Grover's, may well have their most interesting applications in settings that involve the combination of computation and communication. Thus, Grover speeds up the appointment scheduling problem by reducing the amount of communication needed between two parties who want to find a common free slot on their calendars. I will review various other applications of this sort that are being explored. Other distributed computing protocols are required to have other attributes like obliviousness and privacy; I will discuss our recent applications involving quantum data hiding.

Nucleic acid isolation

DOEpatents

Longmire, J.L.; Lewis, A.K.; Hildebrand, C.E.

1988-01-21

A method is provided for isolating DNA from eukaryotic cell and flow sorted chromosomes. When DNA is removed from chromosome and cell structure, detergent and proteolytic digestion products remain with the DNA. These products can be removed with organic extraction, but the process steps associated with organic extraction reduces the size of DNA fragments available for experimental use. The present process removes the waste products by dialyzing a solution containing the DNA against a solution containing polyethylene glycol (PEG). The waste products dialyze into the PEG leaving isolated DNA. The remaining DNA has been prepared with fragments containing more than 160 kb. The isolated DNA has been used in conventional protocols without effect on the protocol.

In-Line Sorting of Harumanis Mango Based on External Quality Using Visible Imaging

PubMed Central

Ibrahim, Mohd Firdaus; Ahmad Sa’ad, Fathinul Syahir; Zakaria, Ammar; Md Shakaff, Ali Yeon

2016-01-01

The conventional method of grading Harumanis mango is time-consuming, costly and affected by human bias. In this research, an in-line system was developed to classify Harumanis mango using computer vision. The system was able to identify the irregularity of mango shape and its estimated mass. A group of images of mangoes of different size and shape was used as database set. Some important features such as length, height, centroid and parameter were extracted from each image. Fourier descriptor and size-shape parameters were used to describe the mango shape while the disk method was used to estimate the mass of the mango. Four features have been selected by stepwise discriminant analysis which was effective in sorting regular and misshapen mango. The volume from water displacement method was compared with the volume estimated by image processing using paired t-test and Bland-Altman method. The result between both measurements was not significantly different (P > 0.05). The average correct classification for shape classification was 98% for a training set composed of 180 mangoes. The data was validated with another testing set consist of 140 mangoes which have the success rate of 92%. The same set was used for evaluating the performance of mass estimation. The average success rate of the classification for grading based on its mass was 94%. The results indicate that the in-line sorting system using machine vision has a great potential in automatic fruit sorting according to its shape and mass. PMID:27801799

In-Line Sorting of Harumanis Mango Based on External Quality Using Visible Imaging.

PubMed

Ibrahim, Mohd Firdaus; Ahmad Sa'ad, Fathinul Syahir; Zakaria, Ammar; Md Shakaff, Ali Yeon

2016-10-27

The conventional method of grading Harumanis mango is time-consuming, costly and affected by human bias. In this research, an in-line system was developed to classify Harumanis mango using computer vision. The system was able to identify the irregularity of mango shape and its estimated mass. A group of images of mangoes of different size and shape was used as database set. Some important features such as length, height, centroid and parameter were extracted from each image. Fourier descriptor and size-shape parameters were used to describe the mango shape while the disk method was used to estimate the mass of the mango. Four features have been selected by stepwise discriminant analysis which was effective in sorting regular and misshapen mango. The volume from water displacement method was compared with the volume estimated by image processing using paired t -test and Bland-Altman method. The result between both measurements was not significantly different (P > 0.05). The average correct classification for shape classification was 98% for a training set composed of 180 mangoes. The data was validated with another testing set consist of 140 mangoes which have the success rate of 92%. The same set was used for evaluating the performance of mass estimation. The average success rate of the classification for grading based on its mass was 94%. The results indicate that the in-line sorting system using machine vision has a great potential in automatic fruit sorting according to its shape and mass.

Optimization of flow cytometric detection and cell sorting of transgenic Plasmodium parasites using interchangeable optical filters

PubMed Central

2012-01-01

Background Malaria remains a major cause of morbidity and mortality worldwide. Flow cytometry-based assays that take advantage of fluorescent protein (FP)-expressing malaria parasites have proven to be valuable tools for quantification and sorting of specific subpopulations of parasite-infected red blood cells. However, identification of rare subpopulations of parasites using green fluorescent protein (GFP) labelling is complicated by autofluorescence (AF) of red blood cells and low signal from transgenic parasites. It has been suggested that cell sorting yield could be improved by using filters that precisely match the emission spectrum of GFP. Methods Detection of transgenic Plasmodium falciparum parasites expressing either tdTomato or GFP was performed using a flow cytometer with interchangeable optical filters. Parasitaemia was evaluated using different optical filters and, after optimization of optics, the GFP-expressing parasites were sorted and analysed by microscopy after cytospin preparation and by imaging cytometry. Results A new approach to evaluate filter performance in flow cytometry using two-dimensional dot blot was developed. By selecting optical filters with narrow bandpass (BP) and maximum position of filter emission close to GFP maximum emission in the FL1 channel (510/20, 512/20 and 517/20; dichroics 502LP and 466LP), AF was markedly decreased and signal-background improve dramatically. Sorting of GFP-expressing parasite populations in infected red blood cells at 90 or 95% purity with these filters resulted in 50-150% increased yield when compared to the standard filter set-up. The purity of the sorted population was confirmed using imaging cytometry and microscopy of cytospin preparations of sorted red blood cells infected with transgenic malaria parasites. Discussion Filter optimization is particularly important for applications where the FP signal and percentage of positive events are relatively low, such as analysis of parasite-infected samples with in the intention of gene-expression profiling and analysis. The approach outlined here results in substantially improved yield of GFP-expressing parasites, and requires decreased sorting time in comparison to standard methods. It is anticipated that this protocol will be useful for a wide range of applications involving rare events. PMID:22950515

Physical knowledge of household waste in Algeria: generation and composition in the town of Annaba.

PubMed

Cheniti, Hamza; Serradj, Tayeb; Brahamia, Khaled; Makhlouf, Ali; Guerraiche, Said

2013-11-01

We investigated the physical composition of household waste in the town of Annaba, Algeria. The study was based on an adequate sampling protocol that takes into account the constraints of Algerian cities. Annaba was taken as a case study to check the situation in Algeria. Ninety to 120 kg was sorted for each type of habitat in the city during four seasons, from 2010 to 2011, according to 11 components of household waste. Variations in the production ratio and percentages of all components were recorded according to the seasons and the type of habitat during the four campaigns of characterization. Analysis of variance showed a significant difference of the waste composition by habitat type. A pairwise multiple comparisons using the Tukey test of the sampled habitat types was also carried out, which indicated no significant differences between the habitat type concerning paper, plastic, composite and glass variables. But for the remaining components, the study revealed, with a significance limit of 0.05, a clear difference in the average composition of the waste according to the type of habitat.

Stationary average consensus protocol for a class of heterogeneous high-order multi-agent systems with application for aircraft

NASA Astrophysics Data System (ADS)

Rezaei, Mohammad Hadi; Menhaj, Mohammad Bagher

2018-01-01

This paper investigates the stationary average consensus problem for a class of heterogeneous-order multi-agent systems. The goal is to bring the positions of agents to the average of their initial positions while letting the other states converge to zero. To this end, three different consensus protocols are proposed. First, based on the auxiliary variables information among the agents under switching directed networks and state-feedback control, a protocol is proposed whereby all the agents achieve stationary average consensus. In the second and third protocols, by resorting to only measurements of relative positions of neighbouring agents under fixed balanced directed networks, two control frameworks are presented with two strategies based on state-feedback and output-feedback control. Finally, simulation results are given to illustrate the effectiveness of the proposed protocols.

MO-E-17A-09: Has Cancer Risk for Pediatric CT Increased Or Decreased? An Analysis of Cohort Data From 2004-2013

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

Brady, S; Kaufman, R

Purpose: To analyze CT radiation dosimetry trends in a pediatric population imaged with modern (2004-2013) CT technology Methods: The institutional review board approved this retrospective review. Two cohorts of pediatric patients that received CT scans for treatment or surveillance for Wilms tumor (n=73) or Neuroblastoma (n=74) from 2004–2013 were included in this study. Patients were scanned during this time period on a GE Ultra (8 slice; 2004–2007), a GE VCT (2008–2011), or a GE VCT-XTe (2011–2013). Each patient's individual or combined chest, abdomen, and pelvic CT exams (n=4138) were loaded onto a PACS workstation (Intelerad, Canada) and measured to calculatemore » their effective diameter and SSDE. Patient SSDE was used to estimate patient organ dosimetry based on previously published data. Patient's organ dosimetry were sorted by gender, weight, age, scan protocol (i.e., chest, abdomen, or pelvis), and CT scanner technology and averaged accordingly to calculate population averaged absolute and effective dose values. Results: Patient radiation dose burden calculated for all genders, weights, and ages decreased at a rate of 0.2 mSv/year (4.2 mGy/year; average organ dose) from 2004–2013; overall levels decreased by 50% from 3.0 mSv (60.0 mGy) to 1.5 mSv (25.9 mGy). Patient dose decreased at equal rates for both male and female, and for individual scan protocols. The greatest dose savings was found for patients between 0–4 years old (65%) followed by 5-9 years old (45%), 10–14 years old (30%), and > 14 years old (21%). Conclusion: Assuming a linear-nothreshold model, there always will be potential risk of cancer induction from CT. However, as demonstrated among these patient populations, effective and organ dose has decreased over the last decade; thus, potential risk of long-term side effects from pediatric CT examinations has also been reduced.« less

The Principle of the Micro-Electronic Neural Bridge and a Prototype System Design.

PubMed

Huang, Zong-Hao; Wang, Zhi-Gong; Lu, Xiao-Ying; Li, Wen-Yuan; Zhou, Yu-Xuan; Shen, Xiao-Yan; Zhao, Xin-Tai

2016-01-01

The micro-electronic neural bridge (MENB) aims to rebuild lost motor function of paralyzed humans by routing movement-related signals from the brain, around the damage part in the spinal cord, to the external effectors. This study focused on the prototype system design of the MENB, including the principle of the MENB, the neural signal detecting circuit and the functional electrical stimulation (FES) circuit design, and the spike detecting and sorting algorithm. In this study, we developed a novel improved amplitude threshold spike detecting method based on variable forward difference threshold for both training and bridging phase. The discrete wavelet transform (DWT), a new level feature coefficient selection method based on Lilliefors test, and the k-means clustering method based on Mahalanobis distance were used for spike sorting. A real-time online spike detecting and sorting algorithm based on DWT and Euclidean distance was also implemented for the bridging phase. Tested by the data sets available at Caltech, in the training phase, the average sensitivity, specificity, and clustering accuracies are 99.43%, 97.83%, and 95.45%, respectively. Validated by the three-fold cross-validation method, the average sensitivity, specificity, and classification accuracy are 99.43%, 97.70%, and 96.46%, respectively.

Concurrent Isolation of 3 Distinct Cardiac Stem Cell Populations From a Single Human Heart Biopsy.

PubMed

Monsanto, Megan M; White, Kevin S; Kim, Taeyong; Wang, Bingyan J; Fisher, Kristina; Ilves, Kelli; Khalafalla, Farid G; Casillas, Alexandria; Broughton, Kathleen; Mohsin, Sadia; Dembitsky, Walter P; Sussman, Mark A

2017-07-07

The relative actions and synergism between distinct myocardial-derived stem cell populations remain obscure. Ongoing debates on optimal cell population(s) for treatment of heart failure prompted implementation of a protocol for isolation of multiple stem cell populations from a single myocardial tissue sample to develop new insights for achieving myocardial regeneration. Establish a robust cardiac stem cell isolation and culture protocol to consistently generate 3 distinct stem cell populations from a single human heart biopsy. Isolation of 3 endogenous cardiac stem cell populations was performed from human heart samples routinely discarded during implantation of a left ventricular assist device. Tissue explants were mechanically minced into 1 mm 3 pieces to minimize time exposure to collagenase digestion and preserve cell viability. Centrifugation removes large cardiomyocytes and tissue debris producing a single cell suspension that is sorted using magnetic-activated cell sorting technology. Initial sorting is based on tyrosine-protein kinase Kit (c-Kit) expression that enriches for 2 c-Kit + cell populations yielding a mixture of cardiac progenitor cells and endothelial progenitor cells. Flowthrough c-Kit - mesenchymal stem cells are positively selected by surface expression of markers CD90 and CD105. After 1 week of culture, the c-Kit + population is further enriched by selection for a CD133 + endothelial progenitor cell population. Persistence of respective cell surface markers in vitro is confirmed both by flow cytometry and immunocytochemistry. Three distinct cardiac cell populations with individualized phenotypic properties consistent with cardiac progenitor cells, endothelial progenitor cells, and mesenchymal stem cells can be successfully concurrently isolated and expanded from a single tissue sample derived from human heart failure patients. © 2017 American Heart Association, Inc.

Management of Toxic Epidermal Necrolysis with Plasmapheresis and Cyclosporine A: Our 10 Years’ Experience

PubMed Central

Giudice, Giuseppe; Maggio, Giulio; Bufano, Loredana; Memeo, Giuseppe

2017-01-01

Background: The management of toxic epidermal necrolysis (TEN) is controversial and there is no uniform strategy. Objective: To share our 10 years’ experience in treating severe TEN with a novel protocol based on the association of cyclosporine A and plasmapheresis. Methods: In this case series, we retrospectively collected and assessed the 12 cases of severe TEN treated from 2005 to 2015 at the Burn Unit of the University of Bari Policlinico hospital. Results: Average body surface area was 77; average SCORETEN was 4.3. The 12 patients had been treated with culprit drug withdrawal, systemic corticosteroids, and/or cyclosporine A with no response. The protocol was successfully administered in all 12 cases. Average time to response from protocol start was 4.9 days. Average time to remission from protocol start was 22 days; average hospital stay at our unit was 24.8 days. Four patients developed severe complications; 1 patient died. No complications linked to the protocol therapeutic measures were observed. The relatively small number of cases given the rarity of the condition is a limitation of this report. Conclusion: Our protocol based on the association of cyclosporine A and plasmapheresis is safe and efficacious in treating severe TEN. PMID:28280663

Highly multiplexed targeted DNA sequencing from single nuclei.

PubMed

Leung, Marco L; Wang, Yong; Kim, Charissa; Gao, Ruli; Jiang, Jerry; Sei, Emi; Navin, Nicholas E

2016-02-01

Single-cell DNA sequencing methods are challenged by poor physical coverage, high technical error rates and low throughput. To address these issues, we developed a single-cell DNA sequencing protocol that combines flow-sorting of single nuclei, time-limited multiple-displacement amplification (MDA), low-input library preparation, DNA barcoding, targeted capture and next-generation sequencing (NGS). This approach represents a major improvement over our previous single nucleus sequencing (SNS) Nature Protocols paper in terms of generating higher-coverage data (>90%), thereby enabling the detection of genome-wide variants in single mammalian cells at base-pair resolution. Furthermore, by pooling 48-96 single-cell libraries together for targeted capture, this approach can be used to sequence many single-cell libraries in parallel in a single reaction. This protocol greatly reduces the cost of single-cell DNA sequencing, and it can be completed in 5-6 d by advanced users. This single-cell DNA sequencing protocol has broad applications for studying rare cells and complex populations in diverse fields of biological research and medicine.

Particle shape-controlled sorting and transport behaviour of mixed siliciclastic/bioclastic sediments in a mesotidal lagoon, South Africa

NASA Astrophysics Data System (ADS)

Flemming, Burghard W.

2017-08-01

This study investigates the effect of particle shape on the transport and deposition of mixed siliciclastic-bioclastic sediments in the lower mesotidal Langebaan Lagoon along the South Atlantic coast of South Africa. As the two sediment components have undergone mutual sorting for the last 7 ka, they can be expected to have reached a highest possible degree of hydraulic equivalence. A comparison of sieve and settling tube data shows that, with progressive coarsening of the size fractions, the mean diameters of individual sediment components increasingly depart from the spherical quartz standard, the experimental data demonstrating the hydraulic incompatibility of the sieve data. Overall, the spatial distribution patterns of textural parameters (mean settling diameter, sorting and skewness) of the siliciclastic and bioclastic sediment components are very similar. Bivariate plots between them reveal linear trends when averaged over small intervals. A systematic deviation is observed in sorting, the trend ranging from uniformity at poorer sorting levels to a progressively increasing lag of the bioclastic component relative to the siliciclastic one as overall sorting improves. The deviation amounts to 0.8 relative sorting units at the optimal sorting level. The small textural differences between the two components are considered to reflect the influence of particle shape, which prevents the bioclastic fraction from achieving complete textural equivalence with the siliciclastic one. This is also reflected in the inferred transport behaviour of the two shape components, the bioclastic fraction moving closer to the bed than the siliciclastic one because of the higher drag experienced by low shape factor particles. As a consequence, the bed-phase development of bioclastic sediments departs significantly from that of siliciclastic sediments. Systematic flume experiments, however, are currently still lacking.

Minimum number of spermatozoa per dose in Mediterranean Italian buffalo (Bubalus bubalis) using sexed frozen semen and conventional artificial insemination.

PubMed

Gaviraghi, A; Puglisi, R; Balduzzi, D; Severgnini, A; Bornaghi, V; Bongioni, G; Frana, A; Gandini, L M; Lukaj, A; Bonacina, C; Galli, A

2013-05-01

In buffaloes, AI with sexed semen is not fully optimized, and the procedure has only been performed using the approach currently in use for cattle. The objective of the present work was to compare the pregnancy rates in Mediterranean Italian buffalo cows inseminated with sexed frozen-thawed semen at 2, 4, 6, and 8 million sperm per dose, using the Ovsynch protocol and conventional AI at a fixed time. Fresh ejaculates from three buffalo bulls were processed according to Beltsville sperm sorting technology, and packaged in 0.25-mL straws with two total concentrations of 2 and 4 million live sorted sperm per straw. After thawing, semen was evaluated for total motility, forward motility, average path velocity, membrane and DNA integrity, and membrane fluidity. Sorting efficiency was estimated using a real time polymerase chain reaction method developed and validated in our laboratory. The artificial inseminations were conducted during the breeding season on 849 Italian Mediterranean buffalo heifers and cows distributed in 13 farms in northern and central Italy. No significant difference in quality parameters was reported between nonsexed and sexed straws produced with 2 and 4 million sperm. Lower pregnancy rate (P < 0.001) was reported when inseminating doses of sexed semen at 2 million were used (53/170; 31.2%), with respect to conventional nonsexed (78/142; 54.9%), and sexed doses at 4, 6, and 8 million spermatozoa (102/205, 49.8%; 84/175, 48.0%; and 74/157, 47.1%, respectively). No differences were evident using conventional doses and sexed semen with sperm numbers equal or higher than 4 million per dose. Pregnancies were not affected by the sire; 39/82 (47.6%), 120/270 (44.4%), and 151/355 (42.5%), respectively, for the three bulls. Variability in pregnancy rates observed in different herds was not significant. Furthermore, no significant difference was reported between pregnancies obtained with sexed semen in heifers and multiparous, respectively, 179/407 (44.0%) and 131/300 (43.7%). The results of the present work indicate that in Mediterranean Italian buffalo the dose of 4 million represents an optimal compromise when using sexed semen with conventional technologies of insemination, together with estrus synchronization, and the minimum number of spermatozoa per dose. In addition, the real time polymerase chain reaction method was optimized and is now available for estimating sorting efficiency in buffalo. Copyright © 2013 Elsevier Inc. All rights reserved.

Organoid culture systems for prostate epithelial tissue and prostate cancer tissue

PubMed Central

Drost, Jarno; Karthaus, Wouter R.; Gao, Dong; Driehuis, Else; Sawyers, Charles L.; Chen, Yu; Clevers, Hans

2016-01-01

Summary This protocol describes a recently developed strategy to generate 3D prostate organoid cultures from healthy mouse and human prostate (either bulk or FAC-sorted single luminal and basal cells), metastatic prostate cancer lesions and circulating tumour cells. Organoids derived from healthy material contain the differentiated luminal and basal cell types, whereas organoids derived from prostate cancer tissue mimic the histology of the tumour. The stepwise establishment of these cultures and the fully defined serum-free conditioned medium that is required to sustain organoid growth are outlined. Organoids established using this protocol can be used to study many different aspects of prostate biology, including homeostasis, tumorigenesis and drug discovery. PMID:26797458

Nucleic acid isolation process

DOEpatents

Longmire, Jonathan L.; Lewis, Annette K.; Hildebrand, Carl E.

1990-01-01

A method is provided for isolating DNA from eukaryotic cell and flow sorted chromosomes. When DNA is removed from chromosome and cell structure, detergent and proteolytic digestion products remain with the DNA. These products can be removed with organic extraction, but the process steps associated with organic extraction reduce the size of DNA fragments available for experimental use. The present process removes the waste products by dialyzing a solution containing the DNA against a solution containing polyethylene glycol (PEG). The waste products dialyze into the PEG leaving isolated DNA. The remaining DNA has been prepared with fragments containing more than 160 kb. The isolated DNA has been used in conventional protocols without affect on the protocol.

Isolation of Eosinophils from the Lamina Propria of the Murine Small Intestine.

PubMed

Berek, Claudia; Beller, Alexander; Chu, Van Trung

2016-01-01

Only recently has it become apparent that eosinophils play a crucial role in mucosal immune homeostasis. Although eosinophils are the main cellular component of the lamina propria of the gastrointestinal tract, they have often been overlooked because they express numerous markers, which are normally used to characterize macrophages and/or dendritic cells. To study their function in mucosal immunity, it is important to isolate them with high purity and viability. Here, we describe a protocol to purify eosinophils from the lamina propria of the murine small intestine. The method involves preparation of the small intestine, removal of epithelial cells and digestion of the lamina propria to release eosinophils. A protocol to sort eosinophils is included.

Active management of labor

PubMed Central

Rogers, Rebecca G; Gardner, Michael O; Tool, Kevin J; Ainsley, Jeanne; Gilson, George

2000-01-01

Objective To compare the costs of a protocol of active management of labor with those of traditional labor management. Design Cost analysis of a randomized controlled trial. Methods From August 1992 to April 1996, we randomly allocated 405 women whose infants were delivered at the University of New Mexico Health Sciences Center, Albuquerque, to an active management of labor protocol that had substantially reduced the duration of labor or a control protocol. We calculated the average cost for each delivery, using both actual costs and charges. Results The average cost for women assigned to the active management protocol was $2,480.79 compared with an average cost of $2,528.61 for women in the control group (P = 0.55). For women whose infant was delivered by cesarean section, the average cost was $4,771.54 for active management of labor and $4,468.89 for the control protocol (P = 0.16). Spontaneous vaginal deliveries cost an average of $27.00 more for actively managed patients compared with the cost for the control protocol. Conclusions The reduced duration of labor by active management did not translate into significant cost savings. Overall, an average cost saving of only $47.91, or 2%, was achieved for labors that were actively managed. This reduction in cost was due to a decrease in the rate of cesarean sections in women whose labor was actively managed and not to a decreased duration of labor. PMID:10778374

Capture of Fluorescence Decay Times by Flow Cytometry

PubMed Central

Naivar, Mark A.; Jenkins, Patrick; Freyer, James P.

2012-01-01

In flow cytometry, the fluorescence decay time of an excitable species has been largely underutilized and is not likely found as a standard parameter on any imaging cytometer, sorting, or analyzing system. Most cytometers lack fluorescence lifetime hardware mainly owing to two central issues. Foremost, research and development with lifetime techniques has lacked proper exploitation of modern laser systems, data acquisition boards, and signal processing techniques. Secondly, a lack of enthusiasm for fluorescence lifetime applications in cells and with bead-based assays has persisted among the greater cytometry community. In this unit, we describe new approaches that address these issues and demonstrate the simplicity of digitally acquiring fluorescence relaxation rates in flow. The unit is divided into protocol and commentary sections in order to provide a most comprehensive discourse on acquiring the fluorescence lifetime with frequency-domain methods. The unit covers (i) standard fluorescence lifetime acquisition (protocol-based) with frequency-modulated laser excitation, (ii) digital frequency-domain cytometry analyses, and (iii) interfacing fluorescence lifetime measurements onto sorting systems. Within the unit is also a discussion on how digital methods are used for aliasing in order to harness higher frequency ranges. Also, a final discussion is provided on heterodyning and processing of waveforms for multi-exponential decay extraction. PMID:25419263

Near-optimal protocols in complex nonequilibrium transformations

DOE PAGES

Gingrich, Todd R.; Rotskoff, Grant M.; Crooks, Gavin E.; ...

2016-08-29

The development of sophisticated experimental means to control nanoscale systems has motivated efforts to design driving protocols that minimize the energy dissipated to the environment. Computational models are a crucial tool in this practical challenge. In this paper, we describe a general method for sampling an ensemble of finite-time, nonequilibrium protocols biased toward a low average dissipation. In addition, we show that this scheme can be carried out very efficiently in several limiting cases. As an application, we sample the ensemble of low-dissipation protocols that invert the magnetization of a 2D Ising model and explore how the diversity of themore » protocols varies in response to constraints on the average dissipation. In this example, we find that there is a large set of protocols with average dissipation close to the optimal value, which we argue is a general phenomenon.« less

The effects of sweep numbers per average and protocol type on the accuracy of the p300-based concealed information test.

PubMed

Dietrich, Ariana B; Hu, Xiaoqing; Rosenfeld, J Peter

2014-03-01

In the first of two experiments, we compared the accuracy of the P300 concealed information test protocol as a function of numbers of trials experienced by subjects and ERP averages analyzed by investigators. Contrary to Farwell et al. (Cogn Neurodyn 6(2):115-154, 2012), we found no evidence that 100 trial based averages are more accurate than 66 or 33 trial based averages (all numbers led to accuracies of 84-94 %). There was actually a trend favoring the lowest trial numbers. The second study compared numbers of irrelevant stimuli recalled and recognized in the 3-stimulus protocol versus the complex trial protocol (Rosenfeld in Memory detection: theory and application of the concealed information test, Cambridge University Press, New York, pp 63-89, 2011). Again, in contrast to expectations from Farwell et al. (Cogn Neurodyn 6(2):115-154, 2012), there were no differences between protocols, although there were more irrelevant stimuli recognized than recalled, and irrelevant 4-digit number group stimuli were neither recalled nor recognized as well as irrelevant city name stimuli. We therefore conclude that stimulus processing in the P300-based complex trial protocol-with no more than 33 sweep averages-is adequate to allow accurate detection of concealed information.

Rapid fabrication of three-dimensional structures for dielectrophoretic sorting of lipid-containing organisms

NASA Astrophysics Data System (ADS)

Schor, Alisha R.; Buie, Cullen R.

2016-10-01

In this work, we demonstrate a microfluidic particle sorter consisting of three-dimensional, conducting microposts. Our sorter uses dielectrophoresis (DEP) to sort high- and low-lipid phenotypes of the yeast Yarrowia lipolytica. Y. lipolytica is one of the many microorganisms being explored as a hydrocarbon source for biodiesel, Omega-3 additives, and other products derived from fatty acids. A rapid, non-destructive, lipid-based sorting tool would accelerate the commercialization of these products. Our device consists of an array of 105, 25 μm wide gold microposts that span the height of a 15 μm channel. This array generates an electric field in a microfluidic device that is uniform through the channel height, but has a custom-shaped non-uniformity in the horizontal directions. This is crucial in order to achieve continuous sorting using DEP, as it ensures all cells are exposed to the same conditions throughout the channel height. By using very low currents (100 μA), we are able to electroplate these post arrays in fewer than 15 min. This is an order of magnitude improvement over previous reports of electroplated microstructures. With an applied signal of 250 MHz, 2.6 V pp in our device, we separate a heterogeneous population with a purity of 97.8% in the low-lipid stream and 71.4% in the high-lipid stream. The high-lipid stream purity can be improved by adjusting the spacing of the array. This unique protocol for the rapid fabrication of 3D microstructures has enabled the creation of a non-invasive sorting tool for genetically engineered, lipid-producing organisms. The ability to screen organisms based on lipid content will alleviate one of the major bottlenecks in commercialization of microbial biofuels.

Through our eyes: exploring African-American men's perspective on factors affecting transition to manhood.

PubMed

Bharmal, Nazleen; Kennedy, David; Jones, Loretta; Lee-Johnson, Charles; Morris, D'Ann; Caldwell, Ben; Brown, Anthony; Houston, Tina; Meeks, Charlene; Vargas, Roberto; Franco, Idalid; Razzak, A Rab; Brown, Arleen F

2012-02-01

Premature mortality and disparities in morbidity observed in African-American men may be associated with factors in their social, economic, and built environments that may be especially influential during the transition to adulthood. To have young, African-American men from Los Angeles County identify and prioritize factors associated with their transition to manhood using photovoice methodology and pile-sorting exercises. Qualitative study using community-based participatory research (CBPR) and photovoice Twelve African-American men, ages 16-26 years, from Los Angeles County, California. We used CBPR principles to form a community advisory board (CAB) whose members defined goals for the partnered project, developed the protocols, and participated in data collection and analysis. Participants were given digital cameras to take 50-300 photographs over three months. Pile-sorting techniques were used to facilitate participants' identification and discussion of the themes in their photos and selected photos of the group. Pile-sorts of group photographs were analyzed using multidimensional scaling and hierarchical cluster analysis to systematically compare participants' themes and identify patterns of associations between sorted photographs. Sub-themes and related quotes were also elicited from the pile-sorting transcripts. The CAB and several study participants met periodically to develop dissemination strategies and design interventions informed by study findings. Four dominant themes emerged during analysis: 1) Struggles face during the transition to manhood, 2) Sources of social support, 3) Role of sports, and 4) Views on Los Angeles lifestyle. The project led to the formation of a young men's group and community events featuring participants. CBPR and photovoice are effective methods to engage young, African-American men to identify and discuss factors affecting their transition to manhood, contextualize research findings, and participate in intervention development.

A real-time traffic control method for the intersection with pre-signals under the phase swap sorting strategy

PubMed Central

Bie, Yiming; Wang, Yinhai

2017-01-01

To deal with the conflicts between left-turn and through traffic streams and increase the discharge capacity, this paper addresses the pre-signal which is implemented at a signalized intersection. Such an intersection with pre-signal is termed as a tandem intersection. For the tandem intersection, phase swap sorting strategy is deemed as the most effective phasing scheme in view of some exclusive merits, such as easier compliance of drivers, and shorter sorting area. However, a major limitation of the phase swap sorting strategy is not considered in previous studies: if one or more vehicle is left at the sorting area after the signal light turns to red, the capacity of the approach would be dramatically dropped. Besides, previous signal control studies deal with a fixed timing plan that is not adaptive with the fluctuation of traffic flows. Therefore, to cope with these two gaps, this paper firstly takes an in-depth analysis of the traffic flow operations at the tandem intersection. Secondly, three groups of loop detectors are placed to obtain the real-time vehicle information for adaptive signalization. The lane selection behavior in the sorting area is considered to set the green time for intersection signals. With the objective of minimizing the vehicle delay, the signal control parameters are then optimized based on a dynamic programming method. Finally, numerical experiments show that average vehicle delay and maximum queue length can be reduced under all scenarios. PMID:28531198

A real-time traffic control method for the intersection with pre-signals under the phase swap sorting strategy.

PubMed

Bie, Yiming; Liu, Zhiyuan; Wang, Yinhai

2017-01-01

To deal with the conflicts between left-turn and through traffic streams and increase the discharge capacity, this paper addresses the pre-signal which is implemented at a signalized intersection. Such an intersection with pre-signal is termed as a tandem intersection. For the tandem intersection, phase swap sorting strategy is deemed as the most effective phasing scheme in view of some exclusive merits, such as easier compliance of drivers, and shorter sorting area. However, a major limitation of the phase swap sorting strategy is not considered in previous studies: if one or more vehicle is left at the sorting area after the signal light turns to red, the capacity of the approach would be dramatically dropped. Besides, previous signal control studies deal with a fixed timing plan that is not adaptive with the fluctuation of traffic flows. Therefore, to cope with these two gaps, this paper firstly takes an in-depth analysis of the traffic flow operations at the tandem intersection. Secondly, three groups of loop detectors are placed to obtain the real-time vehicle information for adaptive signalization. The lane selection behavior in the sorting area is considered to set the green time for intersection signals. With the objective of minimizing the vehicle delay, the signal control parameters are then optimized based on a dynamic programming method. Finally, numerical experiments show that average vehicle delay and maximum queue length can be reduced under all scenarios.

Sorting by COP I-coated vesicles under interphase and mitotic conditions

PubMed Central

1996-01-01

COP I-coated vesicles were analyzed for their content of resident Golgi enzymes (N-acetylgalactosaminyltransferase; N- acetylglucosaminyltransferase I; mannosidase II; galactosyltransferase), cargo (rat serum albumin; polyimmunoglobulin receptor), and recycling proteins (-KDEL receptor; ERGIC-53/p58) using biochemical and morphological techniques. The levels of these proteins were similar when the vesicles were prepared under interphase or mitotic conditions showing that sorting was unaffected. The average density relative to starting membranes for resident enzymes (14-30%), cargo (16-23%), and recycling proteins (81-125%) provides clues to the function of COP I vesicles in transport through the Golgi apparatus. PMID:8830771

Dissecting the Mechanisms of Drug Resistance in BRCA1/2-Mutant Breast Cancers

DTIC Science & Technology

2017-10-01

approval from the Institutional Animal Care and Use Committee (IACUC) (protocol # 08-036) for performing Figure 6. NMNAT-1 deficiency rescues...sorted on day 3, and chromosomal aberrations were analyzed by metaphase spreads. 7 all of the proposed animal experiments at site 2, DFCI. The...ACURO documents/forms have been submitted to DOD for approval. The USAMRMC Animal Care and Use Review Office (ACURO) has received the appropriate forms

Self-organized sorting limits behavioral variability in swarms

PubMed Central

Copenhagen, Katherine; Quint, David A.; Gopinathan, Ajay

2016-01-01

Swarming is a phenomenon where collective motion arises from simple local interactions between typically identical individuals. Here, we investigate the effects of variability in behavior among the agents in finite swarms with both alignment and cohesive interactions. We show that swarming is abolished above a critical fraction of non-aligners who do not participate in alignment. In certain regimes, however, swarms above the critical threshold can dynamically reorganize and sort out excess non-aligners to maintain the average fraction close to the critical value. This persists even in swarms with a distribution of alignment interactions, suggesting a simple, robust and efficient mechanism that allows heterogeneously mixed populations to naturally regulate their composition and remain in a collective swarming state or even differentiate among behavioral phenotypes. We show that, for evolving swarms, this self-organized sorting behavior can couple to the evolutionary dynamics leading to new evolutionarily stable equilibrium populations set by the physical swarm parameters. PMID:27550316

Self-organized sorting limits behavioral variability in swarms

NASA Astrophysics Data System (ADS)

Copenhagen, Katherine; Quint, David A.; Gopinathan, Ajay

2016-08-01

Swarming is a phenomenon where collective motion arises from simple local interactions between typically identical individuals. Here, we investigate the effects of variability in behavior among the agents in finite swarms with both alignment and cohesive interactions. We show that swarming is abolished above a critical fraction of non-aligners who do not participate in alignment. In certain regimes, however, swarms above the critical threshold can dynamically reorganize and sort out excess non-aligners to maintain the average fraction close to the critical value. This persists even in swarms with a distribution of alignment interactions, suggesting a simple, robust and efficient mechanism that allows heterogeneously mixed populations to naturally regulate their composition and remain in a collective swarming state or even differentiate among behavioral phenotypes. We show that, for evolving swarms, this self-organized sorting behavior can couple to the evolutionary dynamics leading to new evolutionarily stable equilibrium populations set by the physical swarm parameters.

Musical auditory stimulus acutely influences heart rate dynamic responses to medication in subjects with well-controlled hypertension.

PubMed

Martiniano, Eli Carlos; Santana, Milana Drumond Ramos; Barros, Érico Luiz Damasceno; do Socorro da Silva, Maria; Garner, David Matthew; de Abreu, Luiz Carlos; Valenti, Vitor E

2018-01-17

Music can improve the efficiency of medical treatment when correctly associated with drug action, reducing risk factors involving deteriorating cardiac function. We evaluated the effect of musical auditory stimulus associated with anti-hypertensive medication on heart rate (HR) autonomic control in hypertensive subjects. We evaluated 37 well-controlled hypertensive patients designated for anti-hypertensive medication. Heart rate variability (HRV) was calculated from the HR monitor recordings of two different, randomly sorted protocols (control and music) on two separate days. Patients were examined in a resting condition 10 minutes before medication and 20 minutes, 40 minutes and 60 minutes after oral medication. Music was played throughout the 60 minutes after medication with the same intensity for all subjects in the music protocol. We noted analogous response of systolic and diastolic arterial pressure in both protocols. HR decreased 60 minutes after medication in the music protocol while it remained unchanged in the control protocol. The effects of anti-hypertensive medication on SDNN (Standard deviation of all normal RR intervals), LF (low frequency, nu), HF (high frequency, nu) and alpha-1 scale were more intense in the music protocol. In conclusion, musical auditory stimulus increased HR autonomic responses to anti-hypertensive medication in well-controlled hypertensive subjects.

Biophotonics sensor acclimatization to stem cells environment

NASA Astrophysics Data System (ADS)

Mohamad Shahimin, Mukhzeer

2017-11-01

The ability to discriminate, characterise and purify biological cells from heterogeneous population of cells is fundamental to numerous prognosis and diagnosis applications; often forming the basis for current and emerging clinical protocols in stem cell therapy. Current sorting approaches exploit differences in cell density, specific immunologic targets, or receptor-ligand interactions to isolate particular cells. Identification of novel properties by which different cell types may be discerned and of new ways for their selective manipulation are clearly fundamental components for improving sorting methodologies. Biophotonics sensor developed by our team are potentially capable of discriminating cells according to their refractive index (which is highly dependable on the organelles inside the cell), size (indicator to cell stage) and shape (in certain cases as an indicator to cell type). The sensor, which already discriminate particles efficiently, is modified to acclimatize into biological environment, especially for stem cell applications.

X-Windows Information Sharing Protocol Widget Class

NASA Technical Reports Server (NTRS)

Barry, Matthew R.

2006-01-01

The X-Windows Information Sharing Protocol (ISP) Widget Class ("Class") is used here in the object-oriented-programming sense of the word) was devised to simplify the task of implementing ISP graphical-user-interface (GUI) computer programs. ISP programming tasks require many method calls to identify, query, and interpret the connections and messages exchanged between a client and an ISP server. Most X-Windows GUI programs use widget sets or toolkits to facilitate management of complex objects. The widget standards facilitate construction of toolkits and application programs. The X-Windows Information Sharing Protocol (ISP) Widget Class encapsulates the client side of the ISP programming libraries within the framework of an X-Windows widget. Using the widget framework, X-Windows GUI programs can interact with ISP services in an abstract way and in the same manner as that of other graphical widgets, making it easier to write ISP GUI client programs. Wrapping ISP client services inside a widget framework enables a programmer to treat an ISP server interface as though it were a GUI. Moreover, an alternate subclass could implement another communication protocol in the same sort of widget.

Three-party Quantum Secure Direct Communication with Single Photons in both Polarization and Spatial-mode Degrees of Freedom

NASA Astrophysics Data System (ADS)

Wang, LiLi; Ma, WenPing; Wang, MeiLing; Shen, DongSu

2016-05-01

We present an efficient three-party quantum secure direct communication (QSDC) protocol with single photos in both polarization and spatial-mode degrees of freedom. The three legal parties' messages can be encoded on the polarization and the spatial-mode states of single photons independently with desired unitary operations. A party can obtain the other two parties' messages simultaneously through a quantum channel. Because no extra public information is transmitted in the classical channels, the drawback of information leakage or classical correlation does not exist in the proposed scheme. Moreover, the comprehensive security analysis shows that the presented QSDC network protocol can defend the outsider eavesdropper's several sorts of attacks. Compared with the single photons with only one degree of freedom, our protocol based on the single photons in two degrees of freedom has higher capacity. Since the preparation and the measurement of single photon quantum states in both the polarization and the spatial-mode degrees of freedom are available with current quantum techniques, the proposed protocol is practical.

Efficient Measurement of Quantum Gate Error by Interleaved Randomized Benchmarking

NASA Astrophysics Data System (ADS)

Magesan, Easwar; Gambetta, Jay M.; Johnson, B. R.; Ryan, Colm A.; Chow, Jerry M.; Merkel, Seth T.; da Silva, Marcus P.; Keefe, George A.; Rothwell, Mary B.; Ohki, Thomas A.; Ketchen, Mark B.; Steffen, M.

2012-08-01

We describe a scalable experimental protocol for estimating the average error of individual quantum computational gates. This protocol consists of interleaving random Clifford gates between the gate of interest and provides an estimate as well as theoretical bounds for the average error of the gate under test, so long as the average noise variation over all Clifford gates is small. This technique takes into account both state preparation and measurement errors and is scalable in the number of qubits. We apply this protocol to a superconducting qubit system and find a bounded average error of 0.003 [0,0.016] for the single-qubit gates Xπ/2 and Yπ/2. These bounded values provide better estimates of the average error than those extracted via quantum process tomography.

Phase Transition in Protocols Minimizing Work Fluctuations

NASA Astrophysics Data System (ADS)

Solon, Alexandre P.; Horowitz, Jordan M.

2018-05-01

For two canonical examples of driven mesoscopic systems—a harmonically trapped Brownian particle and a quantum dot—we numerically determine the finite-time protocols that optimize the compromise between the standard deviation and the mean of the dissipated work. In the case of the oscillator, we observe a collection of protocols that smoothly trade off between average work and its fluctuations. However, for the quantum dot, we find that as we shift the weight of our optimization objective from average work to work standard deviation, there is an analog of a first-order phase transition in protocol space: two distinct protocols exchange global optimality with mixed protocols akin to phase coexistence. As a result, the two types of protocols possess qualitatively different properties and remain distinct even in the infinite duration limit: optimal-work-fluctuation protocols never coalesce with the minimal-work protocols, which therefore never become quasistatic.

4D CT sorting based on patient internal anatomy

NASA Astrophysics Data System (ADS)

Li, Ruijiang; Lewis, John H.; Cerviño, Laura I.; Jiang, Steve B.

2009-08-01

Respiratory motion during free-breathing computed tomography (CT) scan may cause significant errors in target definition for tumors in the thorax and upper abdomen. A four-dimensional (4D) CT technique has been widely used for treatment simulation of thoracic and abdominal cancer radiotherapy. The current 4D CT techniques require retrospective sorting of the reconstructed CT slices oversampled at the same couch position. Most sorting methods depend on external surrogates of respiratory motion recorded by extra instruments. However, respiratory signals obtained from these external surrogates may not always accurately represent the internal target motion, especially when irregular breathing patterns occur. We have proposed a new sorting method based on multiple internal anatomical features for multi-slice CT scan acquired in the cine mode. Four features are analyzed in this study, including the air content, lung area, lung density and body area. We use a measure called spatial coherence to select the optimal internal feature at each couch position and to generate the respiratory signals for 4D CT sorting. The proposed method has been evaluated for ten cancer patients (eight with thoracic cancer and two with abdominal cancer). For nine patients, the respiratory signals generated from the combined internal features are well correlated to those from external surrogates recorded by the real-time position management (RPM) system (average correlation: 0.95 ± 0.02), which is better than any individual internal measures at 95% confidence level. For these nine patients, the 4D CT images sorted by the combined internal features are almost identical to those sorted by the RPM signal. For one patient with an irregular breathing pattern, the respiratory signals given by the combined internal features do not correlate well with those from RPM (correlation: 0.68 ± 0.42). In this case, the 4D CT image sorted by our method presents fewer artifacts than that from the RPM signal. Our 4D CT internal sorting method eliminates the need of externally recorded surrogates of respiratory motion. It is an automatic, accurate, robust, cost efficient and yet simple method and therefore can be readily implemented in clinical settings.

SSMILes: Investigating Various Volcanic Eruptions and Volcano Heights.

ERIC Educational Resources Information Center

Wagner-Pine, Linda; Keith, Donna Graham

1994-01-01

Presents an integrated math/science activity that shows students the differences among the three types of volcanoes using observation, classification, graphing, sorting, problem solving, measurement, averages, pattern relationships, calculators, computers, and research skills. Includes reproducible student worksheet. Lists 13 teacher resources.…

Hot topic: Comparison of sex-sorted and conventional semen within a fixed-time artificial insemination protocol designed for dairy heifers.

PubMed

Mallory, D A; Lock, S L; Woods, D C; Poock, S E; Patterson, D J

2013-02-01

The objective was to compare pregnancy per AI (P/AI) with conventional (CON) or sex-sorted (SS) semen from a single sire within a fixed-time AI (FTAI) program designed for dairy heifers. Holstein heifers (n=240) were assigned to treatment (CON or SS) according to body weight and reproductive tract score. All heifers underwent FTAI by using the "Show-Me-Synch" protocol [controlled internal drug release (CIDR) insert from d 0 to 14 followed by PGF(2α) (25mg i.m.) 16d after insert removal (d 30) with GnRH (100 µg i.m.) and FTAI at 66 h after PGF(2α)]. A single professional technician performed the FTAI. Heifers were fitted with heat detection patches at PGF(2α) to characterize estrous response. Estrous response did not differ between CON (63/120; 53%) and SS (70/120; 58%) treatments. The CON heifers, however, achieved greater FTAI P/AI (82/120; 68%) compared with SS (45/120; 38%) heifers. The P/AI did not differ for CON heifers that exhibited or failed to exhibit estrus before FTAI [44/63 (70%) vs. 38/57(67%), respectively]. For SS heifers, however, those that exhibited estrus had greater P/AI compared with those that failed to exhibit estrus [32/70 (46%) vs. 13/50 (26%)]. Pregnancy per AI resulting from FTAI was greater for heifers that were inseminated with CON semen compared with those that received SS semen. The expression of estrus before FTAI did not affect P/AI when CON semen was used, whereas the P/AI with SS semen was greater for heifers detected in estrus. Further studies are required to develop strategies for using sex-sorted semen when inseminating heifers at predetermined fixed times on the basis of expression of estrus before FTAI. Copyright © 2013 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Combining magnetic sorting of mother cells and fluctuation tests to analyze genome instability during mitotic cell aging in Saccharomyces cerevisiae.

PubMed

Patterson, Melissa N; Maxwell, Patrick H

2014-10-16

Saccharomyces cerevisiae has been an excellent model system for examining mechanisms and consequences of genome instability. Information gained from this yeast model is relevant to many organisms, including humans, since DNA repair and DNA damage response factors are well conserved across diverse species. However, S. cerevisiae has not yet been used to fully address whether the rate of accumulating mutations changes with increasing replicative (mitotic) age due to technical constraints. For instance, measurements of yeast replicative lifespan through micromanipulation involve very small populations of cells, which prohibit detection of rare mutations. Genetic methods to enrich for mother cells in populations by inducing death of daughter cells have been developed, but population sizes are still limited by the frequency with which random mutations that compromise the selection systems occur. The current protocol takes advantage of magnetic sorting of surface-labeled yeast mother cells to obtain large enough populations of aging mother cells to quantify rare mutations through phenotypic selections. Mutation rates, measured through fluctuation tests, and mutation frequencies are first established for young cells and used to predict the frequency of mutations in mother cells of various replicative ages. Mutation frequencies are then determined for sorted mother cells, and the age of the mother cells is determined using flow cytometry by staining with a fluorescent reagent that detects bud scars formed on their cell surfaces during cell division. Comparison of predicted mutation frequencies based on the number of cell divisions to the frequencies experimentally observed for mother cells of a given replicative age can then identify whether there are age-related changes in the rate of accumulating mutations. Variations of this basic protocol provide the means to investigate the influence of alterations in specific gene functions or specific environmental conditions on mutation accumulation to address mechanisms underlying genome instability during replicative aging.

Concurrent Respiratory Motion Correction of Abdominal PET and DCE-MRI using a Compressed Sensing Approach.

PubMed

Fuin, Niccolo; Catalano, Onofrio Antonio; Scipioni, Michele; Canjels, Lisanne P W; Izquierdo, David; Pedemonte, Stefano; Catana, Ciprian

2018-01-25

Purpose: We present an approach for concurrent reconstruction of respiratory motion compensated abdominal DCE-MRI and PET data in an integrated PET/MR scanner. The MR and PET reconstructions share the same motion vector fields (MVFs) derived from radial MR data; the approach is robust to changes in respiratory pattern and do not increase the total acquisition time. Methods: PET and DCE-MRI data of 12 oncological patients were simultaneously acquired for 6 minutes on an integrated PET/MR system after administration of 18 F-FDG and gadoterate meglumine. Golden-angle radial MR data were continuously acquired simultaneously with PET data and sorted into multiple motion phases based on a respiratory signal derived directly from the radial MR data. The resulting multidimensional dataset was reconstructed using a compressed sensing approach that exploits sparsity among respiratory phases. MVFs obtained using the full 6-minute (MC_6-min) and only the last 1 minute (MC_1-min) of data were incorporated into the PET reconstruction to obtain motion-corrected PET images and in an MR iterative reconstruction algorithm to produce a series of motion-corrected DCE-MRI images (moco_GRASP). The motion-correction methods (MC_6-min and MC_1-min) were evaluated by qualitative analysis of the MR images and quantitative analysis of maximum and mean standardized uptake values (SUV max , SUVmean), contrast, signal-to-noise ratio (SNR) and lesion volume in the PET images. Results: Motion corrected MC_6-min PET images demonstrated 30%, 23%, 34% and 18% increases in average SUV max , SUVmean, contrast and SNR, and an average 40% reduction in lesion volume with respect to the non-motion-corrected PET images. The changes in these figures of merit were smaller but still substantial for the MC_1-min protocol: 19%, 10%, 15% and 9% increases in average SUV max , SUVmean, contrast and SNR; and a 28% reduction in lesion volume. Moco_GRASP images were deemed of acceptable or better diagnostic image quality with respect to conventional breath hold cartesian VIBE acquisitions. Conclusion: We presented a method that allows the simultaneous acquisition of respiratory motion-corrected diagnostic quality DCE-MRI and quantitatively accurate PET data in an integrated PET/MR scanner with negligible prolongation in acquisition time compared to routine PET/DCE-MRI protocols. Copyright © 2018 by the Society of Nuclear Medicine and Molecular Imaging, Inc.

Large Brown Oval

NASA Image and Video Library

1996-01-29

This large brown oval, photographed on Mar. 2, 1979 by NASA Voyager 1. Features of this sort are not rare on Jupiter and have an average lifetime of one to two years. Above the feature is the pale orange North Temperate Belt. http://photojournal.jpl.nasa.gov/catalog/PIA00015

Beneath the District Averages: Intradistrict Differences in Teacher Compensation Expenditures

ERIC Educational Resources Information Center

Malkus, Nathaniel

2012-01-01

Previous research indicates that typical district budgeting practices mask large between-school teacher compensation expenditures (TCE) differences, that teacher sorting drives those TCE differences, and that TCE differences drive overall resource inequities. While scarce accurate school-level resource data has hindered intradistrict equity…

Enrichment and isolation of neurons from adult mouse brain for ex vivo analysis.

PubMed

Berl, Sabina; Karram, Khalad; Scheller, Anja; Jungblut, Melanie; Kirchhoff, Frank; Waisman, Ari

2017-05-01

Isolation of neurons from the adult mouse CNS is important in order to study their gene expression during development or the course of different diseases. Here we present two different methods for the enrichment or isolation of neurons from adult mouse CNS. These methods: are either based on flow cytometry sorting of eYFP expressing neurons, or by depletion of non-neuronal cells by sorting with magnetic-beads. Enrichment by FACS sorting of eYFP positive neurons results in a population of 62.4% NeuN positive living neurons. qPCR data shows a 3-5fold upregulation of neuronal markers. The isolation of neurons based on depletion of non-neuronal cells using the Miltenyi Neuron Isolation Kit, reaches a purity of up to 86.5%. qPCR data of these isolated neurons shows an increase in neuronal markers and an absence of glial markers, proving pure neuronal RNA isolation. Former data related to neuronal gene expression are mainly based on histology, which does not allow for high-throughput transcriptome analysis to examine differential gene expression. These protocols can be used to study cell type specific gene expression of neurons to unravel their function in the process of damage to the CNS. Copyright © 2017 Elsevier B.V. All rights reserved.

Exploring Assessment Tools for Research and Evaluation in Astronomy Education and Outreach

NASA Astrophysics Data System (ADS)

Buxner, S. R.; Wenger, M. C.; Dokter, E. F. C.

2011-09-01

The ability to effectively measure knowledge, attitudes, and skills in formal and informal educational settings is an important aspect of astronomy education research and evaluation. Assessments may take the form of interviews, observations, surveys, exams, or other probes to help unpack people's understandings or beliefs. In this workshop, we discussed characteristics of a variety of tools that exist to assess understandings of different concepts in astronomy as well as attitudes towards science and science teaching; these include concept inventories, surveys, interview protocols, observation protocols, card sorting, reflection videos, and other methods currently being used in astronomy education research and EPO program evaluations. In addition, we discussed common questions in the selection of assessment tools including issues of reliability and validity, time to administer, format of implementation, analysis, and human subject concerns.

Collection, Storage, and Preparation of Human Blood Cells

PubMed Central

Dagur, Pradeep K.; McCoy, J. Philip

2015-01-01

Human peripheral blood is often studied by flow cytometry in both the research and clinical laboratories. The methods for collection, storage, and preparation of peripheral blood will vary depending on the cell lineage to be examined as well as the type of assay to be performed. This unit presents protocols for collection of blood, separation of leukocytes from whole blood by lysis of erythrocytes, isolating mononuclear cells by density gradient separation, and assorted non-flow sorting methods, such as magnetic bead separations, for enriching specific cell populations, including monocytes, T lymphocytes, B lymphocytes, neutrophils,, , and platelets prior to flow cytometric analysis. A protocol is also offered for cryopreservation of cells since clinical research often involves retrospective flow cytometric analysis of samples stored over a period of months or years. PMID:26132177

High-resolution FISH on super-stretched flow-sorted plant chromosomes.

PubMed

Valárik, M; Bartos, J; Kovárová, P; Kubaláková, M; de Jong, J H; Dolezel, J

2004-03-01

A novel high-resolution fluorescence in situ hybridisation (FISH) strategy, using super-stretched flow-sorted plant chromosomes as targets, is described. The technique that allows longitudinal extension of chromosomes of more than 100 times their original metaphase size is especially attractive for plant species with large chromosomes, whose pachytene chromosomes are generally too long and heterochromatin patterns too complex for FISH analysis. The protocol involves flow cytometric sorting of metaphase chromosomes, mild proteinase-K digestion of air-dried chromosomes on microscopic slides, followed by stretching with ethanol:acetic acid (3 : 1). Stretching ratios were assessed in a number of FISH experiments with super-stretched chromosomes from barley, wheat, rye and chickpea, hybridised with 45S and 5S ribosomal DNAs and the [GAA]n microsatellite, the [TTTAGGG]n telomeric repeat and a bacterial artificial chromosome (BAC) clone as probes. FISH signals on stretched chromosomes were brighter than those on the untreated control, resulting from better accessibility of the stretched chromatin and maximum observed sensitivity of 1 kbp. Spatial resolution of neighbouring loci was improved down to 70 kbp as compared to 5-10 Mbp after FISH on mitotic chromosomes, revealing details of adjacent DNA sequences hitherto not obtained with any other method. Stretched chromosomes are advantageous over extended DNA fibres from interphase nuclei as targets for FISH studies because they still retain chromosomal integrity. Although the method is confined to species for which chromosome flow sorting has been developed, it provides a unique system for controlling stretching degree of mitotic chromosomes and high-resolution bar-code FISH.

Is the glutamine story over?

PubMed

Smedberg, Marie; Wernerman, Jan

2016-11-10

Glutamine has been launched as a conditionally indispensible amino acid for the critically ill. Supplementation has been recommended in guidelines from international societies. Although data have been presented pointing out that glutamine supplementation may not be for everybody, recommendations for treatments and design of study protocols have included all critically ill patients. Results from more recent studies and meta-analyses indicate that indiscriminate use of glutamine supplementation in critically ill patients may actually cause harm rather than beneficial effects. This viewpoint sorts out arguments of controversy in the glutamine story.

Bottom sediments and nutrients in the tidal Potomac system, Maryland and Virginia

USGS Publications Warehouse

Glenn, Jerry L.

1988-01-01

The characteristics and distributions of near-surface bottom sediments and of nutrients in the sediments provide information on modern sediment and nutrient sources, sedimentation environments, and geochemical reactions in the tidal Potomac system, Maryland and Virginia. This information is fundamental to an improved understanding of sedimentation and eutrophication problems in the tidal Potomac system. The tidal Potomac system consists of 1,230 square kilometers of intertidal to subtidal Potomac mainstem and tributary streambed from the heads-of-tides to Chesapeake Bay. Tidal Potomac sediments are dominantly silt and clay except in local areas. An average sediment sample is about two-thirds silt and clay (fine) particles and one-third sand (coarse) particles. The mean of the median size of all samples is 6.60 phi, or 0.010 millimeters. Sorting generally is poor and the average sediment is skewed toward the fine tail of the size-distribution curve. Mean particle-size measures have large standard deviations. Among geomorphic units, two distinctly different size populations are found; fine (median phi about 9), and poorly sorted (sorting about 3) sediments in the channel and the smooth flat, and coarse (median phi about 2), and well sorted (sorting about 1) sediments in the shoreline flat and the irregular slope. Among mainstem hydrologic divisions, an average sediment from the river and the estuary division is coarser and more variable than an average sediment from the transition division. Substantial concentrations of total carbon, total nitrogen, and total phosphorus, and limited amounts of inorganic carbon, ammonia nitrogen and nitrite plus nitrate nitrogen occur in tidal Potomac sediments. An average tidal Potomac sediment sample weighing 1 kilogram contains about 21,000 milligrams of total carbon, 2,400 milligrams of total nitrogen, 1,200 milligrams of total phosphorus, 600 milligrams of inorganic carbon, 170 milligrams of ammonia nitrogen, and 2 milligrams of nitrite plus nitrate nitrogen. Total carbon, nitrogen, and phosphorus have an average ratio by weight of 18:2:1 and an average ratio by atoms of 94:8:1. Nutrient concentrations and nutrient ratios have large ranges and standard deviations. Nutrient concentrations usually are closely related to particle size; large concentrations are characteristic of fine sediments in the channel and the smooth flat, and small concentrations are typical of coarse sediments in the shoreline flat and the irregular slope. Concentrations typically decrease from the river division to the estuary division. Mainstem and tributaries show no statistically significant difference in mean particle-size measures or mean nutrient concentrations. Tributaries do not contribute large quantities of sediment with diverse texture or nutrient content to the Potomac mainstem. Particle-size measures and nutrient concentrations in the mainstem are significantly related to hydrologic divisions and geomorphic units; that is, particle size and nutrients vary significantly along and across the Potomac mainstem. Lateral variations in particle size and nutrient content are more pronounced and contribute more to significant relations than longitudinal variations contribute. The mean values for the median particle size and for the percentage of sand indicate significant variations among hydrologic divisions for samples from a geomorphic unit, and among geomorphic units, for samples from a hydrologic division. Sediments of channels and smooth flats in the river division commonly are coarser than sediments of channels and smooth flats in the transition and the estuary divisions. Shoreline flats in the estuary division are coarser than shoreline flats in the river division. Shoreline flats and irregular slopes in each hydrologic division generally are significantly coarser than channels and smooth flats. Relations between particle-size measures and geomorphic units show progressively larger cor

Bacterial Microcolonies in Gel Beads for High-Throughput Screening of Libraries in Synthetic Biology.

PubMed

Duarte, José M; Barbier, Içvara; Schaerli, Yolanda

2017-11-17

Synthetic biologists increasingly rely on directed evolution to optimize engineered biological systems. Applying an appropriate screening or selection method for identifying the potentially rare library members with the desired properties is a crucial step for success in these experiments. Special challenges include substantial cell-to-cell variability and the requirement to check multiple states (e.g., being ON or OFF depending on the input). Here, we present a high-throughput screening method that addresses these challenges. First, we encapsulate single bacteria into microfluidic agarose gel beads. After incubation, they harbor monoclonal bacterial microcolonies (e.g., expressing a synthetic construct) and can be sorted according their fluorescence by fluorescence activated cell sorting (FACS). We determine enrichment rates and demonstrate that we can measure the average fluorescent signals of microcolonies containing phenotypically heterogeneous cells, obviating the problem of cell-to-cell variability. Finally, we apply this method to sort a pBAD promoter library at ON and OFF states.

Update of Ireland's national average indoor radon concentration - Application of a new survey protocol.

PubMed

Dowdall, A; Murphy, P; Pollard, D; Fenton, D

2017-04-01

In 2002, a National Radon Survey (NRS) in Ireland established that the geographically weighted national average indoor radon concentration was 89 Bq m -3 . Since then a number of developments have taken place which are likely to have impacted on the national average radon level. Key among these was the introduction of amending Building Regulations in 1998 requiring radon preventive measures in new buildings in High Radon Areas (HRAs). In 2014, the Irish Government adopted the National Radon Control Strategy (NRCS) for Ireland. A knowledge gap identified in the NRCS was to update the national average for Ireland given the developments since 2002. The updated national average would also be used as a baseline metric to assess the effectiveness of the NRCS over time. A new national survey protocol was required that would measure radon in a sample of homes representative of radon risk and geographical location. The design of the survey protocol took into account that it is not feasible to repeat the 11,319 measurements carried out for the 2002 NRS due to time and resource constraints. However, the existence of that comprehensive survey allowed for a new protocol to be developed, involving measurements carried out in unbiased randomly selected volunteer homes. This paper sets out the development and application of that survey protocol. The results of the 2015 survey showed that the current national average indoor radon concentration for homes in Ireland is 77 Bq m -3 , a decrease from the 89 Bq m -3 reported in the 2002 NRS. Analysis of the results by build date demonstrate that the introduction of the amending Building Regulations in 1998 have led to a reduction in the average indoor radon level in Ireland. Copyright © 2016 Elsevier Ltd. All rights reserved.

Basis for paleoenvironmental interpretation of magnetic properties of sediment from Upper Klamath Lake (Oregon): Effects of weathering and mineralogical sorting

USGS Publications Warehouse

Rosenbaum, J.G.; Reynolds, R.L.

2004-01-01

Studies of magnetic properties enable reconstruction of environmental conditions that affected magnetic minerals incorporated in sediments from Upper Klamath Lake. Analyses of stream sediment samples from throughout the catchment of Upper Klamath Lake show that alteration of Fe-oxide minerals during subaerial chemical weathering of basic volcanic rocks has significantly changed magnetic properties of surficial deposits. Titanomagnetite, which is abundant both as phenocrysts and as microcrystals in fresh volcanic rocks, is progressively destroyed during weathering. Because fine-grained magnetite is readily altered due to large surface-to-volume ratios, weathering causes an increase in average magnetic grain size as well as reduction in the quantity of titanomagnetite both absolutely and relative to hematite. Hydrodynamic mineralogical sorting also produces differences in magnetic properties among rock and mineral grains of differing sizes. Importantly, removal of coarse silicate and Fe-oxide grains by sorting concentrated extremely fine-grained magnetite in the resulting sediment. The effects of weathering and sorting of minerals cannot be completely separated. These processes combine to produce the magnetic properties of a non-glacial lithic component of Upper Klamath Lake sediments, which is characterized by relatively low magnetite content and coarse magnetic grain size. Hydrodynamic sorting alone causes significant differences between the magnetic properties of glacial flour in lake sediments and of fresh volcanic rocks in the catchment. In comparison to source volcanic rocks, glacial flour in the lake sediment is highly enriched in extremely fine-grained magnetite.

Desensitization for solid organ and hematopoietic stem cell transplantation

PubMed Central

Zachary, Andrea A; Leffell, Mary S

2014-01-01

Desensitization protocols are being used worldwide to enable kidney transplantation across immunologic barriers, i.e. antibody to donor HLA or ABO antigens, which were once thought to be absolute contraindications to transplantation. Desensitization protocols are also being applied to permit transplantation of HLA mismatched hematopoietic stem cells to patients with antibody to donor HLA, to enhance the opportunity for transplantation of non-renal organs, and to treat antibody-mediated rejection. Although desensitization for organ transplantation carries an increased risk of antibody-mediated rejection, ultimately these transplants extend and enhance the quality of life for solid organ recipients, and desensitization that permits transplantation of hematopoietic stem cells is life saving for patients with limited donor options. Complex patient factors and variability in treatment protocols have made it difficult to identify, precisely, the mechanisms underlying the downregulation of donor-specific antibodies. The mechanisms underlying desensitization may differ among the various protocols in use, although there are likely to be some common features. However, it is likely that desensitization achieves a sort of immune detente by first reducing the immunologic barrier and then by creating an environment in which an autoregulatory process restricts the immune response to the allograft. PMID:24517434

Making sense of the labor market height premium: Evidence from the British Household Panel Survey.

PubMed

Case, Anne; Paxson, Christina; Islam, Mahnaz

2009-03-01

We use data from the British Household Panel Survey to examine the labor market premium in height. Most of the premium is explained by higher average educational attainment and sorting into higher-status occupations and industries by those who are taller.

Multiple enface image averaging for enhanced optical coherence tomography angiography imaging.

PubMed

Uji, Akihito; Balasubramanian, Siva; Lei, Jianqin; Baghdasaryan, Elmira; Al-Sheikh, Mayss; Borrelli, Enrico; Sadda, SriniVas R

2018-05-31

To investigate the effect of multiple enface image averaging on image quality of the optical coherence tomography angiography (OCTA). Twenty-one normal volunteers were enrolled in this study. For each subject, one eye was imaged with 3 × 3 mm scan protocol, and another eye was imaged with the 6 × 6 mm scan protocol centred on the fovea using the ZEISS Angioplex™ spectral-domain OCTA device. Eyes were repeatedly imaged to obtain nine OCTA cube scan sets, and nine superficial capillary plexus (SCP) and deep capillary plexus (DCP) were individually averaged after registration. Eighteen eyes with a 3 × 3 mm scan field and 14 eyes with a 6 × 6 mm scan field were studied. Averaged images showed more continuous vessels and less background noise in both the SCP and the DCP as the number of frames used for averaging increased, with both 3 × 3 and 6 × 6 mm scan protocols. The intensity histogram of the vessels dramatically changed after averaging. Contrast-to-noise ratio (CNR) and subjectively assessed image quality scores also increased as the number of frames used for averaging increased in all image types. However, the additional benefit in quality diminished when averaging more than five frames. Averaging only three frames achieved significant improvement in CNR and the score assigned by certified grades. Use of multiple image averaging in OCTA enface images was found to be both objectively and subjectively effective for enhancing image quality. These findings may of value for developing optimal OCTA imaging protocols for future studies. © 2018 Acta Ophthalmologica Scandinavica Foundation. Published by John Wiley & Sons Ltd.

Intensity non-uniformity correction in MRI: existing methods and their validation.

PubMed

Belaroussi, Boubakeur; Milles, Julien; Carme, Sabin; Zhu, Yue Min; Benoit-Cattin, Hugues

2006-04-01

Magnetic resonance imaging is a popular and powerful non-invasive imaging technique. Automated analysis has become mandatory to efficiently cope with the large amount of data generated using this modality. However, several artifacts, such as intensity non-uniformity, can degrade the quality of acquired data. Intensity non-uniformity consists in anatomically irrelevant intensity variation throughout data. It can be induced by the choice of the radio-frequency coil, the acquisition pulse sequence and by the nature and geometry of the sample itself. Numerous methods have been proposed to correct this artifact. In this paper, we propose an overview of existing methods. We first sort them according to their location in the acquisition/processing pipeline. Sorting is then refined based on the assumptions those methods rely on. Next, we present the validation protocols used to evaluate these different correction schemes both from a qualitative and a quantitative point of view. Finally, availability and usability of the presented methods is discussed.

Proteomic screening of glutamatergic mouse brain synaptosomes isolated by fluorescence activated sorting

PubMed Central

Biesemann, Christoph; Grønborg, Mads; Luquet, Elisa; Wichert, Sven P; Bernard, Véronique; Bungers, Simon R; Cooper, Ben; Varoqueaux, Frédérique; Li, Liyi; Byrne, Jennifer A; Urlaub, Henning; Jahn, Olaf; Brose, Nils; Herzog, Etienne

2014-01-01

For decades, neuroscientists have used enriched preparations of synaptic particles called synaptosomes to study synapse function. However, the interpretation of corresponding data is problematic as synaptosome preparations contain multiple types of synapses and non-synaptic neuronal and glial contaminants. We established a novel Fluorescence Activated Synaptosome Sorting (FASS) method that substantially improves conventional synaptosome enrichment protocols and enables high-resolution biochemical analyses of specific synapse subpopulations. Employing knock-in mice with fluorescent glutamatergic synapses, we show that FASS isolates intact ultrapure synaptosomes composed of a resealed presynaptic terminal and a postsynaptic density as assessed by light and electron microscopy. FASS synaptosomes contain bona fide glutamatergic synapse proteins but are almost devoid of other synapse types and extrasynaptic or glial contaminants. We identified 163 enriched proteins in FASS samples, of which FXYD6 and Tpd52 were validated as new synaptic proteins. FASS purification thus enables high-resolution biochemical analyses of specific synapse subpopulations in health and disease. PMID:24413018

Isolation of circulating tumor cells by immunomagnetic enrichment and fluorescence-activated cell sorting (IE/FACS) for molecular profiling.

PubMed

Magbanua, Mark Jesus M; Park, John W

2013-12-01

Circulating tumor cells (CTCs) are cells shed by the primary tumor into the blood stream capable of initiating distant metastasis. In the past decade, numerous assays have been developed to reliably detect these extremely rare cells. However, methods for purification of CTCs with little or no contamination of normal blood cells for molecular profiling are limited. We have developed a novel protocol to isolate CTCs by combining immunomagnetic enrichment and fluorescence-activated cell sorting (IE/FACS). The two-part assay includes (1) immunomagnetic capture using magnetic beads conjugated to monoclonal antibody against an epithelial cell adhesion marker (EpCAM) to enrich for tumor cells; and (2) FACS analysis using EpCAM to purify tumor cells away from mononuclear cells of hematopoietic lineage. Downstream molecular analyses of single and pooled cells confirmed the isolation of highly pure CTCs with characteristics typical that of malignant cells. Copyright © 2013 Elsevier Inc. All rights reserved.

Methods to study the biogenesis of membrane proteins in yeast mitochondria.

PubMed

Weckbecker, Daniel; Herrmann, Johannes M

2013-01-01

The biogenesis of mitochondrial membrane proteins is an intricate process that relies on the import and submitochondrial sorting of nuclear-encoded preproteins and on the synthesis of mitochondrial translation products in the matrix. Subsequently, these polypeptides need to be inserted into the outer and the inner membranes of the organelle where many of them assemble into multisubunit complexes. In this chapter we provide established protocols to study these different processes experimentally using mitochondria of budding yeast. In particular, methods are described in detail to purify mitochondria, to study mitochondrial protein synthesis, to follow the import of radiolabeled preproteins into isolated mitochondria, and to assess membrane association and the aggregation of mitochondrial proteins by fractionation. These protocols and a list of dos and don'ts shall enable beginners and experienced scientists to address the targeting and assembly of mitochondrial membrane proteins.

Crispr-mediated Gene Targeting of Human Induced Pluripotent Stem Cells.

PubMed

Byrne, Susan M; Church, George M

2015-01-01

CRISPR/Cas9 nuclease systems can create double-stranded DNA breaks at specific sequences to efficiently and precisely disrupt, excise, mutate, insert, or replace genes. However, human embryonic stem or induced pluripotent stem cells (iPSCs) are more difficult to transfect and less resilient to DNA damage than immortalized tumor cell lines. Here, we describe an optimized protocol for genome engineering of human iPSCs using a simple transient transfection of plasmids and/or single-stranded oligonucleotides. With this protocol, we achieve transfection efficiencies greater than 60%, with gene disruption efficiencies from 1-25% and gene insertion/replacement efficiencies from 0.5-10% without any further selection or enrichment steps. We also describe how to design and assess optimal sgRNA target sites and donor targeting vectors; cloning individual iPSC by single cell FACS sorting, and genotyping successfully edited cells.

Serious gaming technology in major incident triage training: a pragmatic controlled trial.

PubMed

Knight, James F; Carley, Simon; Tregunna, Bryan; Jarvis, Steve; Smithies, Richard; de Freitas, Sara; Dunwell, Ian; Mackway-Jones, Kevin

2010-09-01

By exploiting video games technology, serious games strive to deliver affordable, accessible and usable interactive virtual worlds, supporting applications in training, education, marketing and design. The aim of the present study was to evaluate the effectiveness of such a serious game in the teaching of major incident triage by comparing it with traditional training methods. Pragmatic controlled trial. During Major Incident Medical Management and Support Courses, 91 learners were randomly distributed into one of two training groups: 44 participants practiced triage sieve protocol using a card-sort exercise, whilst the remaining 47 participants used a serious game. Following the training sessions, each participant undertook an evaluation exercise, whereby they were required to triage eight casualties in a simulated live exercise. Performance was assessed in terms of tagging accuracy (assigning the correct triage tag to the casualty), step accuracy (following correct procedure) and time taken to triage all casualties. Additionally, the usability of both the card-sort exercise and video game were measured using a questionnaire. Tagging accuracy by participants who underwent the serious game training was significantly higher than those who undertook the card-sort exercise [Chi2=13.126, p=0.02]. Step accuracy was also higher in the serious game group but only for the numbers of participants that followed correct procedure when triaging all eight casualties [Chi2=5.45, p=0.0196]. There was no significant difference in time to triage all casualties (card-sort=435+/-74 s vs video game=456+/-62 s, p=0.155). Serious game technologies offer the potential to enhance learning and improve subsequent performance when compared to traditional educational methods. Copyright 2010 Elsevier Ireland Ltd. All rights reserved.

An improved PRoPHET routing protocol in delay tolerant network.

PubMed

Han, Seung Deok; Chung, Yun Won

2015-01-01

In delay tolerant network (DTN), an end-to-end path is not guaranteed and packets are delivered from a source node to a destination node via store-carry-forward based routing. In DTN, a source node or an intermediate node stores packets in buffer and carries them while it moves around. These packets are forwarded to other nodes based on predefined criteria and finally are delivered to a destination node via multiple hops. In this paper, we improve the dissemination speed of PRoPHET (probability routing protocol using history of encounters and transitivity) protocol by employing epidemic protocol for disseminating message m, if forwarding counter and hop counter values are smaller than or equal to the threshold values. The performance of the proposed protocol was analyzed from the aspect of delivery probability, average delay, and overhead ratio. Numerical results show that the proposed protocol can improve the delivery probability, average delay, and overhead ratio of PRoPHET protocol by appropriately selecting the threshold forwarding counter and threshold hop counter values.

Quality and developmental rate of embryos produced with sex-sorted and conventional semen from superovulated dairy cattle.

PubMed

Mikkola, M; Taponen, J

2017-01-01

This study investigated the effect of sex-sorted semen compared with conventional semen on the outcome of embryo recovery, placing special emphasis on the quality, and developmental stage of embryos. Data were analyzed for 443 embryo collections with sex-sorted semen (SEX group) and 1528 with conventional semen (CONV group) in superovulated dairy heifers and cows. The insemination protocol for conventional semen included two inseminations, comprising a total dose of 30 million sperm passing into the uterine body. For sex-sorted semen, two (30%) to three (70%) deep uterine inseminations were performed, the total dose ranging from eight to 12 million sperm. The data were analyzed separately for heifers and cows. The total number of recovered structures was similar among the groups. The number of viable embryos decreased in the SEX groups compared with the CONV (with 1.4 and 3.2 fewer embryos in heifers and cows, correspondingly, P < 0.001), and correspondingly the proportions of unfertilized ova and degenerated embryos increased in the SEX groups (P < 0.001). The proportion of unsuccessful collections, yielding no transferable embryos, increased in the SEX groups for both heifers (from 7.2% to 11.2%, P = 0.025) and cows (from 9.0% to 20.7%, P < 0.001). Regarding the quality of viable embryos, the quality grades were superior in the CONV group compared with the SEX group for heifers (P < 0.001) and cows (P < 0.001). The proportion of grade 1 embryos decreased by 6.5 percentage points in heifers and 11.9 percentage points in cows when sex-sorted semen was used. Correspondingly, the proportions of grade 2 and 3 embryos increased in heifers and cows when sexed semen was used. The mean developmental stages of embryo collections were numerically slightly lower in the SEX group. In heifers, the delay in developmental stage was statistically significant (P = 0.001), but in cows, there was only a tendency toward that (P = 0.067). In conclusion, sex-sorted sperm decreased the transferable embryo yield and increased the risk of a recovery yielding no transferable embryos. Furthermore, use of sex-sorted semen decreased the proportion of grade 1 embryos. In addition, it also seemed to delay embryonic development, although the delay in embryonic development was minimal and its biological relevance remains undefined. Despite the compromised embryo production, taken into account the optimization of recipient resources, the use of sex-sorted semen is advantageous, especially in superovulated heifers, which are of most importance in the modern breeding strategies using genomic selection. Copyright © 2016 Elsevier Inc. All rights reserved.

A Group Neighborhood Average Clock Synchronization Protocol for Wireless Sensor Networks

PubMed Central

Lin, Lin; Ma, Shiwei; Ma, Maode

2014-01-01

Clock synchronization is a very important issue for the applications of wireless sensor networks. The sensors need to keep a strict clock so that users can know exactly what happens in the monitoring area at the same time. This paper proposes a novel internal distributed clock synchronization solution using group neighborhood average. Each sensor node collects the offset and skew rate of the neighbors. Group averaging of offset and skew rate value are calculated instead of conventional point-to-point averaging method. The sensor node then returns compensated value back to the neighbors. The propagation delay is considered and compensated. The analytical analysis of offset and skew compensation is presented. Simulation results validate the effectiveness of the protocol and reveal that the protocol allows sensor networks to quickly establish a consensus clock and maintain a small deviation from the consensus clock. PMID:25120163

Acoustic sorting models for improved log segregation

Treesearch

Xiping Wang; Steve Verrill; Eini Lowell; Robert J. Ross; Vicki L. Herian

2013-01-01

In this study, we examined three individual log measures (acoustic velocity, log diameter, and log vertical position in a tree) for their ability to predict average modulus of elasticity (MOE) and grade yield of structural lumber obtained from Douglas-fir (Pseudotsuga menziesii [Mirb. Franco]) logs. We found that log acoustic velocity only had a...

Predicting story goodness performance from cognitive measures following traumatic brain injury.

PubMed

Lê, Karen; Coelho, Carl; Mozeiko, Jennifer; Krueger, Frank; Grafman, Jordan

2012-05-01

This study examined the prediction of performance on measures of the Story Goodness Index (SGI; Lê, Coelho, Mozeiko, & Grafman, 2011) from executive function (EF) and memory measures following traumatic brain injury (TBI). It was hypothesized that EF and memory measures would significantly predict SGI outcomes. One hundred sixty-seven individuals with TBI participated in the study. Story retellings were analyzed using the SGI protocol. Three cognitive measures--Delis-Kaplan Executive Function System (D-KEFS; Delis, Kaplan, & Kramer, 2001) Sorting Test, Wechsler Memory Scale--Third Edition (WMS-III; Wechsler, 1997) Working Memory Primary Index (WMI), and WMS-III Immediate Memory Primary Index (IMI)--were entered into a multiple linear regression model for each discourse measure. Two sets of regression analyses were performed, the first with the Sorting Test as the first predictor and the second with it as the last. The first set of regression analyses identified the Sorting Test and IMI as the only significant predictors of performance on measures of the SGI. The second set identified all measures as significant predictors when evaluating each step of the regression function. The cognitive variables predicted performance on the SGI measures, although there were differences in the amount of explained variance. The results (a) suggest that storytelling ability draws on a number of underlying skills and (b) underscore the importance of using discrete cognitive tasks rather than broad cognitive indices to investigate the cognitive substrates of discourse.

Q-sort assessment vs visual analog scale in the evaluation of smile esthetics.

PubMed

Schabel, Brian J; McNamara, James A; Franchi, Lorenzo; Baccetti, Tiziano

2009-04-01

This study was designed to compare the reliability of the Q-sort and visual analog scale (VAS) methods for the assessment of smile esthetics. Furthermore, agreement between orthodontists and parents of orthodontic patients, and between male and female raters, was assessed in terms of subjective evaluation of the smile. Clinical photographs and digital video captures of 48 orthodontically treated patients were rated by 2 panels: 25 experienced orthodontists (15 men, 10 women) and 20 parents of the patients (8 men, 12 women). Interrater reliability of the Q-sort and VAS methods was evaluated by using single-measure and average-measure intraclass correlation (ICC). Kappa agreement and the McNemar test were used to evaluate agreement between orthodontists and parents, and between men and women, for "attractive" and "unattractive" images of smiles captured with clinical photography. The single-measure ICC coefficients showed fair to good reliability of the Q-sort and poor reliability of the VAS for measuring esthetic preferences of an individual orthodontist or parent. Both rating groups agreed significantly (P >0.05) on the total percentage of "attractive" images of smiles captured with clinical photography. Men and women, however, significantly disagreed on the total percentages of "attractive" and "unattractive" smiles. Women rated higher percentages of both image groups as "attractive" than did their male counterparts. The Q-sort was more reliable than the VAS for measuring smile esthetics. Orthodontists and parents of orthodontic patients agreed with respect to "attractive" and "unattractive" smiles. Men and women agreed poorly with respect to "attractive" and "unattractive" smiles.

Internal respiratory surrogate in multislice 4D CT using a combination of Fourier transform and anatomical features

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

Hui, Cheukkai; Suh, Yelin; Robertson, Daniel

Purpose: The purpose of this study was to develop a novel algorithm to create a robust internal respiratory signal (IRS) for retrospective sorting of four-dimensional (4D) computed tomography (CT) images. Methods: The proposed algorithm combines information from the Fourier transform of the CT images and from internal anatomical features to form the IRS. The algorithm first extracts potential respiratory signals from low-frequency components in the Fourier space and selected anatomical features in the image space. A clustering algorithm then constructs groups of potential respiratory signals with similar temporal oscillation patterns. The clustered group with the largest number of similar signalsmore » is chosen to form the final IRS. To evaluate the performance of the proposed algorithm, the IRS was computed and compared with the external respiratory signal from the real-time position management (RPM) system on 80 patients. Results: In 72 (90%) of the 4D CT data sets tested, the IRS computed by the authors’ proposed algorithm matched with the RPM signal based on their normalized cross correlation. For these data sets with matching respiratory signals, the average difference between the end inspiration times (Δt{sub ins}) in the IRS and RPM signal was 0.11 s, and only 2.1% of Δt{sub ins} were more than 0.5 s apart. In the eight (10%) 4D CT data sets in which the IRS and the RPM signal did not match, the average Δt{sub ins} was 0.73 s in the nonmatching couch positions, and 35.4% of them had a Δt{sub ins} greater than 0.5 s. At couch positions in which IRS did not match the RPM signal, a correlation-based metric indicated poorer matching of neighboring couch positions in the RPM-sorted images. This implied that, when IRS did not match the RPM signal, the images sorted using the IRS showed fewer artifacts than the clinical images sorted using the RPM signal. Conclusions: The authors’ proposed algorithm can generate robust IRSs that can be used for retrospective sorting of 4D CT data. The algorithm is completely automatic and requires very little processing time. The algorithm is cost efficient and can be easily adopted for everyday clinical use.« less

Differences in the ability of spermatozoa from individual boar ejaculates to withstand different semen-processing techniques.

PubMed

Parrilla, Inma; del Olmo, David; Sijses, Laurien; Martinez-Alborcia, María J; Cuello, Cristina; Vazquez, Juan M; Martinez, Emilio A; Roca, Jordi

2012-05-01

The present study aimed to evaluate the ability of spermatozoa from individual boar ejaculates to withstand different semen-processing techniques. Eighteen sperm-rich ejaculate samples from six boars (three per boar) were diluted in Beltsville Thawing Solution and split into three aliquots. The aliquots were (1) further diluted to 3×10(7) sperm/mL and stored as a liquid at 17°C for 72 h, (2) frozen-thawed (FT) at 1×10(9) sperm/mL using standard 0.5-mL straw protocols, or (3) sex-sorted with subsequent liquid storage (at 17°C for 6 h) or FT (2×10(7) sperm/mL using a standard 0.25-mL straw protocol). The sperm quality was evaluated based on total sperm motility (the CASA system), viability (plasma membrane integrity assessed using flow cytometry and the LIVE/DEAD Sperm Viability Kit), lipid peroxidation (assessed via indirect measurement of the generation of malondialdehyde (MDA) using the BIOXYTECH MDA-586 Assay Kit) and DNA fragmentation (sperm chromatin dispersion assessed using the Sperm-Sus-Halomax(®) test). Data were normalized to the values assessed for the fresh (for liquid-stored and FT samples) or the sorted semen samples (for liquid stored and the FT sorted spermatozoa). All of the four sperm-processing techniques affected sperm quality (P<0.01), regardless of the semen donor, with reduced percentages of motile and viable sperm and increased MDA generation and percentages of sperm with fragmented DNA. Significant (P<0.05) inter-boar (effect of boars within each semen-processing technique) and intra-boar (effect of semen-processing techniques within each boar) differences were evident for all of the sperm quality parameters assessed, indicating differences in the ability of spermatozoa from individual boars to withstand the semen-processing techniques. These results are the first evidence that ejaculate spermatozoa from individual boars can respond in a boar-dependent manner to different semen-processing techniques. Copyright © 2012 Elsevier B.V. All rights reserved.

A Sorting Statistic with Application in Neurological Magnetic Resonance Imaging of Autism.

PubMed

Levman, Jacob; Takahashi, Emi; Forgeron, Cynthia; MacDonald, Patrick; Stewart, Natalie; Lim, Ashley; Martel, Anne

2018-01-01

Effect size refers to the assessment of the extent of differences between two groups of samples on a single measurement. Assessing effect size in medical research is typically accomplished with Cohen's d statistic. Cohen's d statistic assumes that average values are good estimators of the position of a distribution of numbers and also assumes Gaussian (or bell-shaped) underlying data distributions. In this paper, we present an alternative evaluative statistic that can quantify differences between two data distributions in a manner that is similar to traditional effect size calculations; however, the proposed approach avoids making assumptions regarding the shape of the underlying data distribution. The proposed sorting statistic is compared with Cohen's d statistic and is demonstrated to be capable of identifying feature measurements of potential interest for which Cohen's d statistic implies the measurement would be of little use. This proposed sorting statistic has been evaluated on a large clinical autism dataset from Boston Children's Hospital , Harvard Medical School , demonstrating that it can potentially play a constructive role in future healthcare technologies.

A Sorting Statistic with Application in Neurological Magnetic Resonance Imaging of Autism

PubMed Central

Takahashi, Emi; Lim, Ashley; Martel, Anne

2018-01-01

Effect size refers to the assessment of the extent of differences between two groups of samples on a single measurement. Assessing effect size in medical research is typically accomplished with Cohen's d statistic. Cohen's d statistic assumes that average values are good estimators of the position of a distribution of numbers and also assumes Gaussian (or bell-shaped) underlying data distributions. In this paper, we present an alternative evaluative statistic that can quantify differences between two data distributions in a manner that is similar to traditional effect size calculations; however, the proposed approach avoids making assumptions regarding the shape of the underlying data distribution. The proposed sorting statistic is compared with Cohen's d statistic and is demonstrated to be capable of identifying feature measurements of potential interest for which Cohen's d statistic implies the measurement would be of little use. This proposed sorting statistic has been evaluated on a large clinical autism dataset from Boston Children's Hospital, Harvard Medical School, demonstrating that it can potentially play a constructive role in future healthcare technologies. PMID:29796236

A computationally efficient method for incorporating spike waveform information into decoding algorithms.

PubMed

Ventura, Valérie; Todorova, Sonia

2015-05-01

Spike-based brain-computer interfaces (BCIs) have the potential to restore motor ability to people with paralysis and amputation, and have shown impressive performance in the lab. To transition BCI devices from the lab to the clinic, decoding must proceed automatically and in real time, which prohibits the use of algorithms that are computationally intensive or require manual tweaking. A common choice is to avoid spike sorting and treat the signal on each electrode as if it came from a single neuron, which is fast, easy, and therefore desirable for clinical use. But this approach ignores the kinematic information provided by individual neurons recorded on the same electrode. The contribution of this letter is a linear decoding model that extracts kinematic information from individual neurons without spike-sorting the electrode signals. The method relies on modeling sample averages of waveform features as functions of kinematics, which is automatic and requires minimal data storage and computation. In offline reconstruction of arm trajectories of a nonhuman primate performing reaching tasks, the proposed method performs as well as decoders based on expertly manually and automatically sorted spikes.

Spatial Structures of the Environment and of Dispersal Impact Species Distribution in Competitive Metacommunities

PubMed Central

Ai, Dexiecuo; Gravel, Dominique; Chu, Chengjin; Wang, Gang

2013-01-01

The correspondence between species distribution and the environment depends on species’ ability to track favorable environmental conditions (via dispersal) and to maintain competitive hierarchy against the constant influx of migrants (mass effect) and demographic stochasticity (ecological drift). Here we report a simulation study of the influence of landscape structure on species distribution. We consider lottery competition for space in a spatially heterogeneous environment, where the landscape is represented as a network of localities connected by dispersal. We quantified the contribution of neutrality and species sorting to their spatial distribution. We found that neutrality increases and the strength of species-sorting decreases with the centrality of a community in the landscape when the average dispersal among communities is low, whereas the opposite was found at elevated dispersal. We also found that the strength of species-sorting increases with environmental heterogeneity. Our results illustrate that spatial structure of the environment and of dispersal must be taken into account for understanding species distribution. We stress the importance of spatial geographic structure on the relative importance of niche vs. neutral processes in controlling community dynamics. PMID:23874815

Spatial structures of the environment and of dispersal impact species distribution in competitive metacommunities.

PubMed

Ai, Dexiecuo; Gravel, Dominique; Chu, Chengjin; Wang, Gang

2013-01-01

The correspondence between species distribution and the environment depends on species' ability to track favorable environmental conditions (via dispersal) and to maintain competitive hierarchy against the constant influx of migrants (mass effect) and demographic stochasticity (ecological drift). Here we report a simulation study of the influence of landscape structure on species distribution. We consider lottery competition for space in a spatially heterogeneous environment, where the landscape is represented as a network of localities connected by dispersal. We quantified the contribution of neutrality and species sorting to their spatial distribution. We found that neutrality increases and the strength of species-sorting decreases with the centrality of a community in the landscape when the average dispersal among communities is low, whereas the opposite was found at elevated dispersal. We also found that the strength of species-sorting increases with environmental heterogeneity. Our results illustrate that spatial structure of the environment and of dispersal must be taken into account for understanding species distribution. We stress the importance of spatial geographic structure on the relative importance of niche vs. neutral processes in controlling community dynamics.

Evaluation of amplitude-based sorting algorithm to reduce lung tumor blurring in PET images using 4D NCAT phantom.

PubMed

Wang, Jiali; Byrne, James; Franquiz, Juan; McGoron, Anthony

2007-08-01

develop and validate a PET sorting algorithm based on the respiratory amplitude to correct for abnormal respiratory cycles. using the 4D NCAT phantom model, 3D PET images were simulated in lung and other structures at different times within a respiratory cycle and noise was added. To validate the amplitude binning algorithm, NCAT phantom was used to simulate one case of five different respiratory periods and another case of five respiratory periods alone with five respiratory amplitudes. Comparison was performed for gated and un-gated images and for the new amplitude binning algorithm with the time binning algorithm by calculating the mean number of counts in the ROI (region of interest). an average of 8.87+/-5.10% improvement was reported for total 16 tumors with different tumor sizes and different T/B (tumor to background) ratios using the new sorting algorithm. As both the T/B ratio and tumor size decreases, image degradation due to respiration increases. The greater benefit for smaller diameter tumor and lower T/B ratio indicates a potential improvement in detecting more problematic tumors.

CLUSFAVOR 5.0: hierarchical cluster and principal-component analysis of microarray-based transcriptional profiles

PubMed Central

Peterson, Leif E

2002-01-01

CLUSFAVOR (CLUSter and Factor Analysis with Varimax Orthogonal Rotation) 5.0 is a Windows-based computer program for hierarchical cluster and principal-component analysis of microarray-based transcriptional profiles. CLUSFAVOR 5.0 standardizes input data; sorts data according to gene-specific coefficient of variation, standard deviation, average and total expression, and Shannon entropy; performs hierarchical cluster analysis using nearest-neighbor, unweighted pair-group method using arithmetic averages (UPGMA), or furthest-neighbor joining methods, and Euclidean, correlation, or jack-knife distances; and performs principal-component analysis. PMID:12184816

A rapid and versatile method for the isolation, purification and cryogenic storage of Schwann cells from adult rodent nerves

PubMed Central

Andersen, Natalia D.; Srinivas, Shruthi; Piñero, Gonzalo; Monje, Paula V.

2016-01-01

We herein developed a protocol for the rapid procurement of adult nerve-derived Schwann cells (SCs) that was optimized to implement an immediate enzymatic dissociation of fresh nerve tissue while maintaining high cell viability, improving yields and minimizing fibroblast and myelin contamination. This protocol introduces: (1) an efficient method for enzymatic cell release immediately after removal of the epineurium and extensive teasing of the nerve fibers; (2) an adaptable drop-plating method for selective cell attachment, removal of myelin debris, and expansion of the initial SC population in chemically defined medium; (3) a magnetic-activated cell sorting purification protocol for rapid and effective fibroblast elimination; and (4) an optional step of cryopreservation for the storage of the excess of cells. Highly proliferative SC cultures devoid of myelin and fibroblast growth were obtained within three days of nerve processing. Characterization of the initial, expanded, and cryopreserved cell products confirmed maintenance of SC identity, viability and growth rates throughout the process. Most importantly, SCs retained their sensitivity to mitogens and potential for differentiation even after cryopreservation. To conclude, this easy-to-implement and clinically relevant protocol allows for the preparation of expandable homogeneous SC cultures while minimizing time, manipulation of the cells, and exposure to culture variables. PMID:27549422

Desensitization for solid organ and hematopoietic stem cell transplantation.

PubMed

Zachary, Andrea A; Leffell, Mary S

2014-03-01

Desensitization protocols are being used worldwide to enable kidney transplantation across immunologic barriers, i.e. antibody to donor HLA or ABO antigens, which were once thought to be absolute contraindications to transplantation. Desensitization protocols are also being applied to permit transplantation of HLA mismatched hematopoietic stem cells to patients with antibody to donor HLA, to enhance the opportunity for transplantation of non-renal organs, and to treat antibody-mediated rejection. Although desensitization for organ transplantation carries an increased risk of antibody-mediated rejection, ultimately these transplants extend and enhance the quality of life for solid organ recipients, and desensitization that permits transplantation of hematopoietic stem cells is life saving for patients with limited donor options. Complex patient factors and variability in treatment protocols have made it difficult to identify, precisely, the mechanisms underlying the downregulation of donor-specific antibodies. The mechanisms underlying desensitization may differ among the various protocols in use, although there are likely to be some common features. However, it is likely that desensitization achieves a sort of immune detente by first reducing the immunologic barrier and then by creating an environment in which an autoregulatory process restricts the immune response to the allograft. © 2014 The Authors. Immunological Reviews Published by John Wiley & Sons Ltd.

Beyond Signaling and Human Capital: Education and the Revelation of Ability. NBER Working Paper No. 13951

ERIC Educational Resources Information Center

Arcidiacono, Peter; Bayer, Patrick; Hizmo, Aurel

2008-01-01

In traditional signaling models, education provides a way for individuals to sort themselves by ability. Employers in turn use education to statistically discriminate, paying wages that reflect the average productivity of workers with the same given level of education. In this paper, we provide evidence that education (specifically, attending…

A review on transport layer protocol performance for delivering video on an adhoc network

NASA Astrophysics Data System (ADS)

Suherman; Suwendri; Al-Akaidi, Marwan

2017-09-01

The transport layer protocol is responsible for the end to end data transmission. Transmission control protocol (TCP) provides a reliable connection and user datagram protocol (UDP) offers fast but unguaranteed data transfer. Meanwhile, the 802.11 (wireless fidelity/WiFi) networks have been widely used as internet hotspots. This paper evaluates TCP, TCP variants and UDP performances for video transmission on an adhoc network. The transport protocol - medium access cross-layer is proposed by prioritizing TCP acknowledgement to reduce delay. The NS-2 evaluations show that the average delays increase linearly for all the evaluated protocols and the average packet losses grow logarithmically. UDP produces the lowest transmission delay; 5.4% and 5.8% lower than TCP and TCP variant, but experiences the highest packet loss. Both TCP and TCP Vegas maintain packet loss as low as possible. The proposed cross-layer successfully decreases TCP and TCP Vegas delay about 0.12 % and 0.15%, although losses remain similar.

Topographic control of sorted circle morphology on Svalbard

NASA Astrophysics Data System (ADS)

Voigt, Joana; Hauber, Ernst; Reiss, Dennis; Hiesinger, Harald; Johnsson, Andreas; van Gasselt, Stephan; Balme, Matt; Head, Jim; de Verra, Jean-Pierre; Steinbrügge, Gregor; Jaumann, Ralf

2015-04-01

Patterned ground is a typical phenomenon in polar, subpolar and alpine regions [1]. As it is commonly (but not necessarily!) related to freeze-thaw cycles, its presence on Mars could possibly point to locations and periods where and when liquid water existed in the recent past [2]. Sorted circles are a class of patterned ground that was tentatively identified in Elysium Planitia (Mars) [3], but this interpretation has been challenged on the basis of physical considerations [4]. Without direct access to potential patterned ground on Mars, the analysis of terrestrial analogues can inform the interpretation of Martian landforms. Svalbard (Norway) offers a wide variety of permafrost features that are morphologically analogous to Martian cold-climate landforms [5]. It hosts some of the best examples of sorted circles on Earth, which are located on the westernmost tip of Brøgger peninsula, on a broad strand flat that is characterized by a series of postglacial beach ridges [6]. Here we report on our analysis of sorted circle morphology (especially their plan-view shape, i.e. their "roundness" or ellipticity) and its correlation with local topography (slopes, curvature). Sorted circle morphology was determined from HRSC-AX images (for details on the flight campaign and image properties see ref [5]) and through field work. Topographic information comes from a 50 cm gridded DEM derived from HRSC-AX stereo images. We measured sorted circle morphology (ellipticity, azimuth of major axis) along a WNW-ESE traverse that runs from the inland towards the sea and is oriented perpendicular to the local beach ridge trend. Selected areas with homogeneous sorted circle appearance were visually mapped, and compared to the average slope, aspect, and the calculated topographic wetness index (TWI). Furthermore the whole traverse was classified into four different morphologies of the sorted patterned ground (sorted circles, sorted "ellipses", sorted nets and areas without patterned ground). For these morphologies, we also measured the slope, aspect and TWI to correlate the topographical parameters with the geomorphological characteristics of the patterned ground, and with predictions from modeling [7]. Our results confirm that the dependence of morphology on topography of sorted circles can be measured using a combination of plan-view and topographic remote sensing data. Thus, as the same quality of data is available on Mars, these same measurements could be made there in order to test whether the circle morphology depends on the local relief patterns in the same ways as in our terrestrial study. A positive result would argue that the Martian features may have formed in the same way (freeze-thaw) as the terrestrial ones. [1] Washburn, A.L. (1956) Geol. Soc. Amer. Bull. 67, 823-866. [2] Balme et al. (2013) Prog. Phys. Geog. 37, 289-324. [3] Balme et al. (2009) Icarus 200, 30-38. [4] Kreslavsky, M.A., Head, J.W. (2014) LPSC 45, abstract 2715. [5] Hauber et al. (2011) GSA Spec. Paper 483, 177-201. [6] Tolgensbakk, J., Sollid, J.L. (1987) Kvadehuksletta, Geomorfologi og Kvartærgeologi (geomorphological map; scale 1:10,000), Universitet i Oslo. [7] Kessler, M.A., Werner, B.T. (2003) Science 299, 380-383.

Identifying genes that extend life span using a high-throughput screening system.

PubMed

Chen, Cuiying; Contreras, Roland

2007-01-01

We developed a high-throughput functional genomic screening system that allows identification of genes prolonging lifespan in the baker's yeast Saccharomyces cerevisiae. The method is based on isolating yeast mother cells with a higher than average number of cell divisions as indicated by the number of bud scars on their surface. Fluorescently labeled wheat germ agglutinin (WGA) was used for specific staining of chitin, a major component of bud scars. The critical new steps in our bud-scar-sorting system are the use of small microbeads, which allows successive rounds of purification and regrowth of the mother cells (M-cell), and utilization of flow cytometry to sort and isolate cells with a longer lifespan based on the number of bud scars specifically labeled with WGA.

Cell-cycle synchronisation of bloodstream forms of Trypanosoma brucei using Vybrant DyeCycle Violet-based sorting.

PubMed

Kabani, Sarah; Waterfall, Martin; Matthews, Keith R

2010-01-01

Studies on the cell-cycle of Trypanosoma brucei have revealed several unusual characteristics that differ from the model eukaryotic organisms. However, the inability to isolate homogenous populations of parasites in distinct cell-cycle stages has limited the analysis of trypanosome cell division and complicated the understanding of mutant phenotypes with possible impact on cell-cycle related events. Although hydroxyurea-induced cell-cycle arrest in procyclic and bloodstream forms has been applied recently with success, such block-release protocols can complicate the analysis of cell-cycle regulated events and have the potential to disrupt important cell-cycle checkpoints. An alternative approach based on flow cytometry of parasites stained with Vybrant DyeCycle Orange circumvents this problem, but is restricted to procyclic form parasites. Here, we apply Vybrant Dyecycle Violet staining coupled with flow cytometry to effectively select different cell-cycle stages of bloodstream form trypanosomes. Moreover, the sorted parasites remain viable, although synchrony is rapidly lost. This method enables cell-cycle enrichment of populations of trypanosomes in their mammal infective stage, particularly at the G1 phase.

Cell-cycle synchronisation of bloodstream forms of Trypanosoma brucei using Vybrant DyeCycle Violet-based sorting

PubMed Central

Kabani, Sarah; Waterfall, Martin; Matthews, Keith R.

2010-01-01

Studies on the cell-cycle of Trypanosoma brucei have revealed several unusual characteristics that differ from the model eukaryotic organisms. However, the inability to isolate homogenous populations of parasites in distinct cell-cycle stages has limited the analysis of trypanosome cell division and complicated the understanding of mutant phenotypes with possible impact on cell-cycle related events. Although hydroxyurea-induced cell-cycle arrest in procyclic and bloodstream forms has been applied recently with success, such block-release protocols can complicate the analysis of cell-cycle regulated events and have the potential to disrupt important cell-cycle checkpoints. An alternative approach based on flow cytometry of parasites stained with Vybrant DyeCycle Orange circumvents this problem, but is restricted to procyclic form parasites. Here, we apply Vybrant Dyecycle Violet staining coupled with flow cytometry to effectively select different cell-cycle stages of bloodstream form trypanosomes. Moreover, the sorted parasites remain viable, although synchrony is rapidly lost. This method enables cell-cycle enrichment of populations of trypanosomes in their mammal infective stage, particularly at the G1 phase. PMID:19729042

Fiscal scarcity and the inevitability of bedside budget balancing.

PubMed

Morreim, E H

1989-05-01

Until recently, generous third-party reimbursements enabled physicians to pursue each patient's interests with little regard to costs. Conscious rationing was required only episodically as some particular commodity, eg, transplant organs, was too scarce to meet demand, or as some patients lacked basic access to the health care system. Cost containment and the economic reorganization of medicine introduce a new sort of scarcity, requiring a different sort of rationing. "Fiscal scarcity," the general contraction of health care dollars, means that because every medical decision has its cost, every decision is now subject to scrutiny for its economic as well as its medical wisdom. Therefore, every detail of medicine is an allocation problem. Many observers argue that physicians can nevertheless avoid directly trading patients' interests against economic considerations: through "efficiency protocols" that eliminate marginal benefits, through turning economic rationing decisions over to outside parties, through avoiding cost constraints until society has established a just health care allocation system. This article shows that none of these proposals permits the physician to escape cost-cutting at the bedside.

Danish A.I. field data with sexed semen.

PubMed

Borchersen, S; Peacock, M

2009-01-01

The objective of this study was to compare conception rates, non-return rates and sex ratios of sexed and conventional semen from the same sires in commercial dairy herds in Denmark. The semen was produced from three bulls from each of the three major dairy breeds in Denmark: Holstein, Jersey and Danish Red Dairy Breed (nine bulls total), in order to answer questions on breeds differences in field results. AI was performed by trained technicians using a minimum of 150 doses of sorted sperm and 50 control doses from each bull. During the trial, a total of 2087 doses were used in 63 herds. The trial showed that the conception rate using sorted semen was 5% points lower than with conventional doses for Danish Reds, 7% points for Jerseys, and 12% points for Holsteins. Translating this into non-return rate revealed differences of 10-20% points among bulls. These differences are thought to be a good indicator of what to expect from commercial use of sexed semen. The sex ratios varied from 89% to 93% female calves among breeds, which on average is consistent with the theoretical average sex ratio of 93% females considering the low number of inseminations.

Assessing materials handling and storage capacities in port terminals

NASA Astrophysics Data System (ADS)

Dinu, O.; Roşca, E.; Popa, M.; Roşca, M. A.; Rusca, A.

2017-08-01

Terminals constitute the factual interface between different modes and, as a result, buffer stocks are unavoidable whenever transport flows with different discontinuities meet. This is the reason why assessing materials handling and storage capacities is an important issue in the course of attempting to increase operative planning of logistic processes in terminals. Proposed paper starts with a brief review of the compatibilities between different sorts of materials and corresponding transport modes and after, a literature overview of the studies related to ports terminals and their specialization is made. As a methodology, discrete event simulation stands as a feasible technique for assessing handling and storage capacities at the terminal, taking into consideration the multi-flows interaction and the non-uniform arrivals of vessels and inland vehicles. In this context, a simulation model, that integrates the activities of an inland water terminal and describes the essential interactions between the subsystems which influence the terminal capacity, is developed. Different scenarios are simulated for diverse sorts of materials, leading to bottlenecks identification, performance indicators such as average storage occupancy rate, average dwell or transit times estimations, and their evolution is analysed in order to improve the transfer operations in the logistic process

Optimal protocols for slowly driven quantum systems.

PubMed

Zulkowski, Patrick R; DeWeese, Michael R

2015-09-01

The design of efficient quantum information processing will rely on optimal nonequilibrium transitions of driven quantum systems. Building on a recently developed geometric framework for computing optimal protocols for classical systems driven in finite time, we construct a general framework for optimizing the average information entropy for driven quantum systems. Geodesics on the parameter manifold endowed with a positive semidefinite metric correspond to protocols that minimize the average information entropy production in finite time. We use this framework to explicitly compute the optimal entropy production for a simple two-state quantum system coupled to a heat bath of bosonic oscillators, which has applications to quantum annealing.

Preparation of myeloid derived suppressor cells (MDSC) from naive and pancreatic tumor-bearing mice using flow cytometry and automated magnetic activated cell sorting (AutoMACS).

PubMed

Nelson, Nadine; Szekeres, Karoly; Cooper, Denise; Ghansah, Tomar

2012-06-18

MDSC are a heterogeneous population of immature macrophages, dendritic cells and granulocytes that accumulate in lymphoid organs in pathological conditions including parasitic infection, inflammation, traumatic stress, graft-versus-host disease, diabetes and cancer. In mice, MDSC express Mac-1 (CD11b) and Gr-1 (Ly6G and Ly6C) surface antigens. It is important to note that MDSC are well studied in various tumor-bearing hosts where they are significantly expanded and suppress anti-tumor immune responses compared to naïve counterparts. However, depending on the pathological condition, there are different subpopulations of MDSC with distinct mechanisms and targets of suppression. Therefore, effective methods to isolate viable MDSC populations are important in elucidating their different molecular mechanisms of suppression in vitro and in vivo. Recently, the Ghansah group has reported the expansion of MDSC in a murine pancreatic cancer model. Our tumor-bearing MDSC display a loss of homeostasis and increased suppressive function compared to naïve MDSC. MDSC percentages are significantly less in lymphoid compartments of naïve vs. tumor-bearing mice. This is a major caveat, which often hinders accurate comparative analyses of these MDSC. Therefore, enriching Gr-1(+) leukocytes from naïve mice prior to Fluorescence Activated Cell Sorting (FACS) enhances purity, viability and significantly reduces sort time. However, enrichment of Gr-1(+) leukocytes from tumor-bearing mice is optional as these are in abundance for quick FACS sorting. Therefore, in this protocol, we describe a highly efficient method of immunophenotyping MDSC and enriching Gr-1(+) leukocytes from spleens of naïve mice for sorting MDSC in a timely manner. Immunocompetent C57BL/6 mice are inoculated with murine Panc02 cells subcutaneously whereas naïve mice receive 1XPBS. Approximately 30 days post inoculation; spleens are harvested and processed into single-cell suspensions using a cell dissociation sieve. Splenocytes are then Red Blood Cell (RBC) lysed and an aliquot of these leukocytes are stained using fluorochrome-conjugated antibodies against Mac-1 and Gr-1 to immunophenotype MDSC percentages using Flow Cytometry. In a parallel experiment, whole leukocytes from naïve mice are stained with fluorescent-conjugated Gr-1 antibodies, incubated with PE-MicroBeads and positively selected using an automated Magnetic Activated Cell Sorting (autoMACS) Pro Separator. Next, an aliquot of Gr-1(+) leukocytes are stained with Mac-1 antibodies to identify the increase in MDSC percentages using Flow Cytometry. Now, these Gr1(+) enriched leukocytes are ready for FACS sorting of MDSC to be used in comparative analyses (naïve vs. tumor- bearing) in in vivo and in vitro assays.

SU-F-T-488: Comparison of the TG-51 and TG-51 Addendum Calibration Protocols

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

McCaw, T; Hwang, M; Jang, S

Purpose: To quantify differences between the TG51 and TG51 addendum calibration protocols. Methods: Beam energies of 6X, 6XSRS, 10X, 15X, 23X, 6XFFF, and 10XFFF were calibrated following both the TG51 and TG51 addendum protocols using both a Farmer and a scanning ionization chamber with traceable absorbed dose-to-water calibrations. For the TG51 addendum procedure, the collimating jaws were positioned to define a 10×10cm{sup 2} radiation field, a lead foil was only used for kQ measurements of FFF energies, and a volume-averaging correction was applied based on crossline and inline dose profiles. For the TG51 procedure, the collimating jaws were set tomore » 10×10cm{sup 2} according to the digital readout, and a lead foil was used for kQ measurements of energies greater than 10MV. Results: For beam energies with a flattening filter, absorbed dose-to-water determined by the two protocols differed by 0.1%–0.3%. For FFF beam energies, differences between the protocols were up to 0.2% and 0.8% for the scanning and Farmer ionization chambers, respectively. Differences between the protocols were due to kQ determination, volume-averaging correction, and measurement of raw ionization. Differences in kQ values between the two protocols were up to 0.4% and 0.2% for the scanning and Farmer ionization chambers, respectively. Volume-averaging corrections were less than 0.1% for the scanning ionization chamber, and up to 0.4% and 0.6% for the Farmer ionization chamber in beams with a flattening filter and FFF beams, respectively. Raw ionization measurements differed up to 0.3%±0.07% due to differences in jaw settings. Conclusion: The TG51 and TG51 addendum calibration protocols differed less than 0.3% for the scanning ionization chamber. For the Farmer chamber in FFF energies, volume-averaging corrections of up to 0.6% contributed to calibration differences of up to 0.8%. Failure to verify the radiation field size can produce calibration differences of up to 0.3%.« less

Performance analysis of multi-radio routing protocol in cognitive radio ad hoc networks under different path failure rate

NASA Astrophysics Data System (ADS)

Che-Aron, Z.; Abdalla, A. H.; Abdullah, K.; Hassan, W. H.

2013-12-01

In recent years, Cognitive Radio (CR) technology has largely attracted significant studies and research. Cognitive Radio Ad Hoc Network (CRAHN) is an emerging self-organized, multi-hop, wireless network which allows unlicensed users to opportunistically access available licensed spectrum bands for data communication under an intelligent and cautious manner. However, in CRAHNs, a lot of failures can easily occur during data transmission caused by PU (Primary User) activity, topology change, node fault, or link degradation. In this paper, an attempt has been made to evaluate the performance of the Multi-Radio Link-Quality Source Routing (MR-LQSR) protocol in CRAHNs under different path failure rate. In the MR-LQSR protocol, the Weighted Cumulative Expected Transmission Time (WCETT) is used as the routing metric. The simulations are carried out using the NS-2 simulator. The protocol performance is evaluated with respect to performance metrics like average throughput, packet loss, average end-to-end delay and average jitter. From the simulation results, it is observed that the number of path failures depends on the PUs number and mobility rate of SUs (Secondary Users). Moreover, the protocol performance is greatly affected when the path failure rate is high, leading to major service outages.

Isolation and characterization of living circulating tumor cells in patients by immunomagnetic negative enrichment coupled with flow cytometry.

PubMed

Lu, Yusheng; Liang, Haiyan; Yu, Ting; Xie, Jingjing; Chen, Shuming; Dong, Haiyan; Sinko, Patrick J; Lian, Shu; Xu, Jianguo; Wang, Jichuang; Yu, Suhong; Shao, Jingwei; Yuan, Bo; Wang, Lie; Jia, Lee

2015-09-01

This study was aimed at establishing a sensitive and specific isolation, characterization, and enumeration method for living circulating tumor cells (CTCs) in patients with colorectal carcinoma. Quantitative isolation and characterization of CTCs were performed through a combination of immunomagnetic negative enrichment and fluorescence-activated cell sorting. Isolated CTCs were identified by immunofluorescence staining. The viability and purity of the sorted cells were determined by flow cytometry. Blood samples spiked with HCT116 cells (range, 3-250 cells) were used to determine specificity, recovery, and sensitivity. The method was used to enumerate, characterize, and isolate living CTCs in 10 mL of blood from patients with colorectal carcinoma. The average recovery of HCT116 cells was 61% or more at each spiking level, and the correlation coefficient was 0.992. An analysis of samples from all 18 patients with colorectal carcinoma revealed that 94.4% were positive for CTCs with an average of 33 ± 24 CTCs per 10 mL of blood and with a diameter of 14 to 20 μm (vs 8-12 μm for lymphoma). All patients were CD47(+) , with only 4.3% to 61.2% being CD44(+) . The number of CTCs was well correlated with the patient TNM stage and could be detected in patients at an early cancer stage. The sorted cells could be recultured, and their viability was preserved. This method provides a novel technique for highly sensitive and specific detection and isolation of CTCs in patients with colorectal carcinoma. This method complements the existing approaches for the de novo functional identification of a wide variety of CTC types. It is likely to help in predicting a patient's disease progression and potentially in selecting the appropriate treatment. © 2015 American Cancer Society.

Revisiting the effects of hydrodynamic sorting and sedimentary recycling on chemical weathering indices

NASA Astrophysics Data System (ADS)

Guo, Yulong; Yang, Shouye; Su, Ni; Li, Chao; Yin, Ping; Wang, Zhongbo

2018-04-01

Although the proxies based on elemental geochemistry of siliciclastic sediments have been well developed to indicate the intensity of chemical weathering in various catchments, their geological indications and limitations, and especially how the differentiation of minerals and sediment grain size influences the applications of these proxies needs more clarification. This paper investigates the interactive effects of weathering, hydraulic sorting and sedimentary recycling on river sediment chemistry, and further validates the application of various weathering indices by measuring mineralogical and geochemical compositions of bank sediments and suspended particulate matters (SPMs) from five rivers in East China bearing various sizes, geologic settings and climatic regimes. For a specific river, the silicate weathering intensity registered in the fine SPMs is systematically stronger than that in the coarse-grained bank sediments. Most of the weathering indices not only reflect the integrated weathering history of various catchments but also depend on hydraulic sorting effect during sediment transport and depositional processes. The correlation between CIA (chemical index of alteration) and WIP (weathering index of Parker) offers an approach to predict the weathering trends of the fine SPMs, coarse bank sediments and recycled sediments under the influence of quartz dilution. To minimize the effects of hydrodynamic sorting and sedimentary recycling, we suggest that the fine sediments (e.g. SPMs and <2 μm fraction of bank sediments) in rivers can better reflect the average of present-day weathering crust in catchments and the weathered terrigenous materials into marginal seas and oceans.

Recovery After Prolonged Bed-Rest Deconditioning

NASA Technical Reports Server (NTRS)

Greenleaf, John E.; Quach, David T.

2003-01-01

Recovery data were analyzed from normal healthy test subjects maintained in the horizontal or head-down body position in well-controlled bed rest (BR) studies in which adherence to the well-designed protocol was monitored. Because recovery data were almost always of secondary importance to the data collected during the BR period, there was little consistency in the recovery experimental designs regarding control factors (e.g., diet or exercise), duration, or timing of data collection. Thus, only about half of the BR studies that provided appropriate data were analyzed here. These recovery data were sorted into two groups: those from BR protocols of less than 37 days, and those from protocols greater than 36 days. There was great disparity in the unchanged responses at the end of BR in these two groups. Likewise with the variables that required more than 40 days for recovery; for example, some immune variables required more than 180 days. Knowledge of the recovery process after BR in healthy people should assist rehabilitation workers in differentiating "healthy" BR recovery responses from those of the infirmity of sick or injured patients; this should result in more appropriate and efficient health care.

Efficiency at Sorting Cards in Compressed Air

PubMed Central

Poulton, E. C.; Catton, M. J.; Carpenter, A.

1964-01-01

At a site where compressed air was being used in the construction of a tunnel, 34 men sorted cards twice, once at normal atmospheric pressure and once at 3½, 2½, or 2 atmospheres absolute pressure. An additional six men sorted cards twice at normal atmospheric pressure. When the task was carried out for the first time, all the groups of men performing at raised pressure were found to yield a reliably greater proportion of very slow responses than the group of men performing at normal pressure. There was reliably more variability in timing at 3½ and 2½ atmospheres absolute than at normal pressure. At 3½ atmospheres absolute the average performance was also reliably slower. When the task was carried out for the second time, exposure to 3½ atmospheres absolute pressure had no reliable effect. Thus compressed air affected performance only while the task was being learnt; it had little effect after practice. No reliable differences were found related to age, to length of experience in compressed air, or to the duration of the exposure to compressed air, which was never less than 10 minutes at 3½ atmospheres absolute pressure. PMID:14180485

Quaternion Averaging

NASA Technical Reports Server (NTRS)

Markley, F. Landis; Cheng, Yang; Crassidis, John L.; Oshman, Yaakov

2007-01-01

Many applications require an algorithm that averages quaternions in an optimal manner. For example, when combining the quaternion outputs of multiple star trackers having this output capability, it is desirable to properly average the quaternions without recomputing the attitude from the the raw star tracker data. Other applications requiring some sort of optimal quaternion averaging include particle filtering and multiple-model adaptive estimation, where weighted quaternions are used to determine the quaternion estimate. For spacecraft attitude estimation applications, derives an optimal averaging scheme to compute the average of a set of weighted attitude matrices using the singular value decomposition method. Focusing on a 4-dimensional quaternion Gaussian distribution on the unit hypersphere, provides an approach to computing the average quaternion by minimizing a quaternion cost function that is equivalent to the attitude matrix cost function Motivated by and extending its results, this Note derives an algorithm that deterniines an optimal average quaternion from a set of scalar- or matrix-weighted quaternions. Rirthermore, a sufficient condition for the uniqueness of the average quaternion, and the equivalence of the mininiization problem, stated herein, to maximum likelihood estimation, are shown.

Correlating Structural Order with Structural Rearrangement in Dusty Plasma Liquids: Can Structural Rearrangement be Predicted by Static Structural Information?

NASA Astrophysics Data System (ADS)

Su, Yen-Shuo; Liu, Yu-Hsuan; I, Lin

2012-11-01

Whether the static microstructural order information is strongly correlated with the subsequent structural rearrangement (SR) and their predicting power for SR are investigated experimentally in the quenched dusty plasma liquid with microheterogeneities. The poor local structural order is found to be a good alarm to identify the soft spot and predict the short term SR. For the site with good structural order, the persistent time for sustaining the structural memory until SR has a large mean value but a broad distribution. The deviation of the local structural order from that averaged over nearest neighbors serves as a good second alarm to further sort out the short time SR sites. It has the similar sorting power to that using the temporal fluctuation of the local structural order over a small time interval.

Image classification at low light levels

NASA Astrophysics Data System (ADS)

Wernick, Miles N.; Morris, G. Michael

1986-12-01

An imaging photon-counting detector is used to achieve automatic sorting of two image classes. The classification decision is formed on the basis of the cross correlation between a photon-limited input image and a reference function stored in computer memory. Expressions for the statistical parameters of the low-light-level correlation signal are given and are verified experimentally. To obtain a correlation-based system for two-class sorting, it is necessary to construct a reference function that produces useful information for class discrimination. An expression for such a reference function is derived using maximum-likelihood decision theory. Theoretically predicted results are used to compare on the basis of performance the maximum-likelihood reference function with Fukunaga-Koontz basis vectors and average filters. For each method, good class discrimination is found to result in milliseconds from a sparse sampling of the input image.

Statistical physics in foreign exchange currency and stock markets

NASA Astrophysics Data System (ADS)

Ausloos, M.

2000-09-01

Problems in economy and finance have attracted the interest of statistical physicists all over the world. Fundamental problems pertain to the existence or not of long-, medium- or/and short-range power-law correlations in various economic systems, to the presence of financial cycles and on economic considerations, including economic policy. A method like the detrended fluctuation analysis is recalled emphasizing its value in sorting out correlation ranges, thereby leading to predictability at short horizon. The ( m, k)-Zipf method is presented for sorting out short-range correlations in the sign and amplitude of the fluctuations. A well-known financial analysis technique, the so-called moving average, is shown to raise questions to physicists about fractional Brownian motion properties. Among spectacular results, the possibility of crash predictions has been demonstrated through the log-periodicity of financial index oscillations.

Gene expression profiling of immunomagnetically separated cells directly from stabilized whole blood for multicenter clinical trials

PubMed Central

2014-01-01

Background Clinically useful biomarkers for patient stratification and monitoring of disease progression and drug response are in big demand in drug development and for addressing potential safety concerns. Many diseases influence the frequency and phenotype of cells found in the peripheral blood and the transcriptome of blood cells. Changes in cell type composition influence whole blood gene expression analysis results and thus the discovery of true transcript level changes remains a challenge. We propose a robust and reproducible procedure, which includes whole transcriptome gene expression profiling of major subsets of immune cell cells directly sorted from whole blood. Methods Target cells were enriched using magnetic microbeads and an autoMACS® Pro Separator (Miltenyi Biotec). Flow cytometric analysis for purity was performed before and after magnetic cell sorting. Total RNA was hybridized on HGU133 Plus 2.0 expression microarrays (Affymetrix, USA). CEL files signal intensity values were condensed using RMA and a custom CDF file (EntrezGene-based). Results Positive selection by use of MACS® Technology coupled to transcriptomics was assessed for eight different peripheral blood cell types, CD14+ monocytes, CD3+, CD4+, or CD8+ T cells, CD15+ granulocytes, CD19+ B cells, CD56+ NK cells, and CD45+ pan leukocytes. RNA quality from enriched cells was above a RIN of eight. GeneChip analysis confirmed cell type specific transcriptome profiles. Storing whole blood collected in an EDTA Vacutainer® tube at 4°C followed by MACS does not activate sorted cells. Gene expression analysis supports cell enrichment measurements by MACS. Conclusions The proposed workflow generates reproducible cell-type specific transcriptome data which can be translated to clinical settings and used to identify clinically relevant gene expression biomarkers from whole blood samples. This procedure enables the integration of transcriptomics of relevant immune cell subsets sorted directly from whole blood in clinical trial protocols. PMID:25984272

A robust method to analyze copy number alterations of less than 100 kb in single cells using oligonucleotide array CGH.

PubMed

Möhlendick, Birte; Bartenhagen, Christoph; Behrens, Bianca; Honisch, Ellen; Raba, Katharina; Knoefel, Wolfram T; Stoecklein, Nikolas H

2013-01-01

Comprehensive genome wide analyses of single cells became increasingly important in cancer research, but remain to be a technically challenging task. Here, we provide a protocol for array comparative genomic hybridization (aCGH) of single cells. The protocol is based on an established adapter-linker PCR (WGAM) and allowed us to detect copy number alterations as small as 56 kb in single cells. In addition we report on factors influencing the success of single cell aCGH downstream of the amplification method, including the characteristics of the reference DNA, the labeling technique, the amount of input DNA, reamplification, the aCGH resolution, and data analysis. In comparison with two other commercially available non-linear single cell amplification methods, WGAM showed a very good performance in aCGH experiments. Finally, we demonstrate that cancer cells that were processed and identified by the CellSearch® System and that were subsequently isolated from the CellSearch® cartridge as single cells by fluorescence activated cell sorting (FACS) could be successfully analyzed using our WGAM-aCGH protocol. We believe that even in the era of next-generation sequencing, our single cell aCGH protocol will be a useful and (cost-) effective approach to study copy number alterations in single cells at resolution comparable to those reported currently for single cell digital karyotyping based on next generation sequencing data.

The Leading Group Effect: Illusionary Declines in Scholastic Standard Scores of Mid-Range Japanese Junior High School Pupils

ERIC Educational Resources Information Center

Mori, Kazuo; Uchida, Akitoshi

2012-01-01

Longitudinal change in the average Z scores for four groups of pupils sorted by quartiles was examined for its stability over three years. The data, collected from 1998 to 2009, was obtained from nine cohorts of Japanese junior high school pupils totaling 1,962 subjects. It showed illusionary declines among the mid-range pupils but improvements…

The sociocultural effects on orthopedic surgeries in Taiwan

PubMed Central

Chiu, Shin-Lin; Chu, Chiao-Lee; Lan, Shou-Jen; Chen, Chiu-Liang

2018-01-01

Various sociocultural factors affect healthcare-seeking behaviors. In Taiwanese society, superstitions and lunar festivals play important roles in people’s lives. We investigated the impact of “Ghost Month” (the 7th lunar month) and Chinese New Year (the 12th lunar month and the 1st lunar month of the following year) on the number of elective surgeries and emergent surgeries in Taiwan. The number of total knee replacement (TKR) surgeries and proximal femur fracture (PFF) surgeries in each lunar month from 2000 to 2011 were extracted from the Taiwan National Health Insurance Database, a computerized and population-based database. Patients were then sorted by location of residence or gender. The average number of TKR surgeries performed was significantly lower during the 1st, 7th, and 12th lunar months in urban areas, whereas in rural areas this trend was only evident in the 7th and 12th lunar months. There was however, no significant difference in the average number of PFF surgeries in each lunar month except for an increase seen in the 1st lunar month in rural patients (p<0.05). When sorted by gender, the average number of TKR surgeries was significantly decreased in the 7th and 12th lunar months in male patients, and decreased in the 1st, 7th, and 12th lunar months in female patients. In contrast, there was no difference in the average numbers of PFF surgeries in the 7th and 12th lunar months either in male or female patients. We proposed that the timing of elective surgeries such as TKR might be influenced by Ghost Month and Chinese New Year; however, emergent PFF surgeries were not significantly influenced by sociocultural beliefs and taboos in Taiwan. PMID:29596539

Insights into biodiversity sampling strategies for freshwater microinvertebrate faunas through bioblitz campaigns and DNA barcoding.

PubMed

Laforest, Brandon J; Winegardner, Amanda K; Zaheer, Omar A; Jeffery, Nicholas W; Boyle, Elizabeth E; Adamowicz, Sarah J

2013-04-04

Biodiversity surveys have long depended on traditional methods of taxonomy to inform sampling protocols and to determine when a representative sample of a given species pool of interest has been obtained. Questions remain as to how to design appropriate sampling efforts to accurately estimate total biodiversity. Here we consider the biodiversity of freshwater ostracods (crustacean class Ostracoda) from the region of Churchill, Manitoba, Canada. Through an analysis of observed species richness and complementarity, accumulation curves, and richness estimators, we conduct an a posteriori analysis of five bioblitz-style collection strategies that differed in terms of total duration, number of sites, protocol flexibility to heterogeneous habitats, sorting of specimens for analysis, and primary purpose of collection. We used DNA barcoding to group specimens into molecular operational taxonomic units for comparison. Forty-eight provisional species were identified through genetic divergences, up from the 30 species previously known and documented in literature from the Churchill region. We found differential sampling efficiency among the five strategies, with liberal sorting of specimens for molecular analysis, protocol flexibility (and particularly a focus on covering diverse microhabitats), and a taxon-specific focus to collection having strong influences on garnering more accurate species richness estimates. Our findings have implications for the successful design of future biodiversity surveys and citizen-science collection projects, which are becoming increasingly popular and have been shown to produce reliable results for a variety of taxa despite relying on largely untrained collectors. We propose that efficiency of biodiversity surveys can be increased by non-experts deliberately selecting diverse microhabitats; by conducting two rounds of molecular analysis, with the numbers of samples processed during round two informed by the singleton prevalence during round one; and by having sub-teams (even if all non-experts) focus on select taxa. Our study also provides new insights into subarctic diversity of freshwater Ostracoda and contributes to the broader "Barcoding Biotas" campaign at Churchill. Finally, we comment on the associated implications and future research directions for community ecology analyses and biodiversity surveys through DNA barcoding, which we show here to be an efficient technique enabling rapid biodiversity quantification in understudied taxa.

High frequency mesozooplankton monitoring: Can imaging systems and automated sample analysis help us describe and interpret changes in zooplankton community composition and size structure — An example from a coastal site

NASA Astrophysics Data System (ADS)

Romagnan, Jean Baptiste; Aldamman, Lama; Gasparini, Stéphane; Nival, Paul; Aubert, Anaïs; Jamet, Jean Louis; Stemmann, Lars

2016-10-01

The present work aims to show that high throughput imaging systems can be useful to estimate mesozooplankton community size and taxonomic descriptors that can be the base for consistent large scale monitoring of plankton communities. Such monitoring is required by the European Marine Strategy Framework Directive (MSFD) in order to ensure the Good Environmental Status (GES) of European coastal and offshore marine ecosystems. Time and cost-effective, automatic, techniques are of high interest in this context. An imaging-based protocol has been applied to a high frequency time series (every second day between April 2003 to April 2004 on average) of zooplankton obtained in a coastal site of the NW Mediterranean Sea, Villefranche Bay. One hundred eighty four mesozooplankton net collected samples were analysed with a Zooscan and an associated semi-automatic classification technique. The constitution of a learning set designed to maximize copepod identification with more than 10,000 objects enabled the automatic sorting of copepods with an accuracy of 91% (true positives) and a contamination of 14% (false positives). Twenty seven samples were then chosen from the total copepod time series for detailed visual sorting of copepods after automatic identification. This method enabled the description of the dynamics of two well-known copepod species, Centropages typicus and Temora stylifera, and 7 other taxonomically broader copepod groups, in terms of size, biovolume and abundance-size distributions (size spectra). Also, total copepod size spectra underwent significant changes during the sampling period. These changes could be partially related to changes in the copepod assemblage taxonomic composition and size distributions. This study shows that the use of high throughput imaging systems is of great interest to extract relevant coarse (i.e. total abundance, size structure) and detailed (i.e. selected species dynamics) descriptors of zooplankton dynamics. Innovative zooplankton analyses are therefore proposed and open the way for further development of zooplankton community indicators of changes.

Full-Shift Trunk and Upper Arm Postures and Movements Among Aircraft Baggage Handlers.

PubMed

Wahlström, Jens; Bergsten, Eva; Trask, Catherine; Mathiassen, Svend Erik; Jackson, Jennie; Forsman, Mikael

2016-10-01

The present study assessed full-shift trunk and upper arm postural exposure amplitudes, frequencies, and durations among Swedish airport baggage handlers and aimed to determine whether exposures differ between workers at the ramp (loading and unloading aircraft) and baggage sorting areas. Trunk and upper arm postures were measured using inclinometers during three full work shifts on each of 27 male baggage handlers working at a large Swedish airport. Sixteen of the baggage handlers worked on the ramp and 11 in the sorting area. Variables summarizing postures and movements were calculated, and mean values and variance components between subjects and within subject (between days) were estimated using restricted maximum likelihood algorithms in a one-way random effect model. In total, data from 79 full shifts (651h) were collected with a mean recording time of 495min per shift (range 319-632). On average, baggage handlers worked with the right and left arm elevated >60° for 6.4% and 6.3% of the total workday, respectively. The 90th percentile trunk forward projection (FP) was 34.1°, and the 50th percentile trunk movement velocity was 8° s(-1). For most trunk (FP) and upper arm exposure variables, between-subject variability was considerable, suggesting that the flight baggage handlers were not a homogeneously exposed group. A notable between-days variability pointed to the contents of the job differing on different days. Peak exposures (>90°) were higher for ramp workers than for sorting area workers (trunk 0.6% ramp versus 0.3% sorting; right arm 1.3% ramp versus 0.7% sorting). Trunk and upper arm postures and movements among flight baggage handlers measured by inclinometry were similar to those found in other jobs comprising manual material handling, known to be associated with increased risks for musculoskeletal disorders. The results showed that full-shift trunk (FP) and, to some extent, peak arm exposures were higher for ramp workers compared with sorting workers. © The Author 2016. Published by Oxford University Press on behalf of the British Occupational Hygiene Society.

Protocol for buffer space negotiation

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

Nessett, D.

There are at least two ways to manage the buffer memory of a communications node. On etechnique veiws the buffer as a single resource that is to be reserved and released as a unit for a particular communication transaction. A more common approach treats the node's buffer space as a collection of resources (e.g., bytes, words, packet slots) capable of being allocated among multiple concurrent conversations. To achieve buffer space multiplexing, some sort of negotiation for buffer space must take place between source and sink nodes before a transaction can commence. Results are presented which indicate that, for an applicationmore » involving a CSMA broadcast network, buffer space multiplexing offers better performance than buffer reservation. To achieve this improvement, a simple protocol is presented that features flow-control information traveling both from source to sink as well as from sink to source. It is argued that this bidirectionality allows the sink to allocate buffer space among its active communication paths more effectively. 13 figures.« less

Molecular beacon-enabled purification of living cells by targeting cell type-specific mRNAs.

PubMed

Wile, Brian M; Ban, Kiwon; Yoon, Young-Sup; Bao, Gang

2014-10-01

Molecular beacons (MBs) are dual-labeled oligonucleotides that fluoresce only in the presence of complementary mRNA. The use of MBs to target specific mRNAs allows sorting of specific cells from a mixed cell population. In contrast to existing approaches that are limited by available surface markers or selectable metabolic characteristics, the MB-based method enables the isolation of a wide variety of cells. For example, the ability to purify specific cell types derived from pluripotent stem cells (PSCs) is important for basic research and therapeutics. In addition to providing a general protocol for MB design, validation and nucleofection into cells, we describe how to isolate a specific cell population from differentiating PSCs. By using this protocol, we have successfully isolated cardiomyocytes differentiated from mouse or human PSCs (hPSCs) with ∼ 97% purity, as confirmed by electrophysiology and immunocytochemistry. After designing MBs, their ordering and validation requires 2 weeks, and the isolation process requires 3 h.

Partiality, impartiality and the ethics of triage.

PubMed

Okorie, Ndukaku

2018-06-22

In this paper, I discuss the question of partiality and impartiality in the application of triage. Triage is a process in medical research which recommends that patients should be sorted for treatment according to the degree or severity of their injury. In employing the triage protocol, however, the question of partiality arises because socially vulnerable groups will be neglected since there is the likelihood that the social determinants of a patient's health may diminish her chance of survival. As a process that is based on the severity of a patient's injury, triage will be unfair, and hence negatively partial, to socially vulnerable people. Thus, I aim in this paper to show that the triage protocol fails as an impartial evaluative process because its only aim is to maximize survivability. I contend that: (i) triage would lead to the neglect of the social condition of patients or victims, and (ii) it will only serve the utilitarian purpose of maximization of outcomes which may not be justified in some cases. © 2018 John Wiley & Sons Ltd.

Real-time intraoperative monitoring of brainstem auditory evoked potentials during microvascular decompression for hemifacial spasm.

PubMed

Joo, Byung-Euk; Park, Sang-Ku; Cho, Kyung-Rae; Kong, Doo-Sik; Seo, Dae-Won; Park, Kwan

2016-11-01

OBJECTIVE The aim of this study was to define a new protocol for intraoperative monitoring (IOM) of brainstem auditory evoked potentials (BAEPs) during microvascular decompression (MVD) surgery to treat hemifacial spasm (HFS) and to evaluate the usefulness of this new protocol to prevent hearing impairment. METHODS To define the optimal stimulation rate, estimate the number of trials to be averaged, and identify useful warning criteria in IOM of BAEPs, the authors performed a preliminary study of 13 patients with HFS in 2010. They increased the stimulation rate from 10.1 Hz/sec to 100.1 Hz/sec by 10-Hz increments, and they elevated the average time from 100 times to 1000 times by 100-unit increments at a fixed stimulus rate of 43.9 Hz. After defining the optimal stimulation rate and the number of trials that needed to be averaged for IOM of BAEPs, they also identified the useful warning criteria for this protocol for MVD surgery. From January to December 2013, 254 patients with HFS underwent MVD surgery following the new IOM of BAEPs protocol. Pure-tone audiometry and speech discrimination scoring were performed before surgery and 1 week after surgery. To evaluate the usefulness of the new protocol, the authors compared the incidence of postoperative hearing impairment with the results from the group that underwent MVD surgery prior to the new protocol. RESULTS Through a preliminary study, the authors confirmed that it was possible to obtain a reliable wave when using a stimulation rate of 43.9 Hz/sec and averaging 400 trials. Only a Wave V amplitude loss > 50% was useful as a warning criterion when using the new protocol. A reliable BAEP could be obtained in approximately 9.1 seconds. When the new protocol was used, 2 patients (0.8%) showed no recovery of Wave V amplitude loss > 50%, and only 1 of those 2 patients (0.39%) ultimately had postoperative hearing impairment. When compared with the outcomes in the pre-protocol group, hearing impairment incidence decreased significantly among patients who underwent surgery with the new protocol (0.39% vs 4.02%, p = 0.002). There were no significant differences between the 2 surgery groups regarding other complications, including facial palsy, sixth cranial nerve palsy, and vocal cord palsy. CONCLUSIONS There was a significant decrease in postoperative hearing impairment after MVD for HFS when the new protocol for IOM of BAEPs was used. Real-time IOM of BAEPs, which can obtain a reliable BAEP in less than 10 seconds, is a successful new procedure for preventing hearing impairment during MVD surgery for HFS.

SU-E-P-49: Evaluation of Image Quality and Radiation Dose of Various Unenhanced Head CT Protocols

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

Chen, L; Khan, M; Alapati, K

2015-06-15

Purpose: To evaluate the diagnostic value of various unenhanced head CT protocols and predicate acceptable radiation dose level for head CT exam. Methods: Our retrospective analysis included 3 groups, 20 patients per group, who underwent clinical routine unenhanced adult head CT examination. All exams were performed axially with 120 kVp. Three protocols, 380 mAs without iterative reconstruction and automAs, 340 mAs with iterative reconstruction without automAs, 340 mAs with iterative reconstruction and automAs, were applied on each group patients respectively. The images were reconstructed with H30, J30 for brain window and H60, J70 for bone window. Images acquired with threemore » protocols were randomized and blindly reviewed by three radiologists. A 5 point scale was used to rate each exam The percentage of exam score above 3 and average scores of each protocol were calculated for each reviewer and tissue types. Results: For protocols without automAs, the average scores of bone window with iterative reconstruction were higher than those without iterative reconstruction for each reviewer although the radiation dose was 10 percentage lower. 100 percentage exams were scored 3 or higher and the average scores were above 4 for both brain and bone reconstructions. The CTDIvols are 64.4 and 57.8 mGy of 380 and 340 mAs, respectively. With automAs, the radiation dose varied with head size, resulting in 47.5 mGy average CTDIvol between 39.5 and 56.5 mGy. 93 and 98 percentage exams were scored great than 3 for brain and bone windows, respectively. The diagnostic confidence level and image quality of exams with AutomAs were less than those without AutomAs for each reviewer. Conclusion: According to these results, the mAs was reduced to 300 with automAs OFF for head CT exam. The radiation dose was 20 percentage lower than the original protocol and the CTDIvol was reduced to 51.2 mGy.« less

Geochemical budget of erosion in the Himalayan system

NASA Astrophysics Data System (ADS)

France-Lanord, C.; Lupker, M.; Lavé, J.

2011-12-01

Geochemistry of detrital sediment allow to constrain present and past processes of erosion and may be used to infer large scale budgets. The sediment flux exported by major rivers, corresponds to net physical erosion of a basin and, if combined with the river's dissolved flux, it allows in principle to quantify total erosion rates as well as the balance between chemical and physical erosion. This is nevertheless depending on our ability to quantify riverine fluxes, sediment composition and average source rock composition. Sediment composition results from weathering, attrition, mixing and sorting processes which determine their properties at a given location and time in the drainage basin. Particle sorting during transport exerts a first order control on bulk sediment composition as well as on trace and isotopic compositions. Repeated sampling of river sediments in the Ganga and Brahmaputra Rivers during the monsoon using depth sampling combined to river velocity profiling (ACDP) show the sensitivity of sediment composition to particle sorting effects that can be linked to hydrodynamic conditions. Applied to the Ganga in Bangladesh, and using a Rousean model, we estimate the average grain size and major element composition (Si, Al, Fe) of sediments exported by the Ganga (Lupker et al. 2011, JGR E.S. in press). This leads to a net sediment flux of ca. 380 million tons/yr which is comparable to fluxes reported from hydrological measurements. The average Al/Si ratio of the sediment is 0.23 which is well bellow values reported for the Upper Continental Crust (UCC≈0.27-0.29) and slightly above estimate of the Himalayan Silicate Crust (HSC) composition deduced from a Central Nepal geological sample collection. Deviations from UCC reflect the recycled nature of Himalayan formations having undergone several orogenic cycles and being enriched in quartz. The similarity with HSC suggest that either (1) there is no segregation due to floodplain sequestration, or (2) that the sequestration is limited, or (3) that we overestimate the Al/Si of the HSC. Hypothesis (1) is ruled out by average Siwalik composition or pebble compositions that are enriched in quartz. For hypothesis (3) there is no direct control on USC composition but the average composition of suspended sediments from Himalayan streams, where sediment sorting is limited by turbulence yields Al/Si ratio similar to that of HSC. Therefore, assuming reasonable values for both HSC and floodplain, we suggest that about 10% of the Himalayan erosion flux is presently sequestered in the floodplain. Chemical erosion is revealed by the evolution of sediment composition from the Himalaya to the delta showing a progressive depletion in mobile elements (Na, K, Ca) consistent with progressive weathering of alkaline silicate and carbonate. Quantifying the chemical erosion however requires a careful analysis of the data set, as source effects interfere with weathering proxies such as K/Si, Na/Si. These effects are related to mixing of Himalayan sediments with sediment from the Siwalik or southern tributaries. Quantification of the weathering requires to evaluate the difference between HSC and river sediment.Using detrital sediments to trace weathering and erosion however holds strong promises as, if well modelled, it will enable the use of widely available sedimentary records to address paleo-erosion and weathering studies.

Standardized Protocol for Virtual Surgical Plan and 3-Dimensional Surgical Template-Assisted Single-Stage Mandible Contour Surgery.

PubMed

Fu, Xi; Qiao, Jia; Girod, Sabine; Niu, Feng; Liu, Jian Feng; Lee, Gordon K; Gui, Lai

2017-09-01

Mandible contour surgery, including reduction gonioplasty and genioplasty, has become increasingly popular in East Asia. However, it is technically challenging and, hence, leads to a long learning curve and high complication rates and often needs secondary revisions. The increasing use of 3-dimensional (3D) technology makes accurate single-stage mandible contour surgery with minimum complication rates possible with a virtual surgical plan (VSP) and 3-D surgical templates. This study is to establish a standardized protocol for VSP and 3-D surgical templates-assisted mandible contour surgery and evaluate the accuracy of the protocol. In this study, we enrolled 20 patients for mandible contour surgery. Our protocol is to perform VSP based on 3-D computed tomography data. Then, design and 3-D print surgical templates based on preoperative VSP. The accuracy of the method was analyzed by 3-D comparison of VSP and postoperative results using detailed computer analysis. All patients had symmetric, natural osteotomy lines and satisfactory facial ratios in a single-stage operation. The average relative error of VSP and postoperative result on the entire skull was 0.41 ± 0.13 mm. The average new left gonial error was 0.43 ± 0.77 mm. The average new right gonial error was 0.45 ± 0.69 mm. The average pognion error was 0.79 ± 1.21 mm. Patients were very satisfied with the aesthetic results. Surgeons were very satisfied with the performance of surgical templates to facilitate the operation. Our standardized protocol of VSP and 3-D printed surgical templates-assisted single-stage mandible contour surgery results in accurate, safe, and predictable outcome in a single stage.

Sequential quantum secret sharing in a noisy environment aided with weak measurements

NASA Astrophysics Data System (ADS)

Ray, Maharshi; Chatterjee, Sourav; Chakrabarty, Indranil

2016-05-01

In this work we give a (n,n)-threshold protocol for sequential secret sharing of quantum information for the first time. By sequential secret sharing we refer to a situation where the dealer is not having all the secrets at the same time, at the beginning of the protocol; however if the dealer wishes to share secrets at subsequent phases she/he can realize it with the help of our protocol. First of all we present our protocol for three parties and later we generalize it for the situation where we have more (n> 3) parties. Interestingly, we show that our protocol of sequential secret sharing requires less amount of quantum as well as classical resource as compared to the situation wherein existing protocols are repeatedly used. Further in a much more realistic situation, we consider the sharing of qubits through two kinds of noisy channels, namely the phase damping channel (PDC) and the amplitude damping channel (ADC). When we carry out the sequential secret sharing in the presence of noise we observe that the fidelity of secret sharing at the kth iteration is independent of the effect of noise at the (k - 1)th iteration. In case of ADC we have seen that the average fidelity of secret sharing drops down to ½ which is equivalent to a random guess of the quantum secret. Interestingly, we find that by applying weak measurements one can enhance the average fidelity. This increase of the average fidelity can be achieved with certain trade off with the success probability of the weak measurements.

Effect of patient size on radiation dose for abdominal MDCT with automatic tube current modulation: phantom study.

PubMed

Schindera, Sebastian T; Nelson, Rendon C; Toth, Thomas L; Nguyen, Giao T; Toncheva, Greta I; DeLong, David M; Yoshizumi, Terry T

2008-02-01

The purpose of this study was to evaluate in a phantom study the effect of patient size on radiation dose for abdominal MDCT with automatic tube current modulation. One or two 4-cm-thick circumferential layers of fat-equivalent material were added to the abdomen of an anthropomorphic phantom to simulate patients of three sizes: small (cross-sectional dimensions, 18 x 22 cm), average size (26 x 30 cm), and oversize (34 x 38 cm). Imaging was performed with a 64-MDCT scanner with combined z-axis and xy-axis tube current modulation according to two protocols: protocol A had a noise index of 12.5 H, and protocol B, 15.0 H. Radiation doses to three abdominal organs and the skin were assessed. Image noise also was measured. Despite increasing patient size, the image noise measured was similar for protocol A (range, 11.7-12.2 H) and protocol B (range, 13.9-14.8 H) (p > 0.05). With the two protocols, in comparison with the dose of the small patient, the abdominal organ doses of the average-sized patient and the oversized patient increased 161.5-190.6%and 426.9-528.1%, respectively (p < 0.001). The skin dose increased as much as 268.6% for the average-sized patient and 816.3% for the oversized patient compared with the small patient (p < 0.001). Oversized patients undergoing abdominal MDCT with tube current modulation receive significantly higher doses than do small patients. The noise index needs to be adjusted to the body habitus to ensure dose efficiency.

Time is Money

NASA Astrophysics Data System (ADS)

Ausloos, Marcel; Vandewalle, Nicolas; Ivanova, Kristinka

Specialized topics on financial data analysis from a numerical and physical point of view are discussed when pertaining to the analysis of coherent and random sequences in financial fluctuations within (i) the extended detrended fluctuation analysis method, (ii) multi-affine analysis technique, (iii) mobile average intersection rules and distributions, (iv) sandpile avalanches models for crash prediction, (v) the (m,k)-Zipf method and (vi) the i-variability diagram technique for sorting out short range correlations. The most baffling result that needs further thought from mathematicians and physicists is recalled: the crossing of two mobile averages is an original method for measuring the "signal" roughness exponent, but why it is so is not understood up to now.

Client/Server data serving for high performance computing

NASA Technical Reports Server (NTRS)

Wood, Chris

1994-01-01

This paper will attempt to examine the industry requirements for shared network data storage and sustained high speed (10's to 100's to thousands of megabytes per second) network data serving via the NFS and FTP protocol suite. It will discuss the current structural and architectural impediments to achieving these sorts of data rates cost effectively today on many general purpose servers and will describe and architecture and resulting product family that addresses these problems. The sustained performance levels that were achieved in the lab will be shown as well as a discussion of early customer experiences utilizing both the HIPPI-IP and ATM OC3-IP network interfaces.

4D MR imaging using robust internal respiratory signal

NASA Astrophysics Data System (ADS)

Hui, CheukKai; Wen, Zhifei; Stemkens, Bjorn; Tijssen, R. H. N.; van den Berg, C. A. T.; Hwang, Ken-Pin; Beddar, Sam

2016-05-01

The purpose of this study is to investigate the feasibility of using internal respiratory (IR) surrogates to sort four-dimensional (4D) magnetic resonance (MR) images. The 4D MR images were constructed by acquiring fast 2D cine MR images sequentially, with each slice scanned for more than one breathing cycle. The 4D volume was then sorted retrospectively using the IR signal. In this study, we propose to use multiple low-frequency components in the Fourier space as well as the anterior body boundary as potential IR surrogates. From these potential IR surrogates, we used a clustering algorithm to identify those that best represented the respiratory pattern to derive the IR signal. A study with healthy volunteers was performed to assess the feasibility of the proposed IR signal. We compared this proposed IR signal with the respiratory signal obtained using respiratory bellows. Overall, 99% of the IR signals matched the bellows signals. The average difference between the end inspiration times in the IR signal and bellows signal was 0.18 s in this cohort of matching signals. For the acquired images corresponding to the other 1% of non-matching signal pairs, the respiratory motion shown in the images was coherent with the respiratory phases determined by the IR signal, but not the bellows signal. This suggested that the IR signal determined by the proposed method could potentially correct the faulty bellows signal. The sorted 4D images showed minimal mismatched artefacts and potential clinical applicability. The proposed IR signal therefore provides a feasible alternative to effectively sort MR images in 4D.

CryoEM and image sorting for flexible protein/DNA complexes.

PubMed

Villarreal, Seth A; Stewart, Phoebe L

2014-07-01

Intrinsically disordered regions of proteins and conformational flexibility within complexes can be critical for biological function. However, disorder, flexibility, and heterogeneity often hinder structural analyses. CryoEM and single particle image processing techniques offer the possibility of imaging samples with significant flexibility. Division of particle images into more homogenous subsets after data acquisition can help compensate for heterogeneity within the sample. We present the utility of an eigenimage sorting analysis for examining two protein/DNA complexes with significant conformational flexibility and heterogeneity. These complexes are integral to the non-homologous end joining pathway, and are involved in the repair of double strand breaks of DNA. Both complexes include the DNA-dependent protein kinase catalytic subunit (DNA-PKcs) and biotinylated DNA with bound streptavidin, with one complex containing the Ku heterodimer. Initial 3D reconstructions of the two DNA-PKcs complexes resembled a cryoEM structure of uncomplexed DNA-PKcs without additional density clearly attributable to the remaining components. Application of eigenimage sorting allowed division of the DNA-PKcs complex datasets into more homogeneous subsets. This led to visualization of density near the base of the DNA-PKcs that can be attributed to DNA, streptavidin, and Ku. However, comparison of projections of the subset structures with 2D class averages indicated that a significant level of heterogeneity remained within each subset. In summary, image sorting methods allowed visualization of extra density near the base of DNA-PKcs, suggesting that DNA binds in the vicinity of the base of the molecule and potentially to a flexible region of DNA-PKcs. Copyright © 2013 Elsevier Inc. All rights reserved.

Biogas production from the mechanically pretreated, liquid fraction of sorted organic municipal solid wastes.

PubMed

Alvarado-Lassman, A; Méndez-Contreras, J M; Martínez-Sibaja, A; Rosas-Mendoza, E S; Vallejo-Cantú, N A

2017-06-01

The high liquid content in fruit and vegetable wastes makes it convenient to mechanically separate these wastes into mostly liquid and solid fractions by means of pretreatment. Then, the liquid fraction can be treated using a high-rate anaerobic biofilm reactor to produce biogas, simultaneously reducing the amount of solids that must be landfilled. In this work, the specific composition of municipal solid waste (MSW) in a public market was determined; then, the sorted organic fraction of municipal solid waste was treated mechanically to separate and characterize the mostly liquid and solid fractions. Then, the mesophilic anaerobic digestion for biogas production of the first fraction was evaluated. The anaerobic digestion resulted in a reduced hydraulic retention time of two days with high removal of chemical oxygen demand, that is, 88% on average, with the additional benefit of reducing the mass of the solids that had to be landfilled by about 80%.

Validation of the theoretical domains framework for use in behaviour change and implementation research.

PubMed

Cane, James; O'Connor, Denise; Michie, Susan

2012-04-24

An integrative theoretical framework, developed for cross-disciplinary implementation and other behaviour change research, has been applied across a wide range of clinical situations. This study tests the validity of this framework. Validity was investigated by behavioural experts sorting 112 unique theoretical constructs using closed and open sort tasks. The extent of replication was tested by Discriminant Content Validation and Fuzzy Cluster Analysis. There was good support for a refinement of the framework comprising 14 domains of theoretical constructs (average silhouette value 0.29): 'Knowledge', 'Skills', 'Social/Professional Role and Identity', 'Beliefs about Capabilities', 'Optimism', 'Beliefs about Consequences', 'Reinforcement', 'Intentions', 'Goals', 'Memory, Attention and Decision Processes', 'Environmental Context and Resources', 'Social Influences', 'Emotions', and 'Behavioural Regulation'. The refined Theoretical Domains Framework has a strengthened empirical base and provides a method for theoretically assessing implementation problems, as well as professional and other health-related behaviours as a basis for intervention development.

Carbon Nanotube Composite Ampacity and Metallic CNT Buckypaper Conductivity

NASA Technical Reports Server (NTRS)

De Groh, Henry C., III

2016-01-01

NASA is currently working on developing motors for hybrid electric propulsion applications in aviation. To make electric power more feasible in airplanes higher power to weight ratios are sought for electric motors. One facet to these efforts is to improve (increase) the conductivity and (lower) density of the magnet wire used in motors. Carbon nanotubes (CNT) and composites containing CNT are being explored as a possible way to increase wire conductivity and lower density. Presented here are measurements of the current carrying capacity (ampacity) of a composite made from CNT and copper. The ability of CNT to improve the conductivity of such composites is hindered by the presence of semiconductive CNT (s-CNT) that exist in CNT supplies naturally, and currently, unavoidably. To solve this problem, and avoid s-CNT, various preferential growth and sorting methods are being explored. A supply of sorted 95 metallic CNT (m-CNT) was acquired in the form of thick film Buckypaper (BP) as part of this work and characterized using Raman spectroscopy, resistivity, and density measurements. The ampacity (Acm2) of the Cu-5volCNT composite was 3.8 lower than the same gauge pure Cu wire similarly tested. The lower ampacity in the composite wire is believed to be due to the presence of s-CNT in the composite and the relatively low (proper) level of longitudinal cooling employed in the test method. Although Raman spectroscopy can be used to characterize CNT, a strong relation between the ratios of the primary peaks GGand the relative amounts of m-CNT and s-CNT was not observed. The average effective conductivity of the CNT in the sorted, 95 m-CNT BP was 2.5 times higher than the CNT in the similar but un-sorted BP. This is an indication that improvements in the conductivity of CNT composites can be made by the use of sorted, highly conductive m-CNT.

Highly Conductive Wire: Cu Carbon Nanotube Composite Ampacity and Metallic CNT Buckypaper Conductivity

NASA Technical Reports Server (NTRS)

de Groh, Henry C.

2017-01-01

NASA is currently working on developing motors for hybrid electric propulsion applications in aviation. To make electric power more feasible in airplanes higher power to weight ratios are sought for electric motors. One facet to these efforts is to improve (increase) the conductivity and (lower) density of the magnet wire used in motors. Carbon nanotubes (CNT) and composites containing CNT are being explored as a possible way to increase wire conductivity and lower density. Presented here are measurements of the current carrying capacity (ampacity) of a composite made from CNT and copper. The ability of CNT to improve the conductivity of such composites is hindered by the presence of semiconductive CNT (s-CNT) that exist in CNT supplies naturally, and currently, unavoidably. To solve this problem, and avoid s-CNT, various preferential growth and sorting methods are being explored. A supply of sorted 95 metallic CNT (m-CNT) was acquired in the form of thick film Buckypaper (BP) as part of this work and characterized using Raman spectroscopy, resistivity, and density measurements. The ampacity (Acm2) of the Cu-5volCNT composite was 3.8 lower than the same gauge pure Cu wire similarly tested. The lower ampacity in the composite wire is believed to be due to the presence of s-CNT in the composite and the relatively low (proper) level of longitudinal cooling employed in the test method. Although Raman spectroscopy can be used to characterize CNT, a strong relation between the ratios of the primary peaks GGand the relative amounts of m-CNT and s-CNT was not observed. The average effective conductivity of the CNT in the sorted, 95 m-CNT BP was 2.5 times higher than the CNT in the similar but un-sorted BP. This is an indication that improvements in the conductivity of CNT composites can be made by the use of sorted, highly conductive m-CNT.

Development and validation of the Rapid Estimate of Adolescent Literacy in Medicine (REALM-Teen): a tool to screen adolescents for below-grade reading in health care settings.

PubMed

Davis, Terry C; Wolf, Michael S; Arnold, Connie L; Byrd, Robert S; Long, Sandra W; Springer, Thomas; Kennen, Estela; Bocchini, Joseph A

2006-12-01

The magnitude and consequences of low literacy in adolescent health and health care are unknown. The purpose of this study was to validate the Rapid Estimate of Adolescent Literacy in Medicine (REALM-Teen), a word-recognition test in English that can be used as a brief literacy-screening tool in health care settings. A total of 1533 adolescents aged 10 to 19 years attending 1 of 5 middle schools, 3 high schools, 1 pediatric clinic, or 2 summer programs in Louisiana and North Carolina participated in face-to-face interviews. Demographic information was solicited, and participants were administered a battery of reading tests, including the REALM-Teen, Wide Range Achievement Test-Revised (WRAT-3), and Slosson Oral Reading Test-Revised (SORT-R). Internal consistency for the REALM-Teen was determined using Cronbach's alpha, and criterion validity was established through correlations with both the WRAT-R and SORT-R. Using reading below grade level (according to SORT-R scores) as an outcome, instrument accuracy and corresponding cutoff scores were calculated by plotting receiver operating characteristic curves and stratum-specific likelihood ratios. Participants were 50% black and 53% female; 34% were enrolled in middle school and 66% in high school. The average time required to administer the REALM-Teen was 3 minutes. Internal consistency was excellent, as was test-retest reliability. The REALM-Teen is strongly correlated with both the WRAT-R and SORT-R. Five reading level categories were identified: 3rd grade and below, 4th to 5th grade, 6th to 7th grade, 8th to 9th grade, and 10th grade and above. Forty-six percent of participants were reading below grade level according to the SORT-R and 28% had repeated at least 1 grade. The REALM-Teen is a brief, reliable instrument for assessing adolescent literacy skills and reading below grade level.

Project ArchimedeZ

DTIC Science & Technology

2015-05-18

of information is estimated to average 1 hour per response, including the time for reviewing instructions, searching existing data sources, gathering...describe the proposed content of Project ArchimedeZ, 4 ) describe incentives that Project ArchimedeZ will give to Total Force Airmen to participate and...engaged, most of the time, in some sort of PME but at a manageable level. Rather than a three- hour block, for example, Project ArchimedeZ would deliver

Construction of human chromosome 21-specific yeast artificial chromosomes

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

McCormick, M.K.; Shero, J.H.; Hieter, P.A.

1989-12-01

Chromosome 21-specific yeast artificial chromosomes (YACs) have been constructed by a method that performs all steps in agarose, allowing size selection by pulsed-field gel electrophoresis and the use of nanogram to microgram quantities of DNA. The DNA sources used were hybrid cell line WAV-17, containing chromosome 21 as the only human chromosome and flow-sorted chromosome 21. The transformation efficiency of ligation products was similar to that obtained in aqueous transformations and yielded YACs with sizes ranging from 100 kilobases (kb) to > 1 megabase when polyamines were included in the transformation procedure. Twenty-five YACs containing human DNA have been obtainedmore » from a mouse-human hybrid, ranging in size from 200 to > 1000 kb, with an average size of 410 kb. Ten of these YACs were localized to subregions of chromosome 21 by hybridization of RNA probes to a panel of somatic cell hybrid DNA. Twenty-one human YACs, ranging in size from 100 to 500 kb, with an average size of 150 kb, were obtained from {approx} 50 ng of flow-sorted chromosome 21 DNA. Three were localized to subregions of chromosome 21. YACs will aid the construction of a physical map of human chromosome 21 and the study of disorders associated with chromosome 21 such as Alzheimer disease and Down syndrome.« less

Computational evaluation of new homologous down regulators of Translationally Controlled Tumor Protein (TCTP) targeted for tumor reversion.

PubMed

Nayarisseri, Anuraj; Yadav, Mukesh; Wishard, Rohan

2013-12-01

The Translationally Controlled Tumor Protein (TCTP) has been investigated for tumor reversion and is a target of cancer therapy. Down regulators which suppress the expression of TCTP can trigger the process of tumor reversion leading to the transformation of tumor cells into revertant cells. The present investigation is a novel protein-protein docking approach to target TCTP by a set of proteins similar to the protein: sorting nexin 6 (SNX6) which is an established down regulator of TCTP. The established down regulator along with its set of most similar proteins were modeled using the PYTHON based software - MODELLER v9.9, followed by structure validation using the Procheck Package. Further TCTP was docked with its established and prospective down regulators using the flexible docking protocol suite HADDOCK. The results were evaluated and ranked according to the RMSD values of the complex and the HADDOCK score, which is a weighted sum of van der Waal's energy, electrostatic energy, restraints violation energy and desolvation energy. Results concluded the protein sorting nexin 6 of Mus musculus to be a better down regulator of TCTP, as compared to the suggested down regulator (Homo sapiens snx6).

Efficient induction of dopaminergic neuron differentiation from induced pluripotent stem cells reveals impaired mitophagy in PARK2 neurons.

PubMed

Suzuki, Sadafumi; Akamatsu, Wado; Kisa, Fumihiko; Sone, Takefumi; Ishikawa, Kei-Ichi; Kuzumaki, Naoko; Katayama, Hiroyuki; Miyawaki, Atsushi; Hattori, Nobutaka; Okano, Hideyuki

2017-01-29

Patient-specific induced pluripotent stem cells (iPSCs) show promise for use as tools for in vitro modeling of Parkinson's disease. We sought to improve the efficiency of dopaminergic (DA) neuron induction from iPSCs by the using surface markers expressed in DA progenitors to increase the significance of the phenotypic analysis. By sorting for a CD184 high /CD44 - fraction during neural differentiation, we obtained a population of cells that were enriched in DA neuron precursor cells and achieved higher differentiation efficiencies than those obtained through the same protocol without sorting. This high efficiency method of DA neuronal induction enabled reliable detection of reactive oxygen species (ROS) accumulation and vulnerable phenotypes in PARK2 iPSCs-derived DA neurons. We additionally established a quantitative system using the mt-mKeima reporter system to monitor mitophagy in which mitochondria fuse with lysosomes and, by combining this system with the method of DA neuronal induction described above, determined that mitophagy is impaired in PARK2 neurons. These findings suggest that the efficiency of DA neuron induction is important for the precise detection of cellular phenotypes in modeling Parkinson's disease. Copyright © 2016. Published by Elsevier Inc.

Novel Serial Positive Enrichment Technology Enables Clinical Multiparameter Cell Sorting

PubMed Central

Tschulik, Claudia; Piossek, Christine; Bet, Jeannette; Yamamoto, Tori N.; Schiemann, Matthias; Neuenhahn, Michael; Martin, Klaus; Schlapschy, Martin; Skerra, Arne; Schmidt, Thomas; Edinger, Matthias; Riddell, Stanley R.; Germeroth, Lothar; Busch, Dirk H.

2012-01-01

A general obstacle for clinical cell preparations is limited purity, which causes variability in the quality and potency of cell products and might be responsible for negative side effects due to unwanted contaminants. Highly pure populations can be obtained best using positive selection techniques. However, in many cases target cell populations need to be segregated from other cells by combinations of multiple markers, which is still difficult to achieve – especially for clinical cell products. Therefore, we have generated low-affinity antibody-derived Fab-fragments, which stain like parental antibodies when multimerized via Strep-tag and Strep-Tactin, but can subsequently be removed entirely from the target cell population. Such reagents can be generated for virtually any antigen and can be used for sequential positive enrichment steps via paramagnetic beads. First protocols for multiparameter enrichment of two clinically relevant cell populations, CD4high/CD25high/CD45RAhigh ‘regulatory T cells’ and CD8high/CD62Lhigh/CD45RAneg ‘central memory T cells’, have been established to determine quality and efficacy parameters of this novel technology, which should have broad applicability for clinical cell sorting as well as basic research. PMID:22545138

Evaluation of different protein extraction methods for banana (Musa spp.) root proteome analysis by two-dimensional electrophoresis.

PubMed

Vaganan, M Mayil; Sarumathi, S; Nandakumar, A; Ravi, I; Mustaffa, M M

2015-02-01

Four protocols viz., the trichloroacetic acid-acetone (TCA), phenol-ammonium acetate (PAA), phenol/SDS-ammonium acetate (PSA) and trisbase-acetone (TBA) were evaluated with modifications for protein extraction from banana (Grand Naine) roots, considered as recalcitrant tissues for proteomic analysis. The two-dimensional electrophoresis (2-DE) separated proteins were compared based on protein yield, number of resolved proteins, sum of spot quantity, average spot intensity and proteins resolved in 4-7 pI range. The PAA protocol yielded more proteins (0.89 mg/g of tissues) and protein spots (584) in 2-DE gel than TCA and other protocols. Also, the PAA protocol was superior in terms of sum of total spot quantity and average spot intensity than TCA and other protocols, suggesting phenol as extractant and ammonium acetate as precipitant of proteins were the most suitable for banana rooteomics analysis by 2-DE. In addition, 1:3 ratios of root tissue to extraction buffer and overnight protein precipitation were most efficient to obtain maximum protein yield.

TU-G-BRD-04: A Round Robin Dosimetry Intercomparison of Gamma Stereotactic Radiosurgery Calibration Protocols

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

Drzymala, R; Alvarez, P; Bednarz, G

2015-06-15

Purpose: The purpose of this multi-institutional study was to compare two new gamma stereotactic radiosurgery (GSRS) dosimetry protocols to existing calibration methods. The ultimate goal was to guide AAPM Task Group 178 in recommending a standard GSRS dosimetry protocol. Methods: Nine centers (ten GSRS units) participated in the study. Each institution made eight sets of dose rate measurements: six with two different ionization chambers in three different 160mm-diameter spherical phantoms (ABS plastic, Solid Water and liquid water), and two using the same ionization chambers with a custom in-air positioning jig. Absolute dose rates were calculated using a newly proposed formalismmore » by the IAEA working group for small and non-standard radiation fields and with a new air-kerma based protocol. The new IAEA protocol requires an in-water ionization chamber calibration and uses previously reported Monte-Carlo generated factors to account for the material composition of the phantom, the type of ionization chamber, and the unique GSRS beam configuration. Results obtained with the new dose calibration protocols were compared to dose rates determined by the AAPM TG-21 and TG-51 protocols, with TG-21 considered as the standard. Results: Averaged over all institutions, ionization chambers and phantoms, the mean dose rate determined with the new IAEA protocol relative to that determined with TG-21 in the ABS phantom was 1.000 with a standard deviation of 0.008. For TG-51, the average ratio was 0.991 with a standard deviation of 0.013, and for the new in-air formalism it was 1.008 with a standard deviation of 0.012. Conclusion: Average results with both of the new protocols agreed with TG-21 to within one standard deviation. TG-51, which does not take into account the unique GSRS beam configuration or phantom material, was not expected to perform as well as the new protocols. The new IAEA protocol showed remarkably good agreement with TG-21. Conflict of Interests: Paula Petti, Josef Novotny, Gennady Neyman and Steve Goetsch are consultants for Elekta Instrument A/B; Elekta Instrument AB, PTW Freiburg GmbH, Standard Imaging, Inc., and The Phantom Laboratory, Inc. loaned equipment for use in these experiments; The University of Wisconsin Accredited Dosimetry Calibration Laboratory provided calibration services.« less

Clinical experience with image-guided radiotherapy in an accelerated partial breast intensity-modulated radiotherapy protocol.

PubMed

Leonard, Charles E; Tallhamer, Michael; Johnson, Tim; Hunter, Kari; Howell, Kathryn; Kercher, Jane; Widener, Jodi; Kaske, Terese; Paul, Devchand; Sedlacek, Scot; Carter, Dennis L

2010-02-01

To explore the feasibility of fiducial markers for the use of image-guided radiotherapy (IGRT) in an accelerated partial breast intensity modulated radiotherapy protocol. Nineteen patients consented to an institutional review board approved protocol of accelerated partial breast intensity-modulated radiotherapy with fiducial marker placement and treatment with IGRT. Patients (1 patient with bilateral breast cancer; 20 total breasts) underwent ultrasound guided implantation of three 1.2- x 3-mm gold markers placed around the surgical cavity. For each patient, table shifts (inferior/superior, right/left lateral, and anterior/posterior) and minimum, maximum, mean error with standard deviation were recorded for each of the 10 BID treatments. The dose contribution of daily orthogonal films was also examined. All IGRT patients underwent successful marker placement. In all, 200 IGRT treatment sessions were performed. The average vector displacement was 4 mm (range, 2-7 mm). The average superior/inferior shift was 2 mm (range, 0-5 mm), the average lateral shift was 2 mm (range, 1-4 mm), and the average anterior/posterior shift was 3 mm (range, 1 5 mm). This study shows that the use of IGRT can be successfully used in an accelerated partial breast intensity-modulated radiotherapy protocol. The authors believe that this technique has increased daily treatment accuracy and permitted reduction in the margin added to the clinical target volume to form the planning target volume. Copyright 2010 Elsevier Inc. All rights reserved.

Growth performance and sorting characteristics of corn silage-alfalfa haylage diets with or without forage dilution offered to replacement Holstein dairy heifers.

PubMed

Coblentz, W K; Esser, N M; Hoffman, P C; Akins, M S

2015-11-01

Gravid heifers consuming high-quality forage diets are susceptible to excessive weight gains and overconditioning. One approach for controlling this problem is to dilute diets with low-energy forages, such as straw, that reduce the caloric density and dry matter intake (DMI) of that diet by heifers. These diluting agents are often sortable by dairy heifers, but previous visual evidence has suggested that eastern gamagrass haylage may be a nonsortable alternative. Our objectives were (1) to compare the growth performance of dairy heifers offered a high-quality forage diet (control) with diets containing 1 of 3 diluting agents [eastern gamagrass haylage (EGH), chopped wheat straw (WS), or chopped corn fodder (CF)]; and (2) evaluate sorting behaviors of heifers offered these forage diets. Holstein heifers (n=128) were stratified (32 heifers/block) on the basis of initial body weight (heavy, 560 ± 27.7 kg; medium-heavy, 481 ± 17.7 kg; medium-light, 441 ± 22.0 kg; and light, 399 ± 14.4 kg), and then assigned to 1 of 16 identical research pens (4 pens/block; 8 heifers/pen), where each of the 4 research diets were assigned to 1 pen within each block. Diets were offered in a 118-d feeding trial with heifers crowded to 133% of capacity at the feed bunk. Inclusion of low-energy forages was effective in reducing both diet energy density and DMI. Concentrations of physically effective fiber (pef) particles did not change during the 24-h period following feeding for either the control or EGH diets; however, this response for pef particles masked the competing (and cancelling) responses for individual large and medium particles, which heifers sorted with discrimination and preference, respectively. Sorting against pef particles was detected for WS, and much more severely for the CF diet. Sorting of forage particles by heifers could not be related to heifer performance. Compared with control (1.16 kg/d), average daily gains (ADG) were reduced by dilution in all cases, but were virtually identical between EGH (0.98 kg/d) and CF (0.97 kg/d), which exhibited no sorting and extensive sorting of pef, respectively. Furthermore, ADG for WS was approximately 0.2 kg/d less than EGH or CF, despite exhibiting sorting characteristics intermediate between EGH and CF. Diets diluted with low-energy forages were formulated to be isonitrogenous and isocaloric; within that context, WS was most effective in reducing DMI and maintaining ADG within typical recommendations for Holstein heifers. Copyright © 2015 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Utilization of Information Technology for Non Domestic Waste Management in Semarang City

NASA Astrophysics Data System (ADS)

Ali, Muhammad; Hadi, Sudharto P.; Soemantri, Maman

2018-02-01

Garbage problem is often very complex in urban areas. The handling pattern of collecting, transporting and disposing that has been applied up to this day has not yet produced an appropriate solution. This is evident from the data of statistic centre institution in 2015 that 76.31% of the existing waste in the community has not been sorted, while 10.28% sorted to be used and 13.41% sorted to be discarded, showing the community amount of unsorted garbage large enough to necessitate managerial efforts at the waste sources. In designing a systematic and structured waste management system, the generations, compositions, and characteristics of the waste are indispensable. Therefore, a research is conducted on these three dimensions to the non-domestic waste in Semarang City, which involves commercial waste (from the markets, restaurants, and hotels), institutional waste (from the offices and schools). From the research result the average of 0,24kgs/person/day in weight unit of the City's non-domestical waste generation is derived. The waste composition is dominated by organic waste of around 61.95%, while the rest percentage is inorganic. The management policy is directed with the application of Management Information System model based on Information Technology because of the system's abilities to effectuate the waste management.

Tuning of automatic exposure control strength in lumbar spine CT.

PubMed

D'Hondt, A; Cornil, A; Bohy, P; De Maertelaer, V; Gevenois, P A; Tack, D

2014-05-01

To investigate the impact of tuning the automatic exposure control (AEC) strength curve (specific to Care Dose 4D®; Siemens Healthcare, Forchheim, Germany) from "average" to "strong" on image quality, radiation dose and operator dependency during lumbar spine CT examinations. Two hospitals (H1, H2), both using the same scanners, were considered for two time periods (P1 and P2). During P1, the AEC curve was "average" and radiographers had to select one of two protocols according to the body mass index (BMI): "standard" if BMI <30.0 kg m(-2) (120 kV-330 mAs) or "large" if BMI >30.0 kg m(-2) (140 kV-280 mAs). During P2, the AEC curve was changed to "strong", and all acquisitions were obtained with one protocol (120 kV and 270 mAs). Image quality was scored and patients' diameters calculated for both periods. 497 examinations were analysed. There was no significant difference in mean diameters according to hospitals and periods (p > 0.801) and in quality scores between periods (p > 0.172). There was a significant difference between hospitals regarding how often the "large" protocol was assigned [13 (10%)/132 patients in H1 vs 37 (28%)/133 in H2] (p < 0.001). During P1, volume CT dose index (CTDIvol) was higher in H2 (+13%; p = 0.050). In both hospitals, CTDIvol was reduced between periods (-19.2% in H1 and -29.4% in H2; p < 0.001). An operator dependency in protocol selection, unexplained by patient diameters or highlighted by image quality scores, has been observed. Tuning the AEC curve from average to strong enables suppression of the operator dependency in protocol selection and related dose increase, while preserving image quality. CT acquisition protocols based on weight are responsible for biases in protocol selection. Using an appropriate AEC strength curve reduces the number of protocols to one. Operator dependency of protocol selection is thereby eliminated.

Sr-87/Sr-86 isotopic age determination of upper Cretaceous Santonian, Campanian and Maastrichtian chondrichthyan teeth of the Atlantic and Eastern Gulf Coastal Plains: Implications for sea level cyclicity and macrofossil time-averaging in depositional sequence lag deposits

NASA Astrophysics Data System (ADS)

Becker, Martin Andrew

1997-11-01

Unconformities and fossil rich layers are common elements in the stratigraphic architecture of upper Cretaceous sediments exposed on both the Atlantic and Eastern Gulf Coastal Plains. Contacts between the Eutaw Formation and Tombigbee Sands Member in Alabama, the Blufftown Formation and Cusseta Sands in Georgia and the Wenonah- Mt. Laurel and Navesink Formations in New Jersey are marked by erosional surfaces with overlying blankets and lenses of macrofossil residuum. These contacts correspond to bounding unconformities and transgressive lags separating Santonian-Campanian, lower Campanian-upper Campanian and Campanian-Maastrichtian depositional sequences. Regression and subsequent transgression of sea level at the top of these depositional sequences resulted in hydrodynamic sorting of sediments and fossils that had previously accumulated in shelf and lower shoreface paleoenvironments. Remobilization of sediments by shoreface retreat reworked fossil hard-parts which became concentrated above erosional surfaces as sea level rose. Because of the abundance of chondrichthyan, pelecypod and ammonite fossils, these lags have great biostratigraphic significance and provide a basis for examining time averaging in macrofossil zonation. Chondrichthyan teeth are composed of extremely durable and highly insoluble, biogenic apatite. This tooth apatite accurately records the Sr87/Sr86 isotopic signature of seawater, from which the numerical age of the teeth can be calculated using published age/concentration data. Teeth (e.g. Squalicorax kaupi, Scapanorhynchus texanus) from Santonian-Campanian lag deposits at the contact of the Eutaw Formation and Tombigbee Sands Member in Alabama yield approximate ages of 85-81 Ma. Teeth from lower-upper Campanian lag deposits at the contact of the Blufftown Formation and Cusseta Sands in Georgia yield approximate ages of 83-75 Ma. Teeth from Campanian-Maastrichtian lag deposits at the contact of the Wenonah-Mt. Laurel and Navesink Formations in New Jersey yield approximate ages of 80-76 Ma. Isotopic age determination from these chondrichthyan teeth indicate average hiatus of approximately 3-7 million years occur during the development of lag accumulations and transgressive unconformities. Santonian, Campanian and Maastrichtian macrofossils analyzed in this study are hydrodynamically stable components representing time-averaged fossil assemblages sorted together by physical processes and are not life cohorts. Abrupt appearance and disappearance of organisms found in upper Cretaceous lag deposits of the Atlantic and Eastern Gulf Coastal Plains are artifacts of a physical sorting processes associated with sea-level cyclicity.

Mammographic compression after breast conserving therapy: Controlling pressure instead of force

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

Groot, J. E. de, E-mail: jerry.degroot@sigmascreening.com; Branderhorst, W.; Grimbergen, C. A.

Purpose: X-ray mammography is the primary tool for early detection of breast cancer and for follow-up after breast conserving therapy (BCT). BCT-treated breasts are smaller, less elastic, and more sensitive to pain. Instead of the current force-controlled approach of applying the same force to each breast, pressure-controlled protocols aim to improve standardization in terms of physiology by taking breast contact area and inelasticity into account. The purpose of this study is to estimate the potential for pressure protocols to reduce discomfort and pain, particularly the number of severe pain complaints for BCT-treated breasts. Methods: A prospective observational study including 58more » women having one BCT-treated breast and one untreated nonsymptomatic breast, following our hospital's 18 decanewton (daN) compression protocol was performed. Breast thickness, applied force, contact area, mean pressure, breast volume, and inelasticity (mean E-modulus) were statistically compared between the within-women breast pairs, and data were used as predictors for severe pain, i.e., scores 7 and higher on an 11-point Numerical Rating Scale. Curve-fitting models were used to estimate how pressure-controlled protocols affect breast thickness, compression force, and pain experience. Results: BCT-treated breasts had on average 27% smaller contact areas, 30% lower elasticity, and 30% higher pain scores than untreated breasts (allp < 0.001). Contact area was the strongest predictor for severe pain (p < 0.01). Since BCT-treatment is associated with an average 0.36 dm{sup 2} decrease in contact area, as well as increased pain sensitivity, BCT-breasts had on average 5.3 times higher odds for severe pain than untreated breasts. Model estimations for a pressure-controlled protocol with a 10 kPa target pressure, which is below normal arterial pressure, suggest an average 26% (range 10%–36%) reduction in pain score, and an average 77% (range 46%–95%) reduction of the odds for severe pain. The estimated increase in thickness is +6.4% for BCT breasts. Conclusions: After BCT, women have hardly any choice in avoiding an annual follow-up mammogram. Model estimations show that a 10 kPa pressure-controlled protocol has the potential to reduce pain and severe pain particularly for these women. The results highly motivate conducting further research in larger subject groups.« less

Energy-Aware RFID Anti-Collision Protocol.

PubMed

Arjona, Laura; Simon, Hugo Landaluce; Ruiz, Asier Perallos

2018-06-11

The growing interest in mobile devices is transforming wireless identification technologies. Mobile and battery-powered Radio Frequency Identification (RFID) readers, such as hand readers and smart phones, are are becoming increasingly attractive. These RFID readers require energy-efficient anti-collision protocols to minimize the tag collisions and to expand the reader's battery life. Furthermore, there is an increasing interest in RFID sensor networks with a growing number of RFID sensor tags. Thus, RFID application developers must be mindful of tag anti-collision protocols. Energy-efficient protocols involve a low reader energy consumption per tag. This work presents a thorough study of the reader energy consumption per tag and analyzes the main factor that affects this metric: the frame size update strategy. Using the conclusion of this analysis, the anti-collision protocol Energy-Aware Slotted Aloha (EASA) is presented to decrease the energy consumption per tag. The frame size update strategy of EASA is configured to minimize the energy consumption per tag. As a result, EASA presents an energy-aware frame. The performance of the proposed protocol is evaluated and compared with several state of the art Aloha-based anti-collision protocols based on the current RFID standard. Simulation results show that EASA, with an average of 15 mJ consumed per tag identified, achieves a 6% average improvement in the energy consumption per tag in relation to the strategies of the comparison.

A comparison of VO2max and metabolic variables between treadmill running and treadmill skating.

PubMed

Koepp, Kriston K; Janot, Jeffrey M

2008-03-01

The purpose of this study was to determine differences in VO2max and metabolic variables between treadmill running and treadmill skating. This study also examined VO2max responses during a continuous skating treadmill protocol and a discontinuous skating treadmill protocol. Sixteen male high school hockey players, who had a mean age of 16 +/- 1 years and were of an above-average fitness level, participated in this study. All subjects completed 4 exercise trials: a 1-hour skating treadmill familiarization trial, a treadmill running trial, and 2 randomized skating treadmill trials. Minute ventilation (VE), oxygen consumption VO2), carbon dioxide production VCO2), respiratory exchange ratio (RER), and heart rate were averaged every 15 seconds up to VO2max for each exercise test. The results showed that there was a significant difference (P < 0.05) for VO2max (mL.kg.min) and maximal VCO2 (L.min) between the running treadmill protocol and discontinuous skating treadmill protocol. There was also a significant difference for maximal RER between the discontinuous and continuous skating treadmill protocol and between the discontinuous skating treadmill protocol and running treadmill protocol. In conclusion, the running treadmill elicited a greater VO2max (mL.kg.min) than the skating treadmill did, but when it comes to specificity of ice skating, the skating treadmill may be ideal. Also, there was no significant difference between the discontinuous and continuous skating treadmill protocols. Therefore, a continuous protocol is possible on the skating treadmill without compromising correct skating position and physiologic responses. However, the continuous skating treadmill protocol should undergo validation before other scientists, coaches, and strength and conditioning professionals can apply it correctly.

Spatially averaged flow over a wavy boundary revisited

USGS Publications Warehouse

McLean, S.R.; Wolfe, S.R.; Nelson, J.M.

1999-01-01

Vertical profiles of streamwise velocity measured over bed forms are commonly used to deduce boundary shear stress for the purpose of estimating sediment transport. These profiles may be derived locally or from some sort of spatial average. Arguments for using the latter procedure are based on the assumption that spatial averaging of the momentum equation effectively removes local accelerations from the problem. Using analogies based on steady, uniform flows, it has been argued that the spatially averaged velocity profiles are approximately logarithmic and can be used to infer values of boundary shear stress. This technique of using logarithmic profiles is investigated using detailed laboratory measurements of flow structure and boundary shear stress over fixed two-dimensional bed forms. Spatial averages over the length of the bed form of mean velocity measurements at constant distances from the mean bed elevation yield vertical profiles that are highly logarithmic even though the effect of the bottom topography is observed throughout the water column. However, logarithmic fits of these averaged profiles do not yield accurate estimates of the measured total boundary shear stress. Copyright 1999 by the American Geophysical Union.

PRP: peripheral routing protocol for WSN realistic marginal mobility model

NASA Astrophysics Data System (ADS)

Tudorache, I. G.; Popescu, A. M.; Kemp, A. H.

2017-02-01

This article proposes a new routing protocol called Peripheral Routing Protocol (PRP) for the scenario where the mobile destination (D) moves at the wireless sensor network (WSN) periphery for gathering data. From a connectivity point of view, when D follows the marginal mobility model (MMM), the WSN becomes a hybrid network: a sparse network, because of the interrupted connectivity between D and the rest of the nodes and a well-connected network, because of the connectivity between all the other nodes of the WSN except D. It will be proven through MATLAB simulations that, for a military application scenario where D's connectivity to the WSN varies between 10% and 95%, compared with the 100% case, PRP outperforms routing protocols recommended for Mobile Ad-hoc Networks (MANET) in three ways: it maintains an average Packet Delivery Ratio (PDR) over 90%, a below 10% and 5% increase for the Average End to End Delay (AETED) and energy per transmitted packet.

Development of a novel cell sorting method that samples population diversity in flow cytometry.

PubMed

Osborne, Geoffrey W; Andersen, Stacey B; Battye, Francis L

2015-11-01

Flow cytometry based electrostatic cell sorting is an important tool in the separation of cell populations. Existing instruments can sort single cells into multi-well collection plates, and keep track of cell of origin and sorted well location. However currently single sorted cell results reflect the population distribution and fail to capture the population diversity. Software was designed that implements a novel sorting approach, "Slice and Dice Sorting," that links a graphical representation of a multi-well plate to logic that ensures that single cells are sampled and sorted from all areas defined by the sort region/s. Therefore the diversity of the total population is captured, and the more frequently occurring or rarer cell types are all sampled. The sorting approach was tested computationally, and using functional cell based assays. Computationally we demonstrate that conventional single cell sorting can sample as little as 50% of the population diversity dependant on the population distribution, and that Slice and Dice sorting samples much more of the variety present within a cell population. We then show by sorting single cells into wells using the Slice and Dice sorting method that there are cells sorted using this method that would be either rarely sorted, or not sorted at all using conventional single cell sorting approaches. The present study demonstrates a novel single cell sorting method that samples much more of the population diversity than current methods. It has implications in clonal selection, stem cell sorting, single cell sequencing and any areas where population heterogeneity is of importance. © 2015 International Society for Advancement of Cytometry.

A task analysis of the shift from teacher instructions to self-instructions in performing an in-common task.

PubMed

Grote, I; Rosales, J; Baer, D M

1996-11-01

Three preschool children repeatedly did four kinds of sorts with a deck of stimulus cards: a difficult, untaught target sort and three other sorts considered analytic of self-instructing the target performance. The untaught target sort was to find in a deck of cards those matching what two sample cards had in common. Most preschool children must be taught to mediate this problem. The three other kinds of sorts taught skills involved in the target performance or its mediation. As correct self-instructive talk emerged in the target sorts, it was confirmed. The untaught target sorts were interspersed infrequently among the three alternating directly taught skill sorts, to see if accurate target sorts, and accurate self-instructive talk about the target sorts, would emerge as the three skill sorts were mastered. As all the sorts progressed, increasing accuracy was seen first in the skill sorts and then in the untaught target sorts. All three subjects showed subsequent generalization to new target sorts involving other stimulus sets. Correct spontaneous self-instructions about the target sorts increased from near zero at the beginning of the experiment to consistency at its end. Thus the three skill sorts appeared sufficient for the emergence of a self-instructed solution to the previously insoluble target performance.

Parallel sort with a ranged, partitioned key-value store in a high perfomance computing environment

DOEpatents

Bent, John M.; Faibish, Sorin; Grider, Gary; Torres, Aaron; Poole, Stephen W.

2016-01-26

Improved sorting techniques are provided that perform a parallel sort using a ranged, partitioned key-value store in a high performance computing (HPC) environment. A plurality of input data files comprising unsorted key-value data in a partitioned key-value store are sorted. The partitioned key-value store comprises a range server for each of a plurality of ranges. Each input data file has an associated reader thread. Each reader thread reads the unsorted key-value data in the corresponding input data file and performs a local sort of the unsorted key-value data to generate sorted key-value data. A plurality of sorted, ranged subsets of each of the sorted key-value data are generated based on the plurality of ranges. Each sorted, ranged subset corresponds to a given one of the ranges and is provided to one of the range servers corresponding to the range of the sorted, ranged subset. Each range server sorts the received sorted, ranged subsets and provides a sorted range. A plurality of the sorted ranges are concatenated to obtain a globally sorted result.

Combined Protocol for Acute Malnutrition Study (ComPAS) in rural South Sudan and urban Kenya: study protocol for a randomized controlled trial.

PubMed

Bailey, Jeanette; Lelijveld, Natasha; Marron, Bethany; Onyoo, Pamela; Ho, Lara S; Manary, Mark; Briend, André; Opondo, Charles; Kerac, Marko

2018-04-24

Acute malnutrition is a continuum condition, but severe and moderate forms are treated separately, with different protocols and therapeutic products, managed by separate United Nations agencies. The Combined Protocol for Acute Malnutrition Study (ComPAS) aims to simplify and unify the treatment of uncomplicated severe and moderate acute malnutrition (SAM and MAM) for children 6-59 months into one protocol in order to improve the global coverage, quality, continuity of care and cost-effectiveness of acute malnutrition treatment in resource-constrained settings. This study is a multi-site, cluster randomized non-inferiority trial with 12 clusters in Kenya and 12 clusters in South Sudan. Participants are 3600 children aged 6-59 months with uncomplicated acute malnutrition. This study will evaluate the impact of a simplified and combined protocol for the treatment of SAM and MAM compared to the standard protocol, which is the national treatment protocol in each country. We will assess recovery rate as a primary outcome and coverage, defaulting, death, length of stay, average weekly weight gain and average weekly mid-upper arm circumference (MUAC) gain as secondary outcomes. Recovery rate is defined across both treatment arms as MUAC ≥125 mm and no oedema for two consecutive visits. Per-protocol and intention-to-treat analyses will be conducted. If the combined protocol is shown to be non-inferior to the standard protocol, updating guidelines to use the combined protocol would eliminate the need for separate products, resources and procedures for MAM treatment. This would likely be more cost-effective, increase availability of services, enable earlier case finding and treatment before deterioration of MAM into SAM, promote better continuity of care and improve community perceptions of the programme. ISRCTN, ISRCTN30393230 . Registered on 16 March 2017.

Salmon Spawning Effects on Streambed Stability

NASA Astrophysics Data System (ADS)

Buxton, T. H.; Buffington, J. M.; Yager, E.; Fremier, A. K.; Hassan, M. A.

2014-12-01

Female salmon build nests ("redds") in streambeds to protect their eggs from predation and damage by bed scour. During spawning, streambed material is mixed, fine sediment is winnowed downstream, and sediment is moved into a tailspill mound resembling the shape of a dune. Redd surfaces are coarser and better sorted than unspawned beds, which is thought to increase redd stability because larger grains are heavier and harder to move and sorting leads to higher friction angles for grain mobility. However, spawning also loosens sediment and creates topography that accelerates flow, both of which may increase particle mobility. We address factors controlling the relative stability of redds and unspawned beds using simulated salmon redds and water worked ("unspawned") beds composed of mixed-grain surfaces in a laboratory flume. Results show that simulated spawning lowered packing resistance to particle mobility on redds by an average of 32-39% compared to unspawned beds. Reductions in packing were sufficient to counter the higher inherent stability of relatively coarse, well sorted grains on redds, overall reducing critical shear stress by 8-20% relative to unspawned beds. In addition, boundary shear stress was 13-41% higher on redds due to flow convergence over the tailspill structure. Finally, redd instability relative to unspawned beds was observed in visual measurements of grain mobility, where bed-averaged shear stress was 22% lower at incipient motion and 29% lower at the discharge that mobilized all grain sizes on redds. Results of these complementary observations, along with sediment mass transport rates being nearly five times higher on a redd than an unspawned bed, indicate that redds are unstable compared to unspawned beds. Given these findings, further research is needed to investigate linkages between spawning disturbance and streambed mobility that may affect salmon reproduction in streams, and to assess whether a certain level of bed disturbance from spawning is required to restore ecosystem functions in streams with threatened populations of salmon.

A novel wavelength availability advertisement based ASON routing protocol implementation

NASA Astrophysics Data System (ADS)

Li, Jian; Liu, Juan; Zhang, Jie; Gu, Wanyi

2005-11-01

A novel wavelength availability advertisement based ASON routing protocol implementation is proposed in this paper which is derived from Open Shortest Path First protocol (OSPF) version 2. It can be applied to ASON network with a single control domain and can be easily extended to support routing in the multi-domain scenarios. Two new types of link state advertisement (LSA) are suggested for disseminating wavelength availability and network topology information. The OSPF mechanisms are inherited to ensure that the routing messages are delivered more reliably and converged more quickly while with fewer overheads. The topology auto discovery is realized through LSA flooding interacting with auto neighbor discovery using Link Management Protocol. The new LSA formats are given and how the link state database (LSD) is comprised is described. The new data structures proposed include topology resource list, adjacency list and route table. Then we analyze the differences of ASON in link state exchange, routing information flooding procedure, flushing procedure and new resources participating, i.e. new links or nodes join in an existing ASON. The link or node failure and recovery effect and how to deal with them are settled as well. In order to adopt different Routing and Wavelength Assignment (RWA) algorithms, a standard and efficient interface is designed. After extensive simulation we give the numerical analysis and come to the following conclusions: wavelength availability information flooding Convergence Time is about 30 milliseconds and it is not affected by RWA algorithms and the call traffic load; routing Protocol Average Overhead rises linearly with the increase of traffic load; Average Connection Setup Time decreases with the increase of traffic load because of the decrease of Average Routing Distance of the successfully lightpaths; Wavelength availability advertisement can greatly promote the blocking performance of ASON in relatively low traffic load; ASON operator can make a good trade off between the wavelength availability advertisement Protocol Average Overhead and Blocking Probability by adopting and adjusting the routing update triggers; and the last is that wavelength availability advertisement throughout the optical network is applicable and our ASON routing protocol implementation could be applied in ASON when its scale is not too large and if the calls do not arrive and leave the network in a too frequent pace.

Effect of feed delivery method on the behavior and growth of dairy heifers.

PubMed

Greter, A M; Leslie, K E; Mason, G J; McBride, B W; Devries, T J

2010-04-01

The objective of this study was to determine the effects of feed delivery method on growth, feeding competition, feeding, and sorting behavior of dairy heifers. Thirty-two Holstein heifers (146.2+/-21.9 d of age) were divided into 8 groups of 4 and exposed to 1 of 2 feed delivery treatments for 13 wk. The treatment rations contained 65% grass/alfalfa haylage and 35% textured concentrate (on a dry matter basis) fed as a 1) total mixed ration (TMR) or 2) top-dressed ration (TDR). Group dry matter intakes were recorded daily throughout the experiment. Feeding behavior, recorded using time-lapse video, and sorting behavior were measured for 7 d during each of wk 1, 5, 9, and 13. Sorting activity was determined through particle size analysis of the fresh feed and orts. The particle size separator separated feed into 4 fractions (long, medium, short, and fine). Sorting of each fraction was calculated as actual intake expressed as a percentage of predicted intake. Heifers were fecal scored for consistency of stool twice weekly using a scale from 1 (liquid) to 4 (solid); heifers were weighed every 2 wk. Neither dry matter intake (7.3 kg/d) nor average daily gain (1.3 kg/d) differed between treatments. Heifers fed the TDR tended to consume less neutral detergent fiber than heifers fed the TMR (4.77 vs. 4.91 kg/d). Heifers fed the TDR sorted against long particles (98.9 vs. 96.0%) and consumed short particles (100.3 vs. 101.1%) to a greater extent than did heifers fed the TMR. Daily feeding time did not differ between treatments (201.0 min/d), but heifers on the TDR did spend more time at the bunk in the 2h following feed delivery (50.1 vs. 32.0 min/d). Heifers fed the TDR were displaced from the feed bunk more frequently than heifers fed the TMR (17.6 vs. 8.6 times/d), particularly during the 2-h period following feed delivery. Fecal scores were lower for heifers on the TDR (2.7 vs. 3.4). These results suggest that feeding a TMR to replacement dairy heifers may promote a more even diurnal feeding pattern, minimize feed sorting and feed bunk competition, and promote more solid fecal consistency. Copyright (c) 2010 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

TH-EF-BRA-06: A Novel Retrospective 3D K-Space Sorting 4D-MRI Technique Using a Radial K-Space Acquisition MRI Sequence

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

Liu, Y; Subashi, E; Yin, F

Purpose: Current retrospective 4D-MRI provides superior tumor-to-tissue contrast and accurate respiratory motion information for radiotherapy motion management. The developed 4D-MRI techniques based on 2D-MRI image sorting require a high frame-rate of the MR sequences. However, several MRI sequences provide excellent image quality but have low frame-rate. This study aims at developing a novel retrospective 3D k-space sorting 4D-MRI technique using radial k-space acquisition MRI sequences to improve 4D-MRI image quality and temporal-resolution for imaging irregular organ/tumor respiratory motion. Methods: The method is based on a RF-spoiled, steady-state, gradient-recalled sequence with minimal echo time. A 3D radial k-space data acquisition trajectorymore » was used for sampling the datasets. Each radial spoke readout data line starts from the 3D center of Field-of-View. Respiratory signal can be extracted from the k-space center data point of each spoke. The spoke data was sorted based on its self-synchronized respiratory signal using phase sorting. Subsequently, 3D reconstruction was conducted to generate the time-resolved 4D-MRI images. As a feasibility study, this technique was implemented on a digital human phantom XCAT. The respiratory motion was controlled by an irregular motion profile. To validate using k-space center data as a respiratory surrogate, we compared it with the XCAT input controlling breathing profile. Tumor motion trajectories measured on reconstructed 4D-MRI were compared to the average input trajectory. The mean absolute amplitude difference (D) was calculated. Results: The signal extracted from k-space center data matches well with the input controlling respiratory profile of XCAT. The relative amplitude error was 8.6% and the relative phase error was 3.5%. XCAT 4D-MRI demonstrated a clear motion pattern with little serrated artifacts. D of tumor trajectories was 0.21mm, 0.23mm and 0.23mm in SI, AP and ML directions, respectively. Conclusion: A novel retrospective 3D k-space sorting 4D-MRI technique has been developed and evaluated on human digital phantom. NIH (1R21CA165384-01A1)« less

The Africa Yoga Project: A Participant-Driven Concept Map of Kenyan Teachers' Reported Experiences.

PubMed

Klein, Jessalyn E; Cook-Cottone, Catherine; Giambrone, Carla

2015-01-01

The Africa Yoga Project (AYP) trains and funds Kenyans to teach community yoga classes. Preliminary research with a small sample of AYP teachers suggested the program had a positive impact. This study used concept mapping to explore the experiences of a larger sample. Participants brainstormed statements about how practicing and/or teaching yoga changed them. They sorted statements into self-defined piles and rated them in terms of perceived importance. Multidimensional scaling (MDS) of sort data calculated statement coordinates wherein each statement is placed in proximity to other statements as a function of how frequently statements are sorted together by participants. These results are then and mapped in a two-dimensional space. Hierarchical cluster analysis (HCA) of these data identified clusters (i.e., concepts) among statements. Cluster average importance ratings gave the concept map depth and indicated concept importance. Bridging analysis and researchers' conceptual understanding of yoga literature facilitated HCA interpretive decisions. Of 72 AYP teachers, 52 and 48 teachers participated in brainstorming and sorting/rating activities, respectively. Teachers brainstormed 93 statements about how they had changed. The resultant MDS statement map had adequate validity (stress value = .29). HCA created a 12-cluster solution with the following concepts of perceived change: Identity as a Yoga Teacher; Prosocial Development; Existential Possibility; Genuine Positive Regard; Value and Respect for Others (highest importance); Presence, Acceptance, and Competence; Service and Trust; Non-judgment and Emotion Regulation (lowest importance); Engagement and Connection; Interpersonal Effectiveness; Psychosocial Functioning; and Physical Competence and Security. Teachers perceived the AYP as facilitating change across physical, mental, and spiritual domains. Additional research is needed to quantify and compare this change to other health promotion program outcomes.

How to measure RNA expression in rare senescent cells expressing any specific protein such as p16Ink4a

PubMed Central

Jeyapalan, Jessie C.; Sedivy, John M.

2013-01-01

Here we describe a carefully optimized method for the preparation of high quality RNA by flow sorting of formaldehyde fixed senescent cells immunostained for any intracellular antigen. Replicative cellular senescence is a phenomenon of irreversible growth arrest triggered by the accumulation of a discrete number of cell divisions. The underlying cause of senescence due to replicative exhaustion is telomere shortening. We document here a spontaneous and apparently stochastic process that continuously generates senescent cells in cultures fully immortalized with telomerase. In the course of studying this phenomenon we developed a preparative fluorescence activated flow sorting method based on immunofluorescent staining of intracellular antigens that can also deliver RNA suitable for quantitative analysis of global gene expression. The protocols were developed using normal human diploid fibroblasts (HDF) and up to 5×107 cells could be conveniently processed in a single experiment. The methodology is based on formaldehyde crosslinking of cells, followed by permeabilization, antibody staining, flow sorting, reversal of the crosslinks, and recovery of the RNA. We explored key parameters such as crosslink reversal that affect the fragmentation of RNA. The recovered RNA is of high quality for downstream molecular applications based on short range sequence analysis, such qPCR, hybridization microarrays, and next generation sequencing. The RNA was analyzed by Affymetrix Gene Chip expression profiling and compared to RNA prepared by the direct lysis of cells. The correlation between the data sets was very high, indicating that the procedure does not introduce systematic changes in the mRNA transcriptome. The methods presented in this communication should be of interest to many investigators working in diverse model systems. PMID:23454889

How to measure RNA expression in rare senescent cells expressing any specific protein such as p16Ink4a.

PubMed

Jeyapalan, Jessie C; Sedivy, John M

2013-02-01

Here we describe a carefully optimized method for the preparation of high quality RNA by flow sorting of formaldehyde fixed senescent cells immunostained for any intracellular antigen. Replicative cellular senescence is a phenomenon of irreversible growth arrest triggered by the accumulation of a discrete number of cell divisions. The underlying cause of senescence due to replicative exhaustion is telomere shortening. We document here a spontaneous and apparently stochastic process that continuously generates senescent cells in cultures fully immortalized with telomerase. In the course of studying this phenomenon we developed a preparative fluorescence activated flow sorting method based on immunofluorescent staining of intracellular antigens that can also deliver RNA suitable for quantitative analysis of global gene expression. The protocols were developed using normal human diploid fibroblasts (HDF) and up to 5x107 cells could be conveniently processed in a single experiment. The methodology is based on formaldehyde crosslinking of cells, followed by permeabilization, antibody staining, flow sorting, reversal of the crosslinks, and recovery of the RNA. We explored key parameters such as crosslink reversal that affect the fragmentation of RNA. The recovered RNA is of high quality for downstream molecular applications based on short range sequence analysis, such qPCR, hybridization microarrays, and next generation sequencing. The RNA was analyzed by Affymetrix Gene Chip expression profiling and compared to RNA prepared by the direct lysis of cells. The correlation between the data sets was very high, indicating that the procedure does not introduce systematic changes in the mRNA transcriptome. The methods presented in this communication should be of interest to many investigators working in diverse model systems.

Comparison of three methods of DNA extraction from peripheral blood mononuclear cells and lung fragments of equines.

PubMed

Santos, E M; Paula, J F R; Motta, P M C; Heinemann, M B; Leite, R C; Haddad, J P A; Del Puerto, H L; Reis, J K P

2010-08-17

We compared three different protocols for DNA extraction from horse peripheral blood mononuclear cells (PBMC) and lung fragments, determining average final DNA concentration, purity, percentage of PCR amplification using beta-actin, and cost. Thirty-four samples from PBMC, and 33 samples from lung fragments were submitted to DNA extraction by three different protocols. Protocol A consisted of a phenol-chloroform and isoamylic alcohol extraction, Protocol B used alkaline extraction with NaOH, and Protocol C used the DNAzol((R)) reagent kit. Protocol A was the best option for DNA extraction from lung fragments, producing high DNA concentrations, with high sensitivity in PCR amplification (100%), followed by Protocols C and B. On the other hand, for PBMC samples, Protocol B gave the highest sensitivity in PCR amplification (100%), followed by Protocols C and A. We conclude that Protocol A should be used for PCR diagnosis from lung fragment samples, while Protocol B should be used for PBMC.

Two-step protocol for isolation and culture of cardiospheres.

PubMed

Chen, Lijuan; Pan, Yaohua; Zhang, Lan; Wang, Yingjie; Weintraub, Neal; Tang, Yaoliang

2013-01-01

Cardiac progenitor cells (CPC) are a unique pool of progenitor cells residing in the heart that play an important role in cardiac homeostasis and physiological cardiovascular cell turnover during acute myocardial infarction (MI). Transplanting CPC into the heart has shown promise in two recent clinical trials of cardiac repair (SCIPIO & CADUCEUS). CSCs were originally isolated directly from enzymatically digested hearts followed by cell sorting using stem cell markers. However, long exposure to enzymatic digestion can affect the integrity of stem cell markers on the cell surface and also compromise stem cell function. Here, we describe a two-step procedure in which a large number of intact cardiac progenitor cells can be purified from small amount of heart tissue.

A Three-Dimensional Statistical Average Skull: Application of Biometric Morphing in Generating Missing Anatomy.

PubMed

Teshima, Tara Lynn; Patel, Vaibhav; Mainprize, James G; Edwards, Glenn; Antonyshyn, Oleh M

2015-07-01

The utilization of three-dimensional modeling technology in craniomaxillofacial surgery has grown exponentially during the last decade. Future development, however, is hindered by the lack of a normative three-dimensional anatomic dataset and a statistical mean three-dimensional virtual model. The purpose of this study is to develop and validate a protocol to generate a statistical three-dimensional virtual model based on a normative dataset of adult skulls. Two hundred adult skull CT images were reviewed. The average three-dimensional skull was computed by processing each CT image in the series using thin-plate spline geometric morphometric protocol. Our statistical average three-dimensional skull was validated by reconstructing patient-specific topography in cranial defects. The experiment was repeated 4 times. In each case, computer-generated cranioplasties were compared directly to the original intact skull. The errors describing the difference between the prediction and the original were calculated. A normative database of 33 adult human skulls was collected. Using 21 anthropometric landmark points, a protocol for three-dimensional skull landmarking and data reduction was developed and a statistical average three-dimensional skull was generated. Our results show the root mean square error (RMSE) for restoration of a known defect using the native best match skull, our statistical average skull, and worst match skull was 0.58, 0.74, and 4.4  mm, respectively. The ability to statistically average craniofacial surface topography will be a valuable instrument for deriving missing anatomy in complex craniofacial defects and deficiencies as well as in evaluating morphologic results of surgery.

Instructions to "push as hard as you can" improve average chest compression depth in dispatcher-assisted cardiopulmonary resuscitation.

PubMed

Mirza, Muzna; Brown, Todd B; Saini, Devashish; Pepper, Tracy L; Nandigam, Hari Krishna; Kaza, Niroop; Cofield, Stacey S

2008-10-01

Cardiopulmonary resuscitation (CPR) with adequate chest compression depth appears to improve first shock success in cardiac arrest. We evaluate the effect of simplification of chest compression instructions on compression depth in dispatcher-assisted CPR protocol. Data from two randomized, double-blinded, controlled trials with identical methodology were combined to obtain 332 records for this analysis. Subjects were randomized to either modified Medical Priority Dispatch System (MPDS) v11.2 protocol or a new simplified protocol. The main difference between the protocols was the instruction to "push as hard as you can" in the simplified protocol, compared to "push down firmly 2in. (5cm)" in MPDS. Data were recorded via a Laerdal ResusciAnne SkillReporter manikin. Primary outcome measures included: chest compression depth, proportion of compressions without error, with adequate depth and with total release. Instructions to "push as hard as you can", compared to "push down firmly 2in. (5cm)", resulted in improved chest compression depth (36.4 mm vs. 29.7 mm, p<0.0001), and improved median proportion of chest compressions done to the correct depth (32% vs. <1%, p<0.0001). No significant difference in median proportion of compressions with total release (100% for both) and average compression rate (99.7 min(-1) vs. 97.5 min(-1), p<0.56) was found. Modifying dispatcher-assisted CPR instructions by changing "push down firmly 2in. (5cm)" to "push as hard as you can" achieved improvement in chest compression depth at no cost to total release or average chest compression rate.

The activity of French research ethics committees and characteristics of biomedical research protocols involving humans: a retrospective cohort study.

PubMed

Decullier, Evelyne; Lhéritier, Véronique; Chapuis, François

2005-10-17

Clinical trials throughout the world must be evaluated by research ethics committees. No one has yet attempted to clearly quantify at the national level the activity of ethics committees and describe the characteristics of the protocols submitted. The objectives of this study were to describe 1) the workload and the activity of Research Ethics Committees in France, and 2) the characteristics of protocols approved on a nation-wide basis. Retrospective cohort of 976 protocols approved by a representative sample of 25/48 of French Research Ethics Committees in 1994. Protocols characteristics (design, study size, investigator), number of revisions requested by the ethics committee before approval, time to approval and number of amendments after approval were collected for each protocol by trained research assistant using the committee's files and archives. Thirty-one percent of protocols were approved with no modifications requested in 16 days (95% CI: 14-17). The number of revisions requested by the committee, and amendments submitted by the investigator was on average respectively 39 (95% CI: 25-53) and 37 (95% CI: 27-46), per committee and per year. When revisions were requested, the main reasons were related to information to the patient (28%) and consent modalities (18%). Drugs were the object of research in 68% of the protocols examined. The majority of the research was national (80%) with a predominance of single-centre studies. Workload per protocol has been estimated at twelve and half hours on average for administrative support and at eleven and half hours for expertise. The estimated workload justifies specific and independent administrative and financial support for Research Ethics Committees.

DELAMINATION AND XRF ANALYSIS OF NIST LEAD IN PAINT FILM STANDARDS

EPA Science Inventory

The objectives of this protocol were to remove the laminate coating from lead paint film standards acquired from NIST by means of surface heating. The average XRF value did not change after removal of the polymer coating suggesting that this protocol is satisfactory for renderin...

Evaluation of the Effectiveness of Two Morphine Protocols to Treat Neonatal Abstinence Syndrome in a Level II Nursery in a Community Hospital.

PubMed

DeAtley, Heather N; Burton, Amanda; Fraley, Michelle DeLuca; Haltom, Joan

2017-07-01

The authors sought to evaluate the impact on length of hospital stay and treatment duration of morphine after implementation of a change in the institutional protocol for managing neonatal abstinence syndrome (NAS) in an effort to improve patient outcomes. A single-center, retrospective chart review was conducted at a Level II nursery in a community hospital in Kentucky. Fifty-nine neonates born between January 1, 2014, and December 31, 2015, who were diagnosed with NAS and received morphine for treatment were included. The protocol 1 group consisted of 33 neonates who received an initial dose of morphine 0.04 mg/kg/dose administered orally every 4 hours (January 1-December 31, 2014), and the protocol 2 group consisted of 26 neonates who received an initial dose of morphine 0.06 mg/kg/dose administered orally every 3 hours (January 1-November 30, 2015), after a change in the protocol for managing NAS was implemented on January 1, 2015. Data were reviewed and compared between the two protocol groups to determine the impact that the dosage change had on length of hospital stay and morphine treatment duration. The average length of stay decreased by 7 days in the protocol 2 group compared with the protocol 1 group (21 vs 28.65 days). The average duration of treatment decreased by 7 days in the protocol 2 group compared with the protocol 1 group (18.3 vs 25.4 days). These differences between groups were not statistically significant, however, because the population size was not large enough to achieve adequate power. These results indicate that protocol 2 displayed the potential to decrease length of stay and duration of treatment compared with protocol 1 at this facility; however, balancing higher starting doses with the risk of oversedation will continue to challenge the health care team. Concern for oversedation when using the higher starting dose in protocol 2 has prompted further research (e.g., protocol 3, initial morphine 0.05 mg/kg/dose every 3 hrs). Continued research is also necessary with larger patient populations to enable generalizability to other institutions. © 2017 Pharmacotherapy Publications, Inc.

New Advanced Technology for Muscular Dystrophy

DTIC Science & Technology

2008-03-01

muscles per population) than for M-MDSCs ( gray bars; RI = 109 ± 18; mean ± SEM; n = 10 M-MDSC populations; two to six muscles per population; P = 0.035...experiments) of the latter in 2-week cultures of whole muscle cells ( gray bars) and sorted myogenic cells (black bars). On average, 15–35% of cells...subsequently GTG stained (brief trypsin treatment followed by Giemsa stain). At least ten metaphases were counted for each cell fraction and the

New Advanced Technology for Muscular Dystrophy

DTIC Science & Technology

2009-11-01

per population) than for M-MDSCs ( gray bars; RI = 109 ± 18; mean ± SEM; n = 10 M-MDSC populations; two to six muscles per population; P = 0.035; t...latter in 2-week cultures of whole muscle cells ( gray bars) and sorted myogenic cells (black bars). On average, 15–35% of cells coexpressing... GTG stained (brief trypsin treatment followed by Giemsa stain). At least ten metaphases were counted for each cell fraction and the chromosomes from

Validation of the Pangao PG-800A36 automatic wrist blood pressure monitor according to the European Society of Hypertension and the British Hypertension Society protocols.

PubMed

Zhao, Hairong; Qiao, Weichang; Zhang, Rui; Cui, Peng; Hou, Fanglin; Zhang, Wenli

2018-02-01

The aim of this study was to validate the PG-800A36 automatic wrist blood pressure monitor according to the European Society of Hypertension International Protocol (ESH-IP) revision 2010 and the British Hypertension Society (BHS) protocols. A total of 33 participants were initially included on the basis of the ESH-IP, followed by examination of 85 participants according to the BHS protocol. The procedures and analysis methods of the protocols were followed precisely with left arm/wrist sequential measurements by two trained observers using a mercury sphygmomanometer and one supervisor using the device. The device passed the ESH-IP with an average difference of 1.45±6.46 mmHg for systolic blood pressure and 1.25±5.10 mmHg for diastolic blood pressure. Furthermore, the A/A grade of the BHS protocol was achieved with an average difference of 1.84±6.94 mmHg for systolic blood pressure and 1.15±6.49 mmHg for diastolic blood pressure, and thus, the device also fulfilled the requirements of the Association for the Advancement of Medical Instrumentation. The Pangao PG-800A36 passed the requirements of the ESH-IP revision 2010 and achieved the A/A grade of the BHS protocol, which can be recommended for self-measurement in the general population.

Multi-objective optimization of MOSFETs channel widths and supply voltage in the proposed dual edge-triggered static D flip-flop with minimum average power and delay by using fuzzy non-dominated sorting genetic algorithm-II.

PubMed

Keivanian, Farshid; Mehrshad, Nasser; Bijari, Abolfazl

2016-01-01

D Flip-Flop as a digital circuit can be used as a timing element in many sophisticated circuits. Therefore the optimum performance with the lowest power consumption and acceptable delay time will be critical issue in electronics circuits. The newly proposed Dual-Edge Triggered Static D Flip-Flop circuit layout is defined as a multi-objective optimization problem. For this, an optimum fuzzy inference system with fuzzy rules is proposed to enhance the performance and convergence of non-dominated sorting Genetic Algorithm-II by adaptive control of the exploration and exploitation parameters. By using proposed Fuzzy NSGA-II algorithm, the more optimum values for MOSFET channel widths and power supply are discovered in search space than ordinary NSGA types. What is more, the design parameters involving NMOS and PMOS channel widths and power supply voltage and the performance parameters including average power consumption and propagation delay time are linked. To do this, the required mathematical backgrounds are presented in this study. The optimum values for the design parameters of MOSFETs channel widths and power supply are discovered. Based on them the power delay product quantity (PDP) is 6.32 PJ at 125 MHz Clock Frequency, L = 0.18 µm, and T = 27 °C.

Copy number variability of expression plasmids determined by cell sorting and Droplet Digital PCR.

PubMed

Jahn, Michael; Vorpahl, Carsten; Hübschmann, Thomas; Harms, Hauke; Müller, Susann

2016-12-19

Plasmids are widely used for molecular cloning or production of proteins in laboratory and industrial settings. Constant modification has brought forth countless plasmid vectors whose characteristics in terms of average plasmid copy number (PCN) and stability are rarely known. The crucial factor determining the PCN is the replication system; most replication systems in use today belong to a small number of different classes and are available through repositories like the Standard European Vector Architecture (SEVA). In this study, the PCN was determined in a set of seven SEVA-based expression plasmids only differing in the replication system. The average PCN for all constructs was determined by Droplet Digital PCR and ranged between 2 and 40 per chromosome in the host organism Escherichia coli. Furthermore, a plasmid-encoded EGFP reporter protein served as a means to assess variability in reporter gene expression on the single cell level. Only cells with one type of plasmid (RSF1010 replication system) showed a high degree of heterogeneity with a clear bimodal distribution of EGFP intensity while the others showed a normal distribution. The heterogeneous RSF1010-carrying cell population and one normally distributed population (ColE1 replication system) were further analyzed by sorting cells of sub-populations selected according to EGFP intensity. For both plasmids, low and highly fluorescent sub-populations showed a remarkable difference in PCN, ranging from 9.2 to 123.4 for ColE1 and from 0.5 to 11.8 for RSF1010, respectively. The average PCN determined here for a set of standardized plasmids was generally at the lower end of previously reported ranges and not related to the degree of heterogeneity. Further characterization of a heterogeneous and a homogeneous population demonstrated considerable differences in the PCN of sub-populations. We therefore present direct molecular evidence that the average PCN does not represent the true number of plasmid molecules in individual cells.

Rmax: A systematic approach to evaluate instrument sort performance using center stream catch☆

PubMed Central

Riddell, Andrew; Gardner, Rui; Perez-Gonzalez, Alexis; Lopes, Telma; Martinez, Lola

2015-01-01

Sorting performance can be evaluated with regard to Purity, Yield and/or Recovery of the sorted fraction. Purity is a check on the quality of the sample and the sort decisions made by the instrument. Recovery and Yield definitions vary with some authors regarding both as how efficient the instrument is at sorting the target particles from the original sample, others distinguishing Recovery from Yield, where the former is used to describe the accuracy of the instrument’s sort count. Yield and Recovery are often neglected, mostly due to difficulties in their measurement. Purity of the sort product is often cited alone but is not sufficient to evaluate sorting performance. All of these three performance metrics require re-sampling of the sorted fraction. But, unlike Purity, calculating Yield and/or Recovery calls for the absolute counting of particles in the sorted fraction, which may not be feasible, particularly when dealing with rare populations and precious samples. In addition, the counting process itself involves large errors. Here we describe a new metric for evaluating instrument sort Recovery, defined as the number of particles sorted relative to the number of original particles to be sorted. This calculation requires only measuring the ratios of target and non-target populations in the original pre-sort sample and in the waste stream or center stream catch (CSC), avoiding re-sampling the sorted fraction and absolute counting. We called this new metric Rmax, since it corresponds to the maximum expected Recovery for a particular set of instrument parameters. Rmax is ideal to evaluate and troubleshoot the optimum drop-charge delay of the sorter, or any instrument related failures that will affect sort performance. It can be used as a daily quality control check but can be particularly useful to assess instrument performance before single-cell sorting experiments. Because we do not perturb the sort fraction we can calculate Rmax during the sort process, being especially valuable to check instrument performance during rare population sorts. PMID:25747337

Efficient Ex Vivo Engineering and Expansion of Highly Purified Human Hematopoietic Stem and Progenitor Cell Populations for Gene Therapy.

PubMed

Zonari, Erika; Desantis, Giacomo; Petrillo, Carolina; Boccalatte, Francesco E; Lidonnici, Maria Rosa; Kajaste-Rudnitski, Anna; Aiuti, Alessandro; Ferrari, Giuliana; Naldini, Luigi; Gentner, Bernhard

2017-04-11

Ex vivo gene therapy based on CD34 + hematopoietic stem cells (HSCs) has shown promising results in clinical trials, but genetic engineering to high levels and in large scale remains challenging. We devised a sorting strategy that captures more than 90% of HSC activity in less than 10% of mobilized peripheral blood (mPB) CD34 + cells, and modeled a transplantation protocol based on highly purified, genetically engineered HSCs co-infused with uncultured progenitor cells. Prostaglandin E 2 stimulation allowed near-complete transduction of HSCs with lentiviral vectors during a culture time of less than 38 hr, mitigating the negative impact of standard culture on progenitor cell function. Exploiting the pyrimidoindole derivative UM171, we show that transduced mPB CD34 + CD38 - cells with repopulating potential could be expanded ex vivo. Implementing these findings in clinical gene therapy protocols will improve the efficacy, safety, and sustainability of gene therapy and generate new opportunities in the field of gene editing. Copyright © 2017 The Author(s). Published by Elsevier Inc. All rights reserved.

Thinking in clinical nursing practice: a study of critical care nurses' thinking applying the think-aloud, protocol analysis method.

PubMed

Han, Kyung-Ja; Kim, Hesook Suzie; Kim, Mae-Ja; Hong, Kyung-Ja; Park, Sungae; Yun, Soon-Nyoung; Song, Misoon; Jung, Yoenyi; Kim, Haewon; Kim, Dong-Oak Debbie; Choi, Heejung; Kim, Kyungae

2007-06-01

The purpose of the paper is to discover the patterns and processes of decision-making in clinical nursing practice. A set of think-aloud data from five critical care nurses during 40 to 50 minutes of caregiving in intensive care units were obtained and analyzed by applying the procedures recommended by Ericsson and Simon for protocol analysis. Four thinking processes before acting were identified to constitute various sorts of thoughts in which the nurses were engaged during patient care: reviewing, validation, consideration, rationalization, and action. In addition, three patterns of sequential streaming of thinking (short, intermediate, long) were identified to reveal various ways the nurses dealt with clinical situations involving nursing tasks and responsibilities. This study specifies the initial categories of thoughts for each of the processes and various patterns with which these processes are sequentially combined, providing insights into the ways nurses think about problems and address their concerns. The findings suggest that the thinking in clinical practice involves more than focused decision-making and reasoning, and needs to be examined from a broader perspective.

Diverse food items are similarly categorized by 8- to 13-year-old children.

PubMed

Beltran, Alicia; Knight Sepulveda, Karina; Watson, Kathy; Baranowski, Tom; Baranowski, Janice; Islam, Noemi; Missaghian, Mariam

2008-01-01

Assess how 8- to 13-year-old children categorized and labeled food items for possible use as part of a food search strategy in a computerized 24-hour dietary recall. A set of 62 cards with pictures and names of food items from 18 professionally defined food groups was sorted by each child into piles of similar food items. Participants attended the Children's Nutrition Research Center in the summer 2006. 148 8- to 13-year-old children (132 English speaking, 16 primarily Spanish speaking). Sorting of food items into common groupings and their names. Robinson matrices for identification of clusters of food items. Children created on average 11.1 (+/- 4.4) piles with 5.4 (+/- 4.9) cards per pile. Robinson matrix clusters captured 92.4% of the variance in the sorting of food cards. No substantial differences in Robinson clustering were detected across subcategories for each of the demographic characteristics. The label names provided by the children were most frequently categorized as "Taxonomic-Professional" (42.5%), such as meat, fruit, and drinks; or "Script" (26.4%), such as breakfast food, desserts, and snacks. Children categorized food items into similar clusters but used diverse names to label them. These categories may be used to facilitate food search for researchers in a computerized 24-hour dietary recall for children in this age group.

Fluid resuscitation for major burn patients with the TMMU protocol.

PubMed

Luo, Gaoxing; Peng, Yizhi; Yuan, Zhiqiang; Cheng, Wenguang; Wu, Jun; Tang, Jin; Huang, Yuesheng; Fitzgerald, Mark

2009-12-01

Fluid resuscitation is one of the critical treatments for the major burn patient in the early phases after injury. We evaluated the practice of fluid resuscitation for severely burned patients with the Third Military Medical University (TMMU) protocol, which is most widely used in many regions of China. Patients with major burns (>30% total body surface area (TBSA)) presenting to Southwest Hospital, Third Military Medical University, between January 2005 and October 2007, were included in this study. Fluid resuscitation was initiated by the TMMU protocol. A total of 71 patients were (46 adults and 25 children) included in this study. All patients survived the first 48 h after injury smoothly and none developed abdominal compartment syndrome or other recognised complications associated with fluid resuscitation. The average quantity of fluid infused was 3.3-61.33% more than that calculated based on the TMMU protocol in both adult and paediatric groups. The average urine output during the first 24h after injury was about 1.2 ml per kg body weight per hour in the two groups, but reached 1.2 ml and 1.7 ml during the second 24h in adult and pediatric groups, respectively. This study indicates that the TMMU protocol for fluid resuscitation is a feasible option for burn patients. Individualised resuscitation - guided by the physiological response to fluid administration - is still important as in other protocols.

ECS: efficient communication scheduling for underwater sensor networks.

PubMed

Hong, Lu; Hong, Feng; Guo, Zhongwen; Li, Zhengbao

2011-01-01

TDMA protocols have attracted a lot of attention for underwater acoustic sensor networks (UWSNs), because of the unique characteristics of acoustic signal propagation such as great energy consumption in transmission, long propagation delay and long communication range. Previous TDMA protocols all allocated transmission time to nodes based on discrete time slots. This paper proposes an efficient continuous time scheduling TDMA protocol (ECS) for UWSNs, including the continuous time based and sender oriented conflict analysis model, the transmission moment allocation algorithm and the distributed topology maintenance algorithm. Simulation results confirm that ECS improves network throughput by 20% on average, compared to existing MAC protocols.

Improved momentum-transfer theory for ion mobility. 1. Derivation of the fundamental equation.

PubMed

Siems, William F; Viehland, Larry A; Hill, Herbert H

2012-11-20

For the first time the fundamental ion mobility equation is derived by a bottom-up procedure, with N real atomic ion-atomic neutral collisions replaced by N repetitions of an average collision. Ion drift velocity is identified as the average of all pre- and postcollision velocities in the field direction. To facilitate velocity averaging, collisions are sorted into classes that "cool" and "heat" the ion. Averaging over scattering angles establishes mass-dependent relationships between pre- and postcollision velocities for the cooling and heating classes, and a combined expression for drift velocity is obtained by weighted addition according to relative frequencies of the cooling and heating encounters. At zero field this expression becomes identical to the fundamental low-field ion mobility equation. The bottom-up derivation identifies the low-field drift velocity as 3/4 of the average precollision ion velocity in the field direction and associates the passage from low-field to high-field conditions with the increasing dominance of "cooling" collisions over "heating" collisions. Most significantly, the analysis provides a direct path for generalization to fields of arbitrary strength.

Magnetic cell sorting purification of differentiated embryonic stem cells stably expressing truncated human CD4 as surface marker.

PubMed

David, Robert; Groebner, Michael; Franz, Wolfgang-Michael

2005-04-01

Embryonic stem (ES) cells offer great potential in regenerative medicine and tissue engineering. Clinical applications are still hampered by the lack of protocols for gentle, high-yield isolation of specific cell types for transplantation expressing no immunogenic markers. We describe labeling of stably transfected ES cells expressing a human CD4 molecule lacking its intracellular domain (DeltaCD4) under control of the phosphoglycerate kinase promoter for magnetic cell sorting (MACS). To track the labeled ES cells, we fused DeltaCD4 to an intracellular enhanced green fluorescent protein domain (DeltaCD4EGFP). We showed functionality of the membrane-bound fluorescent fusion protein and its suitability for MACS leading to purities greater than 97%. Likewise, expression of DeltaCD4 yielded up to 98.5% positive cells independently of their differentiation state. Purities were not limited by the initial percentage of DeltaCD4(+) cells, ranging from 0.6%-16%. The viability of MACS-selected cells was demonstrated by reaggregation and de novo formation of embryoid bodies developing all three germ layers. Thus, expression of DeltaCD4 in differentiated ES cells may enable rapid, high-yield purification of a desired cell type for tissue engineering and transplantation studies.

Optimization of Diode Laser System to Treat Benign Prostate Hyperplasia Final Report CRADA No. TSB-1154-95

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

London, Richard A; Byrne, Mark

Benign prostate hyperplasia (BPH) is a pervasive condition of enlargement of the male prostate gland which leads to several urinary difficulties ranging from hesitancy to incontinence to kidney dysfunction in severe cases. Currently the most common therapy is transurethral resection of the prostate (TURP) utilizing an electrosurgical device. Although TURP is largely successful, new BPH therapy methods are desired to reduce the cost and recovery time, improve the success rate, and reduce side effects. Recently, lasers have been introduced for this purpose. Indigo Medical Inc. is currently engaged in the development, testing, and preparation for sales of a new diodemore » laser based BPH therapy system. The development is based on laboratory experiments, animal studies, and a limited FDA-approved clinical trial in the US and in other countries. The addition of sophisticated numerical modeling, of the sort that has been highly developed at Lawrence Livermore National Laboratory, can greatly aid in the design of the system and treatment protocol. The benefits to DOE include the maintenance and advancement of numerical modeling expertise in radiation-matter interactions of the sort essential for the stockpile stewardship, inertial confinement fusion, and advanced manufacturing, and the push on advanced scientific computational methods, ultimately in areas such as 3-D transport.« less

Development of a fluorescence-activated cell sorting method coupled with whole genome amplification to analyze minority and trace Dehalococcoides genomes in microbial communities.

PubMed

Lee, Patrick K H; Men, Yujie; Wang, Shanquan; He, Jianzhong; Alvarez-Cohen, Lisa

2015-02-03

Dehalococcoides mccartyi are functionally important bacteria that catalyze the reductive dechlorination of chlorinated ethenes. However, these anaerobic bacteria are fastidious to isolate, making downstream genomic characterization challenging. In order to facilitate genomic analysis, a fluorescence-activated cell sorting (FACS) method was developed in this study to separate D. mccartyi cells from a microbial community, and the DNA of the isolated cells was processed by whole genome amplification (WGA) and hybridized onto a D. mccartyi microarray for comparative genomics against four sequenced strains. First, FACS was successfully applied to a D. mccartyi isolate as positive control, and then microarray results verified that WGA from 10(6) cells or ∼1 ng of genomic DNA yielded high-quality coverage detecting nearly all genes across the genome. As expected, some inter- and intrasample variability in WGA was observed, but these biases were minimized by performing multiple parallel amplifications. Subsequent application of the FACS and WGA protocols to two enrichment cultures containing ∼10% and ∼1% D. mccartyi cells successfully enabled genomic analysis. As proof of concept, this study demonstrates that coupling FACS with WGA and microarrays is a promising tool to expedite genomic characterization of target strains in environmental communities where the relative concentrations are low.

Starting research in interaction design with visuals for low-functioning children in the autistic spectrum: a protocol.

PubMed

Parés, Narcís; Carreras, Anna; Durany, Jaume; Ferrer, Jaume; Freixa, Pere; Gómez, David; Kruglanski, Orit; Parés, Roc; Ribas, J Ignasi; Soler, Miquel; Sanjurjo, Alex

2006-04-01

On starting to think about interaction design for low-functioning persons in the autistic spectrum (PAS), especially children, one finds a number of questions that are difficult to answer: Can we typify the PAS user? Can we engage the user in interactive communication without generating frustrating or obsessive situations? What sort of visual stimuli can we provide? Will they prefer representational or abstract visual stimuli? Will they understand three-dimensional (3D) graphic representation? What sort of interfaces will they accept? Can we set ambitious goals such as education or therapy? Unfortunately, most of these questions have no answer yet. Hence, we decided to set an apparently simple goal: to design a "fun application," with no intention to reach the level of education or therapy. The goal was to be attained by giving the users a sense of agency--by providing first a sense of control in the interaction dialogue. Our approach to visual stimuli design has been based on the use of geometric, abstract, two-dimensional (2D), real-time computer graphics in a full-body, non-invasive, interactive space. The results obtained within the European-funded project MultiSensory Environment Design for an Interface between Autistic and Typical Expressiveness (MEDIATE) have been extremely encouraging.

Transitions of care from Child and Adolescent Mental Health Services to Adult Mental Health Services (TRACK Study): a study of protocols in Greater London.

PubMed

Singh, Swaran P; Paul, Moli; Ford, Tamsin; Kramer, Tami; Weaver, Tim

2008-06-23

Although young people's transition from Child and Adolescent Mental Health Services (CAMHS) to Adult Mental Health Services (AMHS) in England is a significant health issue for service users, commissioners and providers, there is little evidence available to guide service development. The TRACK study aims to identify factors which facilitate or impede effective transition from CAHMS to AMHS. This paper presents findings from a survey of transition protocols in Greater London. A questionnaire survey (Jan-April 2005) of Greater London CAMHS to identify transition protocols and collect data on team size, structure, transition protocols, population served and referral rates to AMHS. Identified transition protocols were subjected to content analysis. Forty two of the 65 teams contacted (65%) responded to the survey. Teams varied in type (generic/targeted/in-patient), catchment area (locality-based, wider or national) and transition boundaries with AMHS. Estimated annual average number of cases considered suitable for transfer to AMHS, per CAMHS team (mean 12.3, range 0-70, SD 14.5, n = 37) was greater than the annual average number of cases actually accepted by AMHS (mean 8.3, range 0-50, SD 9.5, n = 33). In April 2005, there were 13 active and 2 draft protocols in Greater London. Protocols were largely similar in stated aims and policies, but differed in key procedural details, such as joint working between CAHMS and AMHS and whether protocols were shared at Trust or locality level. While the centrality of service users' involvement in the transition process was identified, no protocol specified how users should be prepared for transition. A major omission from protocols was procedures to ensure continuity of care for patients not accepted by AMHS. At least 13 transition protocols were in operation in Greater London in April 2005. Not all protocols meet all requirements set by government policy. Variation in protocol-sharing organisational units and transition process suggest that practice may vary. There is discontinuity of care provision for some patients who 'graduate' from CAMHS services but are not accepted by adult services.

Transitions of Care from Child and Adolescent Mental Health Services to Adult Mental Health Services (TRACK Study): A study of protocols in Greater London

PubMed Central

Singh, Swaran P; Paul, Moli; Ford, Tamsin; Kramer, Tami; Weaver, Tim

2008-01-01

Background Although young people's transition from Child and Adolescent Mental Health Services (CAMHS) to Adult Mental Health Services (AMHS) in England is a significant health issue for service users, commissioners and providers, there is little evidence available to guide service development. The TRACK study aims to identify factors which facilitate or impede effective transition from CAHMS to AMHS. This paper presents findings from a survey of transition protocols in Greater London. Methods A questionnaire survey (Jan-April 2005) of Greater London CAMHS to identify transition protocols and collect data on team size, structure, transition protocols, population served and referral rates to AMHS. Identified transition protocols were subjected to content analysis. Results Forty two of the 65 teams contacted (65%) responded to the survey. Teams varied in type (generic/targeted/in-patient), catchment area (locality-based, wider or national) and transition boundaries with AMHS. Estimated annual average number of cases considered suitable for transfer to AMHS, per CAMHS team (mean 12.3, range 0–70, SD 14.5, n = 37) was greater than the annual average number of cases actually accepted by AMHS (mean 8.3, range 0–50, SD 9.5, n = 33). In April 2005, there were 13 active and 2 draft protocols in Greater London. Protocols were largely similar in stated aims and policies, but differed in key procedural details, such as joint working between CAHMS and AMHS and whether protocols were shared at Trust or locality level. While the centrality of service users' involvement in the transition process was identified, no protocol specified how users should be prepared for transition. A major omission from protocols was procedures to ensure continuity of care for patients not accepted by AMHS. Conclusion At least 13 transition protocols were in operation in Greater London in April 2005. Not all protocols meet all requirements set by government policy. Variation in protocol-sharing organisational units and transition process suggest that practice may vary. There is discontinuity of care provision for some patients who 'graduate' from CAMHS services but are not accepted by adult services. PMID:18573214

User's guide: Nimbus-7 Earth radiation budget narrow-field-of-view products. Scene radiance tape products, sorting into angular bins products, and maximum likelihood cloud estimation products

NASA Technical Reports Server (NTRS)

Kyle, H. Lee; Hucek, Richard R.; Groveman, Brian; Frey, Richard

1990-01-01

The archived Earth radiation budget (ERB) products produced from the Nimbus-7 ERB narrow field-of-view scanner are described. The principal products are broadband outgoing longwave radiation (4.5 to 50 microns), reflected solar radiation (0.2 to 4.8 microns), and the net radiation. Daily and monthly averages are presented on a fixed global equal area (500 sq km), grid for the period May 1979 to May 1980. Two independent algorithms are used to estimate the outgoing fluxes from the observed radiances. The algorithms are described and the results compared. The products are divided into three subsets: the Scene Radiance Tapes (SRT) contain the calibrated radiances; the Sorting into Angular Bins (SAB) tape contains the SAB produced shortwave, longwave, and net radiation products; and the Maximum Likelihood Cloud Estimation (MLCE) tapes contain the MLCE products. The tape formats are described in detail.

Bubble propagation on a rail: a concept for sorting bubbles by size

NASA Astrophysics Data System (ADS)

Franco-Gómez, Andrés; Thompson, Alice B.; Hazel, Andrew L.; Juel, Anne

We demonstrate experimentally that the introduction of a rail, a small height constriction, within the cross-section of a rectangular channel could be used as a robust passive sorting device in two-phase fluid flows. Single air bubbles carried within silicone oil are generally transported on one side of the rail. However, for flow rates marginally larger than a critical value, a narrow band of bubble sizes can propagate (stably) over the rail, while bubbles of other sizes segregate to the side of the rail. The width of this band of bubble sizes increases with flow rate and the size of the most stable bubble can be tuned by varying the rail width. We present a complementary theoretical analysis based on a depth-averaged theory, which is in qualitative agreement with the experiments. The theoretical study reveals that the mechanism relies on a non-trivial interaction between capillary and viscous forces that is fully dynamic, rather than being a simple modification of capillary static solutions.

Variability of plasma homovanillic acid over 13 months in patients with schizophrenia; relationship with the clinical response and the Wisconsin card sort test.

PubMed

Zumárraga, Mercedes; González-Torres, Miguel A; Arrue, Aurora; Dávila, Ricardo; Dávila, Wendy; Inchausti, Lucía; Pérez-Cabeza, Lucía; Fernández-Rivas, Aránzazu; Bustamante, Sonia; Basterreche, Nieves; Guimón, José

2011-08-01

In the present study we have measured, on a monthly basis, the concentration of plasma homovanillic acid (pHVA) in schizophrenic patients during 13 months of their pharmacological treatment. The average pHVA values of each patient were within the range of 7.30-17.70 ng/ml and the coefficients of variation for each patient (CV %) were within the range of 13-33%. Half of the patients that showed higher pHVA CV% values also showed higher scores on the Brief Psychiatric Rating Scale at the beginning of the study, and improved more after 6 months, when compared to the remaining 50% with lower CV% values. There was no significant relationship between the scores of the Wisconsin Card Sort Test and the concentration or the CV% of the pHVA of each patient. A greater variability in the pHVA may be associated with a greater plasticity of the dopaminergic system and a better clinical response.

Construction and demolition waste as a source of PVC for recycling.

PubMed

Prestes, Sabrina Moretto Darbello; Mancini, Sandro Donnini; Rodolfo, Antonio; Keiroglo, Raquel Carramillo

2012-02-01

Construction and demolition waste can contain considerable amounts of polyvinyl chloride (PVC). This paper describes a study of the recycling of PVC pipes collected from such waste materials. In a sorting facility for the specific disposal of construction and demolition waste, PVC was found to represent one-third of the plastics separated by workers. Pipes were sorted carefully to preclude any possible contamination by poly(ethylene terephthalate) (PET) found in the waste. The material was ground into two distinct particle sizes (final mesh of 12.7 and 8 mm), washed, dried and recycled. The average formulation of the pipes was determined based on ash content tests and used in the fabrication of a similar compound made mainly of virgin PVC. Samples of recycled pipes and of compound based on virgin material were subjected to tensile and impact tests and provided very similar results. These results are a good indication of the application potential of the recycled material and of the fact that longer grinding to obtain finer particles is not necessarily beneficial.

Genome-wide analysis of replication timing by next-generation sequencing with E/L Repli-seq.

PubMed

Marchal, Claire; Sasaki, Takayo; Vera, Daniel; Wilson, Korey; Sima, Jiao; Rivera-Mulia, Juan Carlos; Trevilla-García, Claudia; Nogues, Coralin; Nafie, Ebtesam; Gilbert, David M

2018-05-01

This protocol is an extension to: Nat. Protoc. 6, 870-895 (2014); doi:10.1038/nprot.2011.328; published online 02 June 2011Cycling cells duplicate their DNA content during S phase, following a defined program called replication timing (RT). Early- and late-replicating regions differ in terms of mutation rates, transcriptional activity, chromatin marks and subnuclear position. Moreover, RT is regulated during development and is altered in diseases. Here, we describe E/L Repli-seq, an extension of our Repli-chip protocol. E/L Repli-seq is a rapid, robust and relatively inexpensive protocol for analyzing RT by next-generation sequencing (NGS), allowing genome-wide assessment of how cellular processes are linked to RT. Briefly, cells are pulse-labeled with BrdU, and early and late S-phase fractions are sorted by flow cytometry. Labeled nascent DNA is immunoprecipitated from both fractions and sequenced. Data processing leads to a single bedGraph file containing the ratio of nascent DNA from early versus late S-phase fractions. The results are comparable to those of Repli-chip, with the additional benefits of genome-wide sequence information and an increased dynamic range. We also provide computational pipelines for downstream analyses, for parsing phased genomes using single-nucleotide polymorphisms (SNPs) to analyze RT allelic asynchrony, and for direct comparison to Repli-chip data. This protocol can be performed in up to 3 d before sequencing, and requires basic cellular and molecular biology skills, as well as a basic understanding of Unix and R.

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

Meyer, Jeremy, E-mail: jeremy.meyer@hcuge.ch; Unit of Surgical Research, University of Geneva, Rue Michel-Servet 1, 1206 Genève; Lacotte, Stéphanie, E-mail: stephanie.lacotte@unige.ch

The objective of the present study was to develop an accurate and reproducible method for liver sinusoidal endothelial cell (LSEC) isolation in mice. Non-parenchymal cells were isolated using a modified two-step collagenase digestion combined with Optiprep density gradient centrifugation. LSEC were further purified using two prevalent methods, short-term selective adherence and CD146+ magnetic-activated cell sorting (MACS), and compared in terms of cell yield, viability and purity to our purification technique using CD11b cell depletion combined with long-term selective adherence. LSEC purification using our technique allowed to obtain 7.07±3.80 million LSEC per liver, while CD146+ MACS and short-term selective adherence yieldedmore » 2.94±1.28 and 0.99±0.66 million LSEC, respectively. Purity of the final cell preparation reached 95.10±2.58% when using our method. In contrast, CD146+ MACS and short-term selective adherence gave purities of 86.75±3.26% and 47.95±9.82%, respectively. Similarly, contamination by non-LSEC was the lowest when purification was performed using our technique, with a proportion of contaminating macrophages of only 1.87±0.77%. Further, isolated cells analysed by scanning electron microscopy presented typical LSEC fenestrations organized in sieve plates, demonstrating that the technique allowed to isolate bona fide LSEC. In conclusion, we described a reliable and reproducible technique for the isolation of high yields of pure LSEC in mice. This protocol provides an efficient method to prepare LSEC for studying their biological functions. - Highlights: • This protocol provides an efficient method to prepare primary mouse LSEC for studying their biological functions. • The liver cell dispersion step was improved by performing a retrograde cannulation of the liver. • The cell yield and the purity obtained were higher than comparative techniques in mice. • Contaminating macrophages were removed by introducing a CD11b- magnetic –activated cell sorting step.« less

Kilovoltage cone-beam CT: Comparative dose and image quality evaluations in partial and full-angle scan protocols

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

Kim, Sangroh; Yoo, Sua; Yin Fangfang

2010-07-15

Purpose: To assess imaging dose of partial and full-angle kilovoltage CBCT scan protocols and to evaluate image quality for each protocol. Methods: The authors obtained the CT dose index (CTDI) of the kilovoltage CBCT protocols in an on-board imager by ion chamber (IC) measurements and Monte Carlo (MC) simulations. A total of six new CBCT scan protocols were evaluated: Standard-dose head (100 kVp, 151 mA s, partial-angle), low-dose head (100 kVp, 75 mA s, partial-angle), high-quality head (100 kVp, 754 mA s, partial-angle), pelvis (125 kVp, 706 mA s, full-angle), pelvis spotlight (125 kVp, 752 mA s, partial-angle), and low-dosemore » thorax (110 kVp, 271 mA s, full-angle). Using the point dose method, various CTDI values were calculated by (1) the conventional weighted CTDI (CTDI{sub w}) calculation and (2) Bakalyar's method (CTDI{sub wb}). The MC simulations were performed to obtain the CTDI{sub w} and CTDI{sub wb}, as well as from (3) central slice averaging (CTDI{sub 2D}) and (4) volume averaging (CTDI{sub 3D}) techniques. The CTDI values of the new protocols were compared to those of the old protocols (full-angle CBCT protocols). Image quality of the new protocols was evaluated following the CBCT image quality assurance (QA) protocol [S. Yoo et al., ''A quality assurance program for the on-board imager registered ,'' Med. Phys. 33(11), 4431-4447 (2006)] testing Hounsfield unit (HU) linearity, spatial linearity/resolution, contrast resolution, and HU uniformity. Results: The CTDI{sub w} were found as 6.0, 3.2, 29.0, 25.4, 23.8, and 7.7 mGy for the new protocols, respectively. The CTDI{sub w} and CTDI{sub wb} differed within +3% between IC measurements and MC simulations. Method (2) results were within {+-}12% of method (1). In MC simulations, the CTDI{sub w} and CTDI{sub wb} were comparable to the CTDI{sub 2D} and CTDI{sub 3D} with the differences ranging from -4.3% to 20.6%. The CTDI{sub 3D} were smallest among all the CTDI values. CTDI{sub w} of the new protocols were found as {approx}14 times lower for standard head scan and 1.8 times lower for standard body scan than the old protocols, respectively. In the image quality QA tests, all the protocols except low-dose head and low-dose thorax protocols were within the tolerance in the HU verification test. The HU value for the two protocols was always higher than the nominal value. All the protocols passed the spatial linearity/resolution and HU uniformity tests. In the contrast resolution test, only high-quality head and pelvis scan protocols were within the tolerance. In addition, crescent effect was found in the partial-angle scan protocols. Conclusions: The authors found that CTDI{sub w} of the new CBCT protocols has been significantly reduced compared to the old protocols with acceptable image quality. The CTDI{sub w} values in the point dose method were close to the volume averaging method within 9%-21% for all the CBCT scan protocols. The Bakalyar's method produced more accurate dose estimation within 14%. The HU inaccuracy from low-dose head and low-dose thorax protocols can render incorrect dose results in the treatment planning system. When high soft-tissue contrast data are desired, high-quality head or pelvis scan protocol is recommended depending on the imaging area. The point dose method can be applicable to estimate CBCT dose with reasonable accuracy in the clinical environment.« less

Effect of water addition to a total mixed ration on feed temperature, feed intake, sorting behavior, and milk production of dairy cows.

PubMed

Felton, C A; DeVries, T J

2010-06-01

The objective of this study was to determine the effects of water addition to a high-moisture total mixed ration (TMR) on feed temperature, feed intake, feed sorting behavior, and milk production of dairy cows. Twelve lactating Holstein cows (155.8+/-60.1 DIM), individually fed once daily at 1000 h, were exposed to 3 diets in a Latin square design with 28-d treatment periods. Diets had the same ingredient composition [30.9% corn silage, 30.3% alfalfa haylage, 21.2% high-moisture corn, and 17.6% protein supplement; dry matter (DM) basis] and differed only in DM concentration, which was reduced by the addition of water. Treatment diets averaged 56.3, 50.8, and 44.1% DM. The study was conducted between May and August when environmental temperature was 18.2+/-3.6 degrees C and ambient temperature in the barn was 24.4+/-3.3 degrees C. Dry matter intake (DMI) was monitored for each animal for the last 14 d of each treatment period. For the final 7 d of each period, milk production was monitored, feed temperature and ambient temperature and humidity were recorded (daily at 1000, 1300, and 1600 h), and fresh feed and orts were sampled for determination of sorting. For the final 4 d of each period, milk samples were taken for composition analysis. Samples taken for determining sorting were separated using a Penn State Particle Separator that had 3 screens (19, 8, and 1.18 mm) and a bottom pan, resulting in 4 fractions (long, medium, short, and fine). Sorting was calculated as the actual intake of each particle size fraction expressed as a percentage of the predicted intake of that fraction. Greater amounts of water added to the TMR resulted in greater increases in feed temperature in the hours after feed delivery, greater sorting against long particles, and decreased DMI, reducing the overall intake of starch and neutral detergent fiber. Milk production and composition were not affected by the addition of water to the TMR. Efficiency of production of milk was, however, increased with greater amounts of water added to the TMR. The increases in feed temperature in the hours after feed delivery were enhanced by higher ambient temperatures; this may be indicative of feed spoilage and thus may have contributed to the reduced DMI observed. Overall, these results suggest that the addition of water to high-moisture TMR (less than 60% DM) containing primarily haylage and silage forage sources will not always discourage cows from sorting, but rather may increase this behavior and limit the nutrient consumption of cows, particularly when ambient temperature is high. 2010 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

A Cost Analysis of a Pancreatic Cancer Screening Protocol in High-Risk Populations

PubMed Central

Bruenderman, Elizabeth; Martin, Robert CG

2016-01-01

Background Pancreatic cancer is the 4th leading cause of cancer death in the U.S. A screening protocol is needed to catch early stage, resectable disease. This study suggests a protocol for high-risk individuals and assesses the cost in the context of the Affordable Care Act. Methods Medicare and national average pricing were used for cost analysis of a protocol using MRI/MRCP biannually in high-risk groups. Results: ‘ Costs per year of life added’ based on Medicare and national average costs, respectively, are: $638.62 and $2542.37 for Peutz-Jehgers Syndrome, $945.33 and $3763.44 for Hereditary Pancreatitis, $1141.77 and $4545.45 for Familial Pancreatic Cancer and p16-Leiden mutations, and $356.42 and $1418.92 for new-onset diabetes over age 50 with weight loss or smoking. Conclusion A screening program using MRI/MRCP is affordable in high-risk populations. The U.S. Preventive Services Task Force must reevaluate its pancreatic cancer screening guidelines to make screening more cost-effective for the individual. PMID:26003200

Parallel integer sorting with medium and fine-scale parallelism

NASA Technical Reports Server (NTRS)

Dagum, Leonardo

1993-01-01

Two new parallel integer sorting algorithms, queue-sort and barrel-sort, are presented and analyzed in detail. These algorithms do not have optimal parallel complexity, yet they show very good performance in practice. Queue-sort designed for fine-scale parallel architectures which allow the queueing of multiple messages to the same destination. Barrel-sort is designed for medium-scale parallel architectures with a high message passing overhead. The performance results from the implementation of queue-sort on a Connection Machine CM-2 and barrel-sort on a 128 processor iPSC/860 are given. The two implementations are found to be comparable in performance but not as good as a fully vectorized bucket sort on the Cray YMP.

Sort computation

NASA Technical Reports Server (NTRS)

Dorband, John E.

1988-01-01

Sorting has long been used to organize data in preparation for further computation, but sort computation allows some types of computation to be performed during the sort. Sort aggregation and sort distribution are the two basic forms of sort computation. Sort aggregation generates an accumulative or aggregate result for each group of records and places this result in one of the records. An aggregate operation can be any operation that is both associative and commutative, i.e., any operation whose result does not depend on the order of the operands or the order in which the operations are performed. Sort distribution copies the value from a field of a specific record in a group into that field in every record of that group.

Performance comparison of token ring protocols for hard-real-time communication

NASA Technical Reports Server (NTRS)

Kamat, Sanjay; Zhao, Wei

1992-01-01

The ability to guarantee the deadlines of synchronous messages while maintaining a good aggregate throughput is an important consideration in the design of distributed real-time systems. In this paper, we study two token ring protocols, the priority driven protocol and the timed token protocol, for their suitability for hard real-time systems. Both these protocols use a token to control access to the transmission medium. In a priority driven protocol, messages are assigned priorities and the protocol ensures that messages are transmitted in the order of their priorities. Timed token protocols do not provide for priority arbitration but ensure that the maximum access delay for a station is bounded. For both protocols, we first derive the schedulability conditions under which the transmission deadlines of a given set of synchronous messages can be guaranteed. Subsequently, we use these schedulability conditions to quantitatively compare the average case behavior of the protocols. This comparison demonstrates that each of the protocols has its domain of superior performance and neither dominates the other for the entire range of operating conditions.

Derivation of sorting programs

NASA Technical Reports Server (NTRS)

Varghese, Joseph; Loganantharaj, Rasiah

1990-01-01

Program synthesis for critical applications has become a viable alternative to program verification. Nested resolution and its extension are used to synthesize a set of sorting programs from their first order logic specifications. A set of sorting programs, such as, naive sort, merge sort, and insertion sort, were successfully synthesized starting from the same set of specifications.

Spin-the-bottle Sort and Annealing Sort: Oblivious Sorting via Round-robin Random Comparisons

PubMed Central

Goodrich, Michael T.

2013-01-01

We study sorting algorithms based on randomized round-robin comparisons. Specifically, we study Spin-the-bottle sort, where comparisons are unrestricted, and Annealing sort, where comparisons are restricted to a distance bounded by a temperature parameter. Both algorithms are simple, randomized, data-oblivious sorting algorithms, which are useful in privacy-preserving computations, but, as we show, Annealing sort is much more efficient. We show that there is an input permutation that causes Spin-the-bottle sort to require Ω(n2 log n) expected time in order to succeed, and that in O(n2 log n) time this algorithm succeeds with high probability for any input. We also show there is a specification of Annealing sort that runs in O(n log n) time and succeeds with very high probability. PMID:24550575

Exercise Increases the Cardiovascular Stimulus Provided by Artificial Gravity

NASA Technical Reports Server (NTRS)

Howarth, M. S.; Moore, F. B.; Hinghofer-Szalkay, H.; Jezova, D.; Diedrich, A.; Ferris, M. B.; Schlegel, T. T.; Pathwardhan, A. R.; Knapp, C. F.; Evans, J. M.

2008-01-01

We investigated fluid shifts and regulatory responses to variations of posture, exercise, Gz level and radius of rotation in subjects riding NASA Ames 20G centrifuge. Results are from 4 protocols that address radius and exercise effects only. Protocol A: After 10 min supine control, 12 healthy men (35 plus or minus 9 yr, 82.8 plus or minus 7.9 kg) were exposed to rotational 1 Gz (2.5 m radius) for 2 min followed by 20 min alternating between 1 and 1.25 Gz. Blood samples were taken pre and post spin. Protocol B: Same as A, but lower limb exercise (70% V02max) preceded ramps to 1.25 Gz. Protocol C: Same as A but radius of rotation 8.3 m. Protocol D: Same as B but at 8.3 m. The 8 subjects who completed all protocols, increased heart rate (HR) from control, on average, by: A: 5, B: 39, C: 11, D: 44 bpm. For thoracic fluid volume, (bioimpedance), the 8 subjects changed from control, on average: A: -394, B: -548, C: -537, D: -708 mL. For thigh fluid volume, changes from control, on average, were: A: -137, B: 129, C: -75, D: 159 mL. Hematocrit changes from control were: A: 2.3, B: 3.5, C: 2.3, D: 4.3 %. Radius effects were mild and included greater loss of fluid from the thorax, less fluid loss from the thigh and increased heart rate at the longer radius. Pre-acceleration exercise effects were more dramatic and included additional loss of fluid from the chest, increased fluid volume of the thigh, increased hematocrit and greater heart rate increases. We propose that short bouts of intense exercise can be used to magnify the cardiovascular stress delivered by artificial gravity (AG) training and the combination of AG with exercise training can be fine-tuned to preserve orthostatic tolerance of astronauts during spaceflight.

Continuous tunnel kiln direct-fired with bark to dry 1.75-inch southern pine in 12 hours.

Treesearch

P. Koch; W.L. Wellford

1977-01-01

Length-sorted lumber is surfaced on one side to 1.75-inch thickness, mechanically stacked 5 feet wide and 10 feet high on 1-1/4-inch-thick sticks, and continuously transported through a zone-controlled tunnel kiln at 8 ft./hr. to yield 500,000 fbm of lumber dried to 9 percent average MC per 168-hour week. In the tunnel, the lumber is dried for 8 (possibly 10) hours at...

Continuous tunnel kiln direct-fired with bark to dry 1.75-inch southern pine in 12 hours

Treesearch

Peter Koch; Walker L. Wellford

1976-01-01

Length-sorted lumber is surfaced on one side to 1.75-inch thickness, mechanically stacked 5 feet wide and 10 feet high on 1-1/4-inch-thick sticks, and continuously transported through a zone-controlled tunnel kiln at 8 ft./hr. to yield 500,000 fbm of lumber dried to 9 percent average MC per 168-hour week. In the tunnel, the lumber is dried for 8 (possibly 10) hours of...

A Plan for Collecting Ada Software Development Cost, Schedule, and Environment Data.

DTIC Science & Technology

1987-04-02

separate comment section for events that affected individual CSCIs. I C-31 S% S g S. SYSTEM LEVEL OR CSCI LEVEL DOCUMENTATION PORN INSTRUCTIONS This...J*~ *.p.N. COMPUTER SOFTVARE CONFIGURATION ITEM SUMMART DATA PORN INSTRUCTIONS 4.1.4. Development Methods Experience Enter the average number of...users see what is happening and view results). It is often a video display terminal of some sort, although it could be a hard copy printer and keyboard or

Safe sorting of GFP-transduced live cells for subsequent culture using a modified FACS vantage.

PubMed

Sørensen, T U; Gram, G J; Nielsen, S D; Hansen, J E

1999-12-01

A stream-in-air cell sorter enables rapid sorting to a high purity, but it is not well suited for sorting of infectious material due to the risk of airborne spread to the surroundings. A FACS Vantage cell sorter was modified for safe use with potentially HIV infected cells. Safety tests with bacteriophages were performed to evaluate the potential spread of biologically active material during cell sorting. Cells transduced with a retroviral vector carrying the gene for GFP were sorted on the basis of their GFP fluorescence, and GFP expression was followed during subsequent culture. The bacteriophage sorting showed that the biologically active material was confined to the sorting chamber. A failure mode simulating a nozzle blockage resulted in detectable droplets inside the sorting chamber, but no droplets could be detected when an additional air suction from the sorting chamber had been put on. The GFP transduced cells were sorted to 99% purity. Cells not expressing GFP at the time of sorting did not turn on the gene during subsequent culture. Un-sorted cells and cells sorted to be positive for GFP showed a decrease in the fraction of GFP positive cells during culture. Sorting of live infected cells can be performed safely and with no deleterious effects on vector expression using the modified FACS Vantage instrument. Copyright 1999 Wiley-Liss, Inc.

Economic comparison of common treatment protocols and J5 vaccination for clinical mastitis in dairy herds using optimized culling decisions.

PubMed

Kessels, J A; Cha, E; Johnson, S K; Welcome, F L; Kristensen, A R; Gröhn, Y T

2016-05-01

This study used an existing dynamic optimization model to compare costs of common treatment protocols and J5 vaccination for clinical mastitis in US dairy herds. Clinical mastitis is an infection of the mammary gland causing major economic losses in dairy herds due to reduced milk production, reduced conception, and increased risk of mortality and culling for infected cows. Treatment protocols were developed to reflect common practices in dairy herds. These included targeted therapy following pathogen identification, and therapy without pathogen identification using a broad-spectrum antimicrobial or treating with the cheapest treatment option. The cost-benefit of J5 vaccination was also estimated. Effects of treatment were accounted for as changes in treatment costs, milk loss due to mastitis, milk discarded due to treatment, and mortality. Following ineffective treatments, secondary decisions included extending the current treatment, alternative treatment, discontinuing treatment, and pathogen identification followed by recommended treatment. Average net returns for treatment protocols and vaccination were generated using an existing dynamic programming model. This model incorporates cow and pathogen characteristics to optimize management decisions to treat, inseminate, or cull cows. Of the treatment protocols where 100% of cows received recommended treatment, pathogen-specific identification followed by recommended therapy yielded the highest average net returns per cow per year. Out of all treatment scenarios, the highest net returns were achieved with selecting the cheapest treatment option and discontinuing treatment, or alternate treatment with a similar spectrum therapy; however, this may not account for the full consequences of giving nonrecommended therapies to cows with clinical mastitis. Vaccination increased average net returns in all scenarios. Copyright © 2016 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Instructions to “push as hard as you can” improve average chest compression depth in dispatcher-assisted Cardiopulmonary Resuscitation

PubMed Central

Mirza, Muzna; Brown, Todd B.; Saini, Devashish; Pepper, Tracy L; Nandigam, Hari Krishna; Kaza, Niroop; Cofield, Stacey S.

2008-01-01

Background and Objective Cardiopulmonary Resuscitation (CPR) with adequate chest compression depth appears to improve first shock success in cardiac arrest. We evaluate the effect of simplification of chest compression instructions on compression depth in dispatcher-assisted CPR protocol. Methods Data from two randomized, double-blinded, controlled trials with identical methodology were combined to obtain 332 records for this analysis. Subjects were randomized to either modified Medical Priority Dispatch System (MPDS) v11.2 protocol or a new simplified protocol. The main difference between the protocols was the instruction to “push as hard as you can” in the simplified protocol, compared to “push down firmly 2 inches (5cm)” in MPDS. Data were recorded via a Laerdal® ResusciAnne® SkillReporter™ manikin. Primary outcome measures included: chest compression depth, proportion of compressions without error, with adequate depth and with total release. Results Instructions to “push as hard as you can”, compared to “push down firmly 2 inches (5cm)”, resulted in improved chest compression depth (36.4 vs 29.7 mm, p<0.0001), and improved median proportion of chest compressions done to the correct depth (32% vs <1%, p<0.0001). No significant difference in median proportion of compressions with total release (100% for both) and average compression rate (99.7 vs 97.5 per min, p<0.56) was found. Conclusions Modifying dispatcher-assisted CPR instructions by changing “push down firmly 2 inches (5cm)” to “push as hard as you can” achieved improvement in chest compression depth at no cost to total release or average chest compression rate. PMID:18635306

Safety of a DVT chemoprophylaxis protocol following traumatic brain injury: a single center quality improvement initiative.

PubMed

Nickele, Christopher M; Kamps, Timothy K; Medow, Joshua E

2013-04-01

Venous thromboembolism (VTE) is a complication that affects approximately 30 % of moderate and severe traumatic brain injury (TBI) patients when pharmacologic prophylaxis is not used. Following TBI, specifically in the case of contusions, the safety and efficacy of pharmacologic thromboembolism prophylaxis (PTP) has been studied only in small sample sizes. In this study, we attempt to assess the safety and efficacy of a PTP protocol for TBI patients, as a quality improvement (QI) initiative, in the neuroscience intensive care unit (NSICU). Between January 1st and December 31st, 2009, consecutive patients discharged from the University of Wisconsin NSICU after >a 48 h minimum stay were evaluated as part of a QI project. A protocol for the initiation of PTP was designed and implemented for NSICU patients. The protocol did not vary based on type of intracranial injury. The rate of VTE was reported as was heparin-induced thrombocytopenia and PTP-related expansion of intracranial hemorrhage (IH) requiring reoperation. The number of patients receiving PTP and the timing of therapy were tracked. Patients were excluded for persistent coagulopathy, other organ system bleeding (such as the gastrointestinal tract), or pregnancy. Faculty could opt out of the protocol without reason. Using the same criteria, patients discharged during the preceding 6 months, from July 1st to December 31st, 2008, were evaluated as controls as the PTP protocol was not in effect during this time. During the control period, there were 48 head trauma admissions who met the inclusion criteria. In 22 patients (45.8 %), PTP was initiated at an average of 4.9 ± 5.4 days after admission. During the protocol period, there were 87 head trauma admissions taken from 1,143 total NSICU stays who met criteria. In 63 patients (72.4 %), the care team in the NSICU successfully initiated PTP, at an average of 3.4 ± 2.8 days after admission. All 87 trauma patients were analyzed, and the rate of clinically significant deep venous thrombosis (DVT) was 6.9 % (6 of 87). Three protocol patients (3.45 %) went to the operating room for surgery after the initiation of PTP; none of these patients had a measurable change in hemorrhage size on head CT. The change in percentage of patients receiving PTP was significantly increased by the protocol (p < 0.0001); while the average days to first PTP dose trended down with institution of the protocol, this change was not statistically significant. A PTP protocol in the NSICU is useful in controlling the number of complications from DVT and pulmonary embolism while avoiding additional IH. This protocol, based on a published body of literature, allowed for VTE rates similar to published rates, while having no PTP-related hemorrhage expansion. The protocol significantly changed physician behavior, increasing the percentage of patients receiving PTP during their hospitalization; whether long-term patient outcomes are affected is a potential goal for future study.

Differences in Preferential Sorting of Fine Particles in the Panama Basin Over the Past 25 kyr: Effects on 230Th-derived Focusing Factors

NASA Astrophysics Data System (ADS)

Loveley, M. R.; Marcantonio, F.; Lyle, M. W.; Wang, J. K.

2013-12-01

In this study, we attempt to understand how preferential sorting of fine particles during redistribution processes in the Panama Basin affects the 230Th constant-flux proxy. Fine particles likely contain greater amounts of 230Th, so that preferential sorting of fine particles may bias sediment mass accumulation rates (MARs). We examined sediments that span the past 25 kyr from two new sediment cores retrieved within about 56 km of each other in the northern part of the basin (MV1013-01-'4JC', 5° 44.699'N 85° 45.498' W, 1730 m depth; MV1014-01-'8JC', 6° 14.038'N 86° 2.613' W, 1993 m depth). Core 4JC, closer to the ridge top that bounds the basin (Cocos Ridge), has a thin sediment drape, while the deeper core 8JC, has a thicker sediment drape and lies further from the ridge top. 230Th-derived focusing factors from 4JC are similar and suggest winnowing with average values of about 0.5 and 0.6 during the Holocene and the last glacial, respectively. For 8JC, calculated average focusing factors are significantly different and suggest focusing with values of about 2 during the Holocene and 4 during the last glacial. Since the two sites are close to each other, one would expect similar rain rates and, therefore, similar 230Th-derived MARs within similar windows of time, i.e., the rain rate should not vary significantly at each site temporally. In addition, the radiocarbon-derived sand (>63μm) MARs should behave similarly since coarser particles are likely not transported by bottom currents. Sand MARs are, indeed, similar during the Holocene and the last glacial at each site. During the last glacial, however, sand MARs are about a factor of 3 higher than those during the Holocene. On the other hand, there is little variability in the 230Th-derived MARs both spatially and temporally. We interpret the discrepancies between the radiocarbon-derived sand and 230Th-derived MARs as being due to preferential sorting of fine particles during the redistribution of sediments by deep-sea currents. The 230Th-derived focusing factors are being overestimated at the deeper site and vice versa at the shallower site, and the degree of inaccuracy varies temporally. We discuss this temporal variability and its relationship to deep-sea current velocities.

Design and realization of sort manipulator of crystal-angle sort machine

NASA Astrophysics Data System (ADS)

Wang, Ming-shun; Chen, Shu-ping; Guan, Shou-ping; Zhang, Yao-wei

2005-12-01

It is a current tendency of development in automation technology to replace manpower with manipulators in working places where dangerous, harmful, heavy or repetitive work is involved. The sort manipulator is installed in a crystal-angle sort machine to take the place of manpower, and engaged in unloading and sorting work. It is the outcome of combing together mechanism, electric transmission, and pneumatic element and micro-controller control. The step motor makes the sort manipulator operate precisely. The pneumatic elements make the sort manipulator be cleverer. Micro-controller's software bestows some simple artificial intelligence on the sort manipulator, so that it can precisely repeat its unloading and sorting work. The combination of manipulator's zero position and step motor counting control puts an end to accumulating error in long time operation. A sort manipulator's design in the practice engineering has been proved to be correct and reliable.

40 CFR 61.356 - Recordkeeping requirements.

Code of Federal Regulations, 2010 CFR

2010-07-01

... test protocol and the means by which sampling variability and analytical variability were accounted for... also establish the design minimum and average temperature in the combustion zone and the combustion... the design minimum and average temperatures across the catalyst bed inlet and outlet. (C) For a boiler...

A Task Analysis of the Shift from Teacher Instructions to Self-Instructions in Performing an In-Common Task.

ERIC Educational Resources Information Center

Grote, Irene; And Others

1996-01-01

Three preschoolers performed four sorts with stimulus cards--an untaught target sort and three directly taught alternating sorts considered to self-instruct the target performance. Accuracy increased first in the skill sorts and then in the untaught target sorts. All subjects generalized to new target sorts. Correct spontaneous self-instructions…

A Novel Process Audit for Standardized Perioperative Handoff Protocols.

PubMed

Pallekonda, Vinay; Scholl, Adam T; McKelvey, George M; Amhaz, Hassan; Essa, Deanna; Narreddy, Spurthy; Tan, Jens; Templonuevo, Mark; Ramirez, Sasha; Petrovic, Michelle A

2017-11-01

A perioperative handoff protocol provides a standardized delivery of communication during a handoff that occurs from the operating room to the postanestheisa care unit or ICU. The protocol's success is dependent, in part, on its continued proper use over time. A novel process audit was developed to help ensure that a perioperative handoff protocol is used accurately and appropriately over time. The Audit Observation Form is used for the Audit Phase of the process audit, while the Audit Averages Form is used for the Data Analysis Phase. Employing minimal resources and using quantitative methods, the process audit provides the necessary means to evaluate the proper execution of any perioperative handoff protocol. Copyright © 2017 The Joint Commission. Published by Elsevier Inc. All rights reserved.

To sort or not to sort: the impact of spike-sorting on neural decoding performance.

PubMed

Todorova, Sonia; Sadtler, Patrick; Batista, Aaron; Chase, Steven; Ventura, Valérie

2014-10-01

Brain-computer interfaces (BCIs) are a promising technology for restoring motor ability to paralyzed patients. Spiking-based BCIs have successfully been used in clinical trials to control multi-degree-of-freedom robotic devices. Current implementations of these devices require a lengthy spike-sorting step, which is an obstacle to moving this technology from the lab to the clinic. A viable alternative is to avoid spike-sorting, treating all threshold crossings of the voltage waveform on an electrode as coming from one putative neuron. It is not known, however, how much decoding information might be lost by ignoring spike identity. We present a full analysis of the effects of spike-sorting schemes on decoding performance. Specifically, we compare how well two common decoders, the optimal linear estimator and the Kalman filter, reconstruct the arm movements of non-human primates performing reaching tasks, when receiving input from various sorting schemes. The schemes we tested included: using threshold crossings without spike-sorting; expert-sorting discarding the noise; expert-sorting, including the noise as if it were another neuron; and automatic spike-sorting using waveform features. We also decoded from a joint statistical model for the waveforms and tuning curves, which does not involve an explicit spike-sorting step. Discarding the threshold crossings that cannot be assigned to neurons degrades decoding: no spikes should be discarded. Decoding based on spike-sorted units outperforms decoding based on electrodes voltage crossings: spike-sorting is useful. The four waveform based spike-sorting methods tested here yield similar decoding efficiencies: a fast and simple method is competitive. Decoding using the joint waveform and tuning model shows promise but is not consistently superior. Our results indicate that simple automated spike-sorting performs as well as the more computationally or manually intensive methods used here. Even basic spike-sorting adds value to the low-threshold waveform-crossing methods often employed in BCI decoding.

To sort or not to sort: the impact of spike-sorting on neural decoding performance

NASA Astrophysics Data System (ADS)

Todorova, Sonia; Sadtler, Patrick; Batista, Aaron; Chase, Steven; Ventura, Valérie

2014-10-01

Objective. Brain-computer interfaces (BCIs) are a promising technology for restoring motor ability to paralyzed patients. Spiking-based BCIs have successfully been used in clinical trials to control multi-degree-of-freedom robotic devices. Current implementations of these devices require a lengthy spike-sorting step, which is an obstacle to moving this technology from the lab to the clinic. A viable alternative is to avoid spike-sorting, treating all threshold crossings of the voltage waveform on an electrode as coming from one putative neuron. It is not known, however, how much decoding information might be lost by ignoring spike identity. Approach. We present a full analysis of the effects of spike-sorting schemes on decoding performance. Specifically, we compare how well two common decoders, the optimal linear estimator and the Kalman filter, reconstruct the arm movements of non-human primates performing reaching tasks, when receiving input from various sorting schemes. The schemes we tested included: using threshold crossings without spike-sorting; expert-sorting discarding the noise; expert-sorting, including the noise as if it were another neuron; and automatic spike-sorting using waveform features. We also decoded from a joint statistical model for the waveforms and tuning curves, which does not involve an explicit spike-sorting step. Main results. Discarding the threshold crossings that cannot be assigned to neurons degrades decoding: no spikes should be discarded. Decoding based on spike-sorted units outperforms decoding based on electrodes voltage crossings: spike-sorting is useful. The four waveform based spike-sorting methods tested here yield similar decoding efficiencies: a fast and simple method is competitive. Decoding using the joint waveform and tuning model shows promise but is not consistently superior. Significance. Our results indicate that simple automated spike-sorting performs as well as the more computationally or manually intensive methods used here. Even basic spike-sorting adds value to the low-threshold waveform-crossing methods often employed in BCI decoding.

Sorting nexin-2 is associated with tubular elements of the early endosome, but is not essential for retromer-mediated endosome-to-TGN transport

PubMed Central

Carlton, Jez G.; Bujny, Miriam V.; Peter, Brian J.; Oorschot, Viola M. J.; Rutherford, Anna; Arkell, Rebecca S.; Klumperman, Judith; McMahon, Harvey T.; Cullen, Peter J.

2006-01-01

Summary Sorting nexins are a large family of phox-homology-domain-containing proteins that have been implicated in the control of endosomal sorting. Sorting nexin-1 is a component of the mammalian retromer complex that regulates retrieval of the cation-independent mannose 6-phosphate receptor from endosomes to the trans-Golgi network. In yeast, retromer is composed of Vps5p (the orthologue of sorting nexin-1), Vps17p (a related sorting nexin) and a cargo selective subcomplex composed of Vps26p, Vps29p and Vps35p. With the exception of Vps17p, mammalian orthologues of all yeast retromer components have been identified. For Vps17p, one potential mammalian orthologue is sorting nexin-2. Here we show that, like sorting nexin-1, sorting nexin-2 binds phosphatidylinositol 3-monophosphate and phosphatidylinositol 3,5-bisphosphate, and possesses a Bin/Amphiphysin/Rvs domain that can sense membrane curvature. However, in contrast to sorting nexin-1, sorting nexin-2 could not induce membrane tubulation in vitro or in vivo. Functionally, we show that endogenous sorting nexin-1 and sorting nexin-2 co-localise on high curvature tubular elements of the 3-phosphoinositide-enriched early endosome, and that suppression of sorting nexin-2 does not perturb the degradative sorting of receptors for epidermal growth factor or transferrin, nor the steady-state distribution of the cation-independent mannose 6-phosphate receptor. However, suppression of sorting nexin-2 results in a subtle alteration in the kinetics of cation-independent mannose 6-phosphate receptor retrieval. These data suggest that although sorting nexin-2 may be a component of the retromer complex, its presence is not essential for the regulation of endosome-to-trans Golgi network retrieval of the cation-independent mannose 6-phosphate receptor. PMID:16179610

ECS: Efficient Communication Scheduling for Underwater Sensor Networks

PubMed Central

Hong, Lu; Hong, Feng; Guo, Zhongwen; Li, Zhengbao

2011-01-01

TDMA protocols have attracted a lot of attention for underwater acoustic sensor networks (UWSNs), because of the unique characteristics of acoustic signal propagation such as great energy consumption in transmission, long propagation delay and long communication range. Previous TDMA protocols all allocated transmission time to nodes based on discrete time slots. This paper proposes an efficient continuous time scheduling TDMA protocol (ECS) for UWSNs, including the continuous time based and sender oriented conflict analysis model, the transmission moment allocation algorithm and the distributed topology maintenance algorithm. Simulation results confirm that ECS improves network throughput by 20% on average, compared to existing MAC protocols. PMID:22163775

Optimizing radiologist e-prescribing of CT oral contrast agent using a protocoling portal.

PubMed

Wasser, Elliot J; Galante, Nicholas J; Andriole, Katherine P; Farkas, Cameron; Khorasani, Ramin

2013-12-01

The purpose of this study is to quantify the time expenditure associated with radiologist ordering of CT oral contrast media when using an integrated protocoling portal and to determine radiologists' perceptions of the ordering process. This prospective study was performed at a large academic tertiary care facility. Detailed timing information for CT inpatient oral contrast orders placed via the computerized physician order entry (CPOE) system was gathered over a 14-day period. Analyses evaluated the amount of physician time required for each component of the ordering process. Radiologists' perceptions of the ordering process were assessed by survey. Descriptive statistics and chi-square analysis were performed. A total of 96 oral contrast agent orders were placed by 13 radiologists during the study period. The average time necessary to create a protocol for each case was 40.4 seconds (average range by subject, 20.0-130.0 seconds; SD, 37.1 seconds), and the average total time to create and sign each contrast agent order was 27.2 seconds (range, 10.0-50.0 seconds; SD, 22.4 seconds). Overall, 52.5% (21/40) of survey respondents indicated that radiologist entry of oral contrast agent orders improved patient safety. A minority of respondents (15% [6/40]) indicated that contrast agent order entry was either very or extremely disruptive to workflow. Radiologist e-prescribing of CT oral contrast agents using CPOE can be embedded in a protocol workflow. Integration of health IT tools can help to optimize user acceptance and adoption.

Effect of modulated ultrasound parameters on ultrasound-induced thrombolysis.

PubMed

Soltani, Azita; Volz, Kim R; Hansmann, Doulas R

2008-12-07

The potential of ultrasound to enhance enzyme-mediated thrombolysis by application of constant operating parameters (COP) has been widely demonstrated. In this study, the effect of ultrasound with modulated operating parameters (MOP) on enzyme-mediated thrombolysis was investigated. The MOP protocol was applied to an in vitro model of thrombolysis. The results were compared to a COP with the equivalent soft tissue thermal index (TIS) over the duration of ultrasound exposure of 30 min (p < 0.14). To explore potential differences in the mechanism responsible for ultrasound-induced thrombolysis, a perfusion model was used to measure changes in average fibrin pore size of clot before, after and during exposure to MOP and COP protocols and cavitational activity was monitored in real time for both protocols using a passive cavitation detection system. The relative lysis enhancement by each COP and MOP protocol compared to alteplase alone yielded values of 33.69 +/- 12.09% and 63.89 +/- 15.02% in a thrombolysis model, respectively (p < 0.007). Both COP and MOP protocols caused an equivalent significant increase in average clot pore size of 2.09 x 10(-2) +/- 0.01 microm and 1.99 x 10(-2) +/- 0.004 microm, respectively (p < 0.74). No signatures of inertial or stable cavitation were observed for either acoustic protocol. In conclusion, due to mechanisms other than cavitation, application of ultrasound with modulated operating parameters has the potential to significantly enhance the relative lysis enhancement compared to application of ultrasound with constant operating parameters.

Quantitative Assessment of In-solution Digestion Efficiency Identifies Optimal Protocols for Unbiased Protein Analysis*

PubMed Central

León, Ileana R.; Schwämmle, Veit; Jensen, Ole N.; Sprenger, Richard R.

2013-01-01

The majority of mass spectrometry-based protein quantification studies uses peptide-centric analytical methods and thus strongly relies on efficient and unbiased protein digestion protocols for sample preparation. We present a novel objective approach to assess protein digestion efficiency using a combination of qualitative and quantitative liquid chromatography-tandem MS methods and statistical data analysis. In contrast to previous studies we employed both standard qualitative as well as data-independent quantitative workflows to systematically assess trypsin digestion efficiency and bias using mitochondrial protein fractions. We evaluated nine trypsin-based digestion protocols, based on standard in-solution or on spin filter-aided digestion, including new optimized protocols. We investigated various reagents for protein solubilization and denaturation (dodecyl sulfate, deoxycholate, urea), several trypsin digestion conditions (buffer, RapiGest, deoxycholate, urea), and two methods for removal of detergents before analysis of peptides (acid precipitation or phase separation with ethyl acetate). Our data-independent quantitative liquid chromatography-tandem MS workflow quantified over 3700 distinct peptides with 96% completeness between all protocols and replicates, with an average 40% protein sequence coverage and an average of 11 peptides identified per protein. Systematic quantitative and statistical analysis of physicochemical parameters demonstrated that deoxycholate-assisted in-solution digestion combined with phase transfer allows for efficient, unbiased generation and recovery of peptides from all protein classes, including membrane proteins. This deoxycholate-assisted protocol was also optimal for spin filter-aided digestions as compared with existing methods. PMID:23792921

A retrospective comparison of smart prep and test bolus multi-detector CT pulmonary angiography protocols

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

Suckling, Tara; Smith, Tony; Reed, Warren

2013-06-15

Optimal arterial opacification is crucial in imaging the pulmonary arteries using computed tomography (CT). This poses the challenge of precisely timing data acquisition to coincide with the transit of the contrast bolus through the pulmonary vasculature. The aim of this quality assurance exercise was to investigate if a change in CT pulmonary angiography (CTPA) scanning protocol resulted in improved opacification of the pulmonary arteries. Comparison was made between the smart prep protocol (SPP) and the test bolus protocol (TBP) for opacification in the pulmonary trunk. A total of 160 CTPA examinations (80 using each protocol) performed between January 2010 andmore » February 2011 were assessed retrospectively. CT attenuation coefficients were measured in Hounsfield Units (HU) using regions of interest at the level of the pulmonary trunk. The average pixel value, standard deviation (SD), maximum, and minimum were recorded. For each of these variables a mean value was then calculated and compared for these two CTPA protocols. Minimum opacification of 200 HU was achieved in 98% of the TBP sample but only 90% of the SPP sample. The average CT attenuation over the pulmonary trunk for the SPP was 329 (SD = ±21) HU, whereas for the TBP it was 396 (SD = ±22) HU (P = 0.0017). The TBP also recorded higher maximum (P = 0.0024) and minimum (P = 0.0039) levels of opacification. This study has found that a TBP resulted in significantly better opacification of the pulmonary trunk than the SPP.« less

Design of monitoring system for mail-sorting based on the Profibus S7 series PLC

NASA Astrophysics Data System (ADS)

Zhang, W.; Jia, S. H.; Wang, Y. H.; Liu, H.; Tang, G. C.

2017-01-01

With the rapid development of the postal express, the workload of mail sorting is increasing, but the automatic technology of mail sorting is not mature enough. In view of this, the system uses Siemens S7-300 PLC as the main station controller, PLC of Siemens S7-200/400 is from the station controller, through the man-machine interface configuration software MCGS, PROFIBUS-DP communication, RFID technology and mechanical sorting hand achieve mail classification sorting monitoring. Among them, distinguish mail-sorting by scanning RFID posted in the mail electronic bar code (fixed code), the system uses the corresponding controller on the acquisition of information processing, the processed information transmit to the sorting manipulator by PROFIBUS-DP. The system can realize accurate and efficient mail sorting, which will promote the development of mail sorting technology.

Dissecting Stop Transfer versus Conservative Sorting Pathways for Mitochondrial Inner Membrane Proteins in Vivo*

PubMed Central

Park, Kwangjin; Botelho, Salomé Calado; Hong, Joonki; Österberg, Marie; Kim, Hyun

2013-01-01

Mitochondrial inner membrane proteins that carry an N-terminal presequence are sorted by one of two pathways: stop transfer or conservative sorting. However, the sorting pathway is known for only a small number of proteins, in part due to the lack of robust experimental tools with which to study. Here we present an approach that facilitates determination of inner membrane protein sorting pathways in vivo by fusing a mitochondrial inner membrane protein to the C-terminal part of Mgm1p containing the rhomboid cleavage region. We validated the Mgm1 fusion approach using a set of proteins for which the sorting pathway is known, and determined sorting pathways of inner membrane proteins for which the sorting mode was previously uncharacterized. For Sdh4p, a multispanning membrane protein, our results suggest that both conservative sorting and stop transfer mechanisms are required for insertion. Furthermore, the sorting process of Mgm1 fusion proteins was analyzed under different growth conditions and yeast mutant strains that were defective in the import motor or the m-AAA protease function. Our results show that the sorting of mitochondrial proteins carrying moderately hydrophobic transmembrane segments is sensitive to cellular conditions, implying that mitochondrial import and membrane sorting in the physiological environment may be dynamically tuned. PMID:23184936

Dose reduction for abdominal and pelvic MDCT after change to graduated weight-based protocol for selecting quality reference tube current, peak kilovoltage, and slice collimation.

PubMed

Herts, Brian R; Baker, Mark E; Obuchowski, Nancy; Primak, Andrew; Schneider, Erika; Rhana, Harpreet; Dong, Frank

2013-06-01

The purpose of this article is to determine the decrease in volume CT dose index (CTDI(vol)) and dose-length product (DLP) achieved by switching from fixed quality reference tube current protocols with automatic tube current modulation to protocols adjusting the quality reference tube current, slice collimation, and peak kilovoltage according to patient weight. All adult patients who underwent CT examinations of the abdomen or abdomen and pelvis during 2010 using weight-based protocols who also underwent a CT examination in 2008 or 2009 using fixed quality reference tube current protocols were identified from the radiology information system. Protocol pages were electronically retrieved, and the CT model, examination date, scan protocol, CTDI(vol), and DLP were extracted from the DICOM header or by optical character recognition. There were 15,779 scans with dose records for 2700 patients. Changes in CTDI(vol) and DLP were compared only between examinations of the same patient and same CT system model for examinations performed in 2008 or 2009 and those performed in 2010. The final analysis consisted of 1117 comparisons in 1057 patients, and 1209 comparisons in 988 patients for CTDI(vol) and DLP, respectively. The change to a weight-based protocol resulted in a statistically significant reduction in CTDI(vol) and DLP on three MDCT system models (p < 0.001). The largest average CTDI(vol) decrease was 13.9%, and the largest average DLP decrease was 16.1% on a 64-MDCT system. Both the CTDI(vol) and DLP decreased the most for patients who weighed less than 250 lb (112.5 kg). Adjusting the CT protocol by selecting parameters according to patient weight is a viable method for reducing CT radiation dose. The largest reductions occurred in the patients weighing less than 250 lb.

Seminal plasma affects sperm sex sorting in boars.

PubMed

Alkmin, Diego V; Parrilla, Inmaculada; Tarantini, Tatiana; Del Olmo, David; Vazquez, Juan M; Martinez, Emilio A; Roca, Jordi

2016-04-01

Two experiments were conducted in boar semen samples to evaluate how both holding time (24h) and the presence of seminal plasma (SP) before sorting affect sperm sortability and the ability of sex-sorted spermatozoa to tolerate liquid storage. Whole ejaculate samples were divided into three aliquots immediately after collection: one was diluted (1:1, v/v) in Beltsville thawing solution (BTS; 50% SP); the SP of the other two aliquots was removed and the sperm pellets were diluted with BTS + 10% of their own SP (10% SP) or BTS alone (0% SP). The three aliquots of each ejaculate were divided into two portions, one that was processed immediately for sorting and a second that was sorted after 24h storage at 15-17°C. In the first experiment, the ability to exhibit well-defined X- and Y-chromosome-bearing sperm peaks (split) in the cytometry histogram and the subsequent sorting efficiency were assessed (20 ejaculates). In contrast with holding time, the SP proportion influenced the parameters examined, as evidenced by the higher number of ejaculates exhibiting split and better sorting efficiency (P<0.05) in semen samples with 0-10% SP compared with those with 50% SP. In a second experiment, the quality (viability, total and progressive motility) and functionality (plasma membrane fluidity and intracellular generation of reactive oxygen species) of sex-sorted spermatozoa were evaluated after 0, 72 and 120h storage at 15-17°C (10 ejaculates). Holding time and SP proportion did not influence the quality or functionality of stored sex-sorted spermatozoa. In conclusion, a holding time as long as 24h before sorting did not negatively affect sex sorting efficiency or the ability of sorted boar spermatozoa to tolerate long-term liquid storage. A high proportion of SP (50%) in the semen samples before sorting reduced the number of ejaculates to be sorted and negatively influenced the sorting efficiency, but did not affect the ability of sex-sorted spermatozoa to tolerate liquid storage.

Types and Frequency of Infusion Pump Alarms: Protocol for a Retrospective Data Analysis.

PubMed

Glover, Kevin R; Vitoux, Rachel R; Schuster, Catherine; Curtin, Christopher R

2018-06-14

The variety of alarms from all types of medical devices has increased from 6 to 40 in the last three decades, with today's most critically ill patients experiencing as many as 45 alarms per hour. Alarm fatigue has been identified as a critical safety issue for clinical staff that can lead to potentially dangerous delays or nonresponse to actionable alarms, resulting in serious patient injury and death. To date, most research on medical device alarms has focused on the nonactionable alarms of physiological monitoring devices. While there have been some reports in the literature related to drug library alerts during the infusion pump programing sequence, research related to the types and frequencies of actionable infusion pump alarms remains largely unexplored. The objectives of this study protocol are to establish baseline data related to the types and frequency of infusion pump alarms from the B. Braun Outlook 400ES Safety Infusion System with the accompanying DoseTrac Infusion Management Software. The most recent consecutive 60-day period of backup hospital data received between April 2014 and February 2017 from 32 United States-based hospitals will be selected for analysis. Microsoft SQL Server (2012 - 11.0.5343.0 X64) will be used to manage the data with unique code written to sort data and perform descriptive analyses. A validated data management methodology will be utilized to clean and analyze the data. Data management procedures will include blinding, cleaning, and review of existing infusion data within the DoseTrac Infusion Management Software databases at each hospital. Patient-identifying data will be removed prior to merging into a dedicated and secure data repository. This pooled data will then be analyzed. This exploratory study will analyze the aggregate alarm data for each hospital by care area, drug infused, time of day, and day of week, including: overall infusion pump alarm frequency (number of alarms per active infusion), duration of alarms (average, range, median), and type and frequency of alarms distributed by care area. Infusion pump alarm data collected and analyzed in this study will be used to help establish a baseline of infusion pump alarm types and relative frequencies. Understanding the incidences and characteristics of infusion pump alarms will result in more informed quality improvement recommendations to decrease and/or modify infusion pump alarms, and potentially reduce clinical staff alarm fatigue and improve patient safety. . RR1-10.2196/10446. ©Kevin R Glover, Rachel R Vitoux, Catherine Schuster, Christopher R Curtin. Originally published in JMIR Research Protocols (http://www.researchprotocols.org), 14.06.2018.

[Norm study of occupational stress on the professionals in Chengdu and Chongqing area].

PubMed

Zeng, Fan-Hua; Wang, Zhi-Ming; Wang, Mian-Zhen; Lan, Ya-Jia

2004-12-01

To establish the norm of occupational stress on the professionals in Chengdu and Chongqing area. According to the "Occupation Sorting Canon in the People's Republic of China", the professionals of the above-mentioned area were sorted out and randomly stratified. The normative data were derived from a sample of 2 064 participants. The modified Occupation Stress Inventory Revised Edition (OSI-R) was used to test the targets' occupational stress level (including stressors, strain and coping resources). (1) In these professionals, the sex ratio was about 1:1, average age (36.4 +/- 9.4) years, average length of service (15.9 +/- 10.0) years, 63.07% people were college educated and over 80% married. (2) Descriptive statistics for OSI-R scale scores for the total normative sample, for gender samples and for occupational group samples were modulated. (3) The gender norm showed that there were heavier role overload and stronger occupational strains in males than those in females (P < 0.01). The score of personal resources in the males was not different from that in females (P > 0.05). (4) In terms of different occupations, the scores of occupational role and personal strain among various groups indicated significant differences (P < 0.01). The score of personal resources did not manifest difference (P > 0.05). (5) The major factors influencing OSI-R were sex, occupation and length of service. The norm established can basically represent the occupational stress on professionals in Chengdu and Chongqing area.

Purification of Bone Marrow Clonal Cells from Patients with Myelodysplastic Syndrome via IGF-IR

PubMed Central

He, Qi; Chang, Chun-Kang; Xu, Feng; Zhang, Qing-Xia; Shi, Wen-Hui; Li, Xiao

2015-01-01

Malignant clonal cells purification can greatly benefit basic and clinical studies in myelodysplastic syndrome (MDS). In this study, we investigated the potential of using type 1 insulin-like growth factor receptor (IGF-IR) as a marker for purification of malignant bone marrow clonal cells from patients with MDS. The average percentage of IGF-IR expression in CD34+ bone marrow cells among 15 normal controls was 4.5%, 70% of which also express the erythroid lineage marker CD235a. This indicates that IGF-IR mainly express in erythropoiesis. The expression of IGF-IR in CD34+ cells of 55 MDS patients was significantly higher than that of cells from the normal controls (54.0 vs. 4.5%). Based on the pattern of IGF-IR expression in MDS patients and normal controls, sorting of IGF-IR-positive and removal of CD235a-positive erythroid lineage cells with combination of FISH detection were performed on MDS samples with chromosomal abnormalities. The percentage of malignant clonal cells significantly increased after sorting. The enrichment effect was more significant in clonal cells with a previous percentage lower than 50%. This enrichment effect was present in samples from patients with +8, 5q-/-5, 20q-/-20 or 7q-/-7 chromosomal abnormalities. These data suggest that IGF-IR can be used as a marker for MDS bone marrow clonal cells and using flow cytometry for positive IGF-IR sorting may effectively purify MDS clonal cells. PMID:26469401

Stochastic Model of Vesicular Sorting in Cellular Organelles

NASA Astrophysics Data System (ADS)

Vagne, Quentin; Sens, Pierre

2018-02-01

The proper sorting of membrane components by regulated exchange between cellular organelles is crucial to intracellular organization. This process relies on the budding and fusion of transport vesicles, and should be strongly influenced by stochastic fluctuations, considering the relatively small size of many organelles. We identify the perfect sorting of two membrane components initially mixed in a single compartment as a first passage process, and we show that the mean sorting time exhibits two distinct regimes as a function of the ratio of vesicle fusion to budding rates. Low ratio values lead to fast sorting but result in a broad size distribution of sorted compartments dominated by small entities. High ratio values result in two well-defined sorted compartments but sorting is exponentially slow. Our results suggest an optimal balance between vesicle budding and fusion for the rapid and efficient sorting of membrane components and highlight the importance of stochastic effects for the steady-state organization of intracellular compartments.

Identification and genetic analysis of cancer cells with PCR-activated cell sorting

PubMed Central

Eastburn, Dennis J.; Sciambi, Adam; Abate, Adam R.

2014-01-01

Cell sorting is a central tool in life science research for analyzing cellular heterogeneity or enriching rare cells out of large populations. Although methods like FACS and FISH-FC can characterize and isolate cells from heterogeneous populations, they are limited by their reliance on antibodies, or the requirement to chemically fix cells. We introduce a new cell sorting technology that robustly sorts based on sequence-specific analysis of cellular nucleic acids. Our approach, PCR-activated cell sorting (PACS), uses TaqMan PCR to detect nucleic acids within single cells and trigger their sorting. With this method, we identified and sorted prostate cancer cells from a heterogeneous population by performing >132 000 simultaneous single-cell TaqMan RT-PCR reactions targeting vimentin mRNA. Following vimentin-positive droplet sorting and downstream analysis of recovered nucleic acids, we found that cancer-specific genomes and transcripts were significantly enriched. Additionally, we demonstrate that PACS can be used to sort and enrich cells via TaqMan PCR reactions targeting single-copy genomic DNA. PACS provides a general new technical capability that expands the application space of cell sorting by enabling sorting based on cellular information not amenable to existing approaches. PMID:25030902

Robust Characterization of Loss Rates

NASA Astrophysics Data System (ADS)

Wallman, Joel J.; Barnhill, Marie; Emerson, Joseph

2015-08-01

Many physical implementations of qubits—including ion traps, optical lattices and linear optics—suffer from loss. A nonzero probability of irretrievably losing a qubit can be a substantial obstacle to fault-tolerant methods of processing quantum information, requiring new techniques to safeguard against loss that introduce an additional overhead that depends upon the loss rate. Here we present a scalable and platform-independent protocol for estimating the average loss rate (averaged over all input states) resulting from an arbitrary Markovian noise process, as well as an independent estimate of detector efficiency. Moreover, we show that our protocol gives an additional constraint on estimated parameters from randomized benchmarking that improves the reliability of the estimated error rate and provides a new indicator for non-Markovian signatures in the experimental data. We also derive a bound for the state-dependent loss rate in terms of the average loss rate.

Development of Information Assurance Protocol for Low Bandwidth Nanosatellite Communications

DTIC Science & Technology

2017-09-01

INFORMATION ASSURANCE PROTOCOL FOR LOW BANDWIDTH NANOSATELLITE COMMUNICATIONS by Cervando A. Banuelos II September 2017 Thesis Advisor...reporting burden for this collection of information is estimated to average 1 hour per response, including the time for reviewing instruction...searching existing data sources, gathering and maintaining the data needed, and completing and reviewing the collection of information . Send comments

Building America House Simulation Protocols

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

Hendron, Robert; Engebrecht, Cheryn

2010-09-01

The House Simulation Protocol document was developed to track and manage progress toward Building America's multi-year, average whole-building energy reduction research goals for new construction and existing homes, using a consistent analytical reference point. This report summarizes the guidelines for developing and reporting these analytical results in a consistent and meaningful manner for all home energy uses using standard operating conditions.

VehiHealth: An Emergency Routing Protocol for Vehicular Ad Hoc Network to Support Healthcare System.

PubMed

Bhoi, S K; Khilar, P M

2016-03-01

Survival of a patient depends on effective data communication in healthcare system. In this paper, an emergency routing protocol for Vehicular Ad hoc Network (VANET) is proposed to quickly forward the current patient status information from the ambulance to the hospital to provide pre-medical treatment. As the ambulance takes time to reach the hospital, ambulance doctor can provide sudden treatment to the patient in emergency by sending patient status information to the hospital through the vehicles using vehicular communication. Secondly, the experienced doctors respond to the information by quickly sending a treatment information to the ambulance. In this protocol, data is forwarded through that path which has less link breakage problem between the vehicles. This is done by calculating an intersection value I v a l u e for the neighboring intersections by using the current traffic information. Then the data is forwarded through that intersection which has minimum I v a l u e . Simulation results show VehiHealth performs better than P-GEDIR, GyTAR, A-STAR and GSR routing protocols in terms of average end-to-end delay, number of link breakage, path length, and average response time.

Evaluation of motility, membrane status and DNA integrity of frozen-thawed bottlenose dolphin (Tursiops truncatus) spermatozoa after sex-sorting and recryopreservation.

PubMed

Montano, G A; Kraemer, D C; Love, C C; Robeck, T R; O'Brien, J K

2012-06-01

Artificial insemination (AI) with sex-sorted frozen-thawed spermatozoa has led to enhanced management of ex situ bottlenose dolphin populations. Extended distance of animals from the sorting facility can be overcome by the use of frozen-thawed, sorted and recryopreserved spermatozoa. Although one bottlenose dolphin calf had been born using sexed frozen-thawed spermatozoa derived from frozen semen, a critical evaluation of in vitro sperm quality is needed to justify the routine use of such samples in AI programs. Sperm motility parameters and plasma membrane integrity were influenced by stage of the sex-sorting process, sperm type (non-sorted and sorted) and freezing method (straw and directional) (P<0.05). After recryopreservation, sorted spermatozoa frozen with the directional freezing method maintained higher (P<0.05) motility parameters over a 24-h incubation period compared to spermatozoa frozen using straws. Quality of sperm DNA of non-sorted spermatozoa, as assessed by the sperm chromatin structure assay (SCSA), was high and remained unchanged throughout freeze-thawing and incubation processes. Though a possible interaction between Hoechst 33342 and the SCSA-derived acridine orange was observed in stained and sorted samples, the proportion of sex-sorted, recryopreserved spermatozoa exhibiting denatured DNA was low (6.6±4.1%) at 6 h after the second thawing step and remained unchanged (P>0.05) at 24 h. The viability of sorted spermatozoa was higher (P<0.05) than that of non-sorted spermatozoa across all time points after recryopreservation. Collective results indicate that bottlenose dolphin spermatozoa undergoing cryopreservation, sorting and recryopreservation are of adequate quality for use in AI.

Static stretching vs. dynamic warm-ups: a comparison of their effects on torque and electromyography output of the quadriceps and hamstring muscles.

PubMed

Williams, N; Coburn, J; Gillum, T

2015-11-01

The aim of this paper was to determine if two different warm-up protocols differently affect torque of the quadriceps and hamstrings, and electromyography (EMG) output of the rectus femoris (RF) and vastus lateralis (VL) when completing 30 maximal leg extensions and curls. Twenty-one healthy male (N.=8) and female (N.=13) subjects volunteered to participate in a familiarization session and three testing sessions. The three testing sessions control, dynamic, and static were completed in a counterbalanced order on non-consecutive days. First, subjects warmed-up on a treadmill for five minutes before completing six dynamic movements, six static-stretches, or no stretches. They then rested for five minutes before completing 30 maximal leg extensions and curls at a speed of 60 s-1. A significant decrease in quadriceps torque output over time was determined for the dynamic protocol when compared to the control (P<0.01) and static (P<0.05) protocols. A significant decrease was found in peak quadriceps torque for the dynamic protocol (P<0.01) when compared to the static, and a significant increase was found for the static protocol (P<0.05) when compared to the control. A significant decrease in average quadriceps torque was found for the dynamic protocol when compared to the static (P<0.05) and control (P<0.01) protocols. No difference was found in hamstring torque or EMG output of the RF and VL. Short duration static-stretching has the ability to increase peak and average torque of the leg extensors, while some types of anaerobic exercise involving maximal contractions to fatigue may be hindered by performing dynamic movements as part of the warm-up.

Titrating Oxygen Requirements During Exercise: Evaluation of a Standardized Single Walk Test Protocol.

PubMed

Giovacchini, Coral X; Mathews, Anne M; Lawlor, Brian R; MacIntyre, Neil R

2018-04-01

Oxygen supplementation for exercise-induced hypoxemia is a common clinical practice that improves exercise tolerance. However, we know of no standardized exercise oxygen titration protocol using a single walk test. We report our experience with a protocol developed in our laboratory. Our protocol is based on the 6-min walk test (6MWT). Pulse oximetry readings (oxygen saturation [Spo 2 ]) are monitored, and supplemental oxygen is added in 2 L/min increments to keep Spo 2 > 88%. This continues for at least 6 min of walking with the Spo 2 remaining > 88% for at least 3 min. The records of consecutive patients over 4 months undergoing this procedure were reviewed for test performance, oxygen titration results, and adverse events. Two hundred twenty-two patients were tested; only two prematurely terminated the protocol because of intractable dyspnea. One hundred fifty-six patients (38%) required oxygen supplementation, with the first titration most commonly occurring between 1 and 2 min of walking. Nine of the patients had the first titration after 5 min of walking. The average test duration was 7 min (maximum, 15 min). The average number of titrations was 2.2 (maximum six). Sixteen patients could not maintain Spo 2 > 88% for 3 min despite administration of 15 L/min of supplemental oxygen (maximal dose). Our protocol was easily performed as a modification of a standard 6MWT with no serious adverse events. Because it is based on a widely accepted measurement of functional capabilities, and because it determined a stable final oxygen dose for ≥ 3 min of walking in most patients, we believe this protocol can be easily adapted for clinical use. Copyright © 2017 American College of Chest Physicians. Published by Elsevier Inc. All rights reserved.

Response of bed surface patchiness to reductions in sediment supply

NASA Astrophysics Data System (ADS)

Nelson, Peter A.; Venditti, Jeremy G.; Dietrich, William E.; Kirchner, James W.; Ikeda, Hiroshi; Iseya, Fujiko; Sklar, Leonard S.

2009-06-01

River beds are often arranged into patches of similar grain size and sorting. Patches can be distinguished into "free patches," which are zones of sorted material that move freely, such as bed load sheets; "forced patches," which are areas of sorting forced by topographic controls; and "fixed patches" of bed material rendered immobile through localized coarsening that remain fairly persistent through time. Two sets of flume experiments (one using bimodal, sand-rich sediment and the other using unimodal, sand-free sediment) are used to explore how fixed and free patches respond to stepwise reductions in sediment supply. At high sediment supply, migrating bed load sheets formed even in unimodal, sand-free sediment, yet grain interactions visibly played a central role in their formation. In both sets of experiments, reductions in supply led to the development of fixed coarse patches, which expanded at the expense of finer, more mobile patches, narrowing the zone of active bed load transport and leading to the eventual disappearance of migrating bed load sheets. Reductions in sediment supply decreased the migration rate of bed load sheets and increased the spacing between successive sheets. One-dimensional morphodynamic models of river channel beds generally are not designed to capture the observed variability, but should be capable of capturing the time-averaged character of the channel. When applied to our experiments, a 1-D morphodynamic model (RTe-bookAgDegNormGravMixPW.xls) predicted the bed load flux well, but overpredicted slope changes and was unable to predict the substantial variability in bed load flux (and load grain size) because of the migration of mobile patches. Our results suggest that (1) the distribution of free and fixed patches is primarily a function of sediment supply, (2) the dynamics of bed load sheets are primarily scaled by sediment supply, (3) channels with reduced sediment supply may inherently be unable to transport sediment uniformly across their width, and (4) cross-stream variability in shear stress and grain size can produce potentially large errors in width-averaged sediment flux calculations.

Sampling solution traces for the problem of sorting permutations by signed reversals

PubMed Central

2012-01-01

Background Traditional algorithms to solve the problem of sorting by signed reversals output just one optimal solution while the space of all optimal solutions can be huge. A so-called trace represents a group of solutions which share the same set of reversals that must be applied to sort the original permutation following a partial ordering. By using traces, we therefore can represent the set of optimal solutions in a more compact way. Algorithms for enumerating the complete set of traces of solutions were developed. However, due to their exponential complexity, their practical use is limited to small permutations. A partial enumeration of traces is a sampling of the complete set of traces and can be an alternative for the study of distinct evolutionary scenarios of big permutations. Ideally, the sampling should be done uniformly from the space of all optimal solutions. This is however conjectured to be ♯P-complete. Results We propose and evaluate three algorithms for producing a sampling of the complete set of traces that instead can be shown in practice to preserve some of the characteristics of the space of all solutions. The first algorithm (RA) performs the construction of traces through a random selection of reversals on the list of optimal 1-sequences. The second algorithm (DFALT) consists in a slight modification of an algorithm that performs the complete enumeration of traces. Finally, the third algorithm (SWA) is based on a sliding window strategy to improve the enumeration of traces. All proposed algorithms were able to enumerate traces for permutations with up to 200 elements. Conclusions We analysed the distribution of the enumerated traces with respect to their height and average reversal length. Various works indicate that the reversal length can be an important aspect in genome rearrangements. The algorithms RA and SWA show a tendency to lose traces with high average reversal length. Such traces are however rare, and qualitatively our results show that, for testable-sized permutations, the algorithms DFALT and SWA produce distributions which approximate the reversal length distributions observed with a complete enumeration of the set of traces. PMID:22704580

MO-F-CAMPUS-J-03: Sorting 2D Dynamic MR Images Using Internal Respiratory Signal for 4D MRI

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

Wen, Z; Hui, C; Beddar, S

Purpose: To develop a novel algorithm to extract internal respiratory signal (IRS) for sorting dynamic magnetic resonance (MR) images in order to achieve four-dimensional (4D) MR imaging. Methods: Dynamic MR images were obtained with the balanced steady state free precession by acquiring each two-dimensional sagittal slice repeatedly for more than one breathing cycle. To generate a robust IRS, we used 5 different representative internal respiratory surrogates in both the image space (body area) and the Fourier space (the first two low-frequency phase components in the anterior-posterior direction, and the first two low-frequency phase components in the superior-inferior direction). A clusteringmore » algorithm was then used to search for a group of similar individual internal signals, which was then used to formulate the final IRS. A phantom study and a volunteer study were performed to demonstrate the effectiveness of this algorithm. The IRS was compared to the signal from the respiratory bellows. Results: The IRS computed by our algorithm matched well with the bellows signal in both the phantom and the volunteer studies. On average, the normalized cross correlation between the IRS and the bellows signal was 0.97 in the phantom study and 0.87 in the volunteer study, respectively. The average difference between the end inspiration times in the IRS and bellows signal was 0.18 s in the phantom study and 0.14 s in the volunteer study, respectively. 4D images sorted based on the IRS showed minimal mismatched artifacts, and the motion of the anatomy was coherent with the respiratory phases. Conclusion: A novel algorithm was developed to generate IRS from dynamic MR images to achieve 4D MR imaging. The performance of the IRS was comparable to that of the bellows signal. It can be easily implemented into the clinic and potentially could replace the use of external respiratory surrogates. This research was partially funded by the the Center for Radiation Oncology Research from UT MD Anderson Cancer Center.« less

Clock Scan Protocol for Image Analysis: ImageJ Plugins.

PubMed

Dobretsov, Maxim; Petkau, Georg; Hayar, Abdallah; Petkau, Eugen

2017-06-19

The clock scan protocol for image analysis is an efficient tool to quantify the average pixel intensity within, at the border, and outside (background) a closed or segmented convex-shaped region of interest, leading to the generation of an averaged integral radial pixel-intensity profile. This protocol was originally developed in 2006, as a visual basic 6 script, but as such, it had limited distribution. To address this problem and to join similar recent efforts by others, we converted the original clock scan protocol code into two Java-based plugins compatible with NIH-sponsored and freely available image analysis programs like ImageJ or Fiji ImageJ. Furthermore, these plugins have several new functions, further expanding the range of capabilities of the original protocol, such as analysis of multiple regions of interest and image stacks. The latter feature of the program is especially useful in applications in which it is important to determine changes related to time and location. Thus, the clock scan analysis of stacks of biological images may potentially be applied to spreading of Na + or Ca ++ within a single cell, as well as to the analysis of spreading activity (e.g., Ca ++ waves) in populations of synaptically-connected or gap junction-coupled cells. Here, we describe these new clock scan plugins and show some examples of their applications in image analysis.

A Binary Array Asynchronous Sorting Algorithm with Using Petri Nets

NASA Astrophysics Data System (ADS)

Voevoda, A. A.; Romannikov, D. O.

2017-01-01

Nowadays the tasks of computations speed-up and/or their optimization are actual. Among the approaches on how to solve these tasks, a method applying approaches of parallelization and asynchronization to a sorting algorithm is considered in the paper. The sorting methods are ones of elementary methods and they are used in a huge amount of different applications. In the paper, we offer a method of an array sorting that based on a division into a set of independent adjacent pairs of numbers and their parallel and asynchronous comparison. And this one distinguishes the offered method from the traditional sorting algorithms (like quick sorting, merge sorting, insertion sorting and others). The algorithm is implemented with the use of Petri nets, like the most suitable tool for an asynchronous systems description.

A Quality Sorting of Fruit Using a New Automatic Image Processing Method

NASA Astrophysics Data System (ADS)

Amenomori, Michihiro; Yokomizu, Nobuyuki

This paper presents an innovative approach for quality sorting of objects such as apples sorting in an agricultural factory, using an image processing algorithm. The objective of our approach are; firstly to sort the objects by their colors precisely; secondly to detect any irregularity of the colors surrounding the apples efficiently. An experiment has been conducted and the results have been obtained and compared with that has been preformed by human sorting process and by color sensor sorting devices. The results demonstrate that our approach is capable to sort the objects rapidly and the percentage of classification valid rate was 100 %.

TU-F-17A-04: Respiratory Phase-Resolved 3D MRI with Isotropic High Spatial Resolution: Determination of the Average Breathing Motion Pattern for Abdominal Radiotherapy Planning

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

Deng, Z; Pang, J; Yang, W

Purpose: To develop a retrospective 4D-MRI technique (respiratory phase-resolved 3D-MRI) for providing an accurate assessment of tumor motion secondary to respiration. Methods: A 3D projection reconstruction (PR) sequence with self-gating (SG) was developed for 4D-MRI on a 3.0T MRI scanner. The respiration-induced shift of the imaging target was recorded by SG signals acquired in the superior-inferior direction every 15 radial projections (i.e. temporal resolution 98 ms). A total of 73000 radial projections obtained in 8-min were retrospectively sorted into 10 time-domain evenly distributed respiratory phases based on the SG information. Ten 3D image sets were then reconstructed offline. The techniquemore » was validated on a motion phantom (gadolinium-doped water-filled box, frequency of 10 and 18 cycles/min) and humans (4 healthy and 2 patients with liver tumors). Imaging protocol included 8-min 4D-MRI followed by 1-min 2D-realtime (498 ms/frame) MRI as a reference. Results: The multiphase 3D image sets with isotropic high spatial resolution (1.56 mm) permits flexible image reformatting and visualization. No intra-phase motion-induced blurring was observed. Comparing to 2D-realtime, 4D-MRI yielded similar motion range (phantom: 10.46 vs. 11.27 mm; healthy subject: 25.20 vs. 17.9 mm; patient: 11.38 vs. 9.30 mm), reasonable displacement difference averaged over the 10 phases (0.74mm; 3.63mm; 1.65mm), and excellent cross-correlation (0.98; 0.96; 0.94) between the two displacement series. Conclusion: Our preliminary study has demonstrated that the 4D-MRI technique can provide high-quality respiratory phase-resolved 3D images that feature: a) isotropic high spatial resolution, b) a fixed scan time of 8 minutes, c) an accurate estimate of average motion pattern, and d) minimal intra-phase motion artifact. This approach has the potential to become a viable alternative solution to assess the impact of breathing on tumor motion and determine appropriate treatment margins. Comparison with 4D-CT in a clinical setting is warranted to assess the value of 4D-MRI in radiotherapy planning. This work supported in part by grant 1R03CA173273-01.« less

Large-Scale Expansion of Human iPSC-Derived Skeletal Muscle Cells for Disease Modeling and Cell-Based Therapeutic Strategies.

PubMed

van der Wal, Erik; Herrero-Hernandez, Pablo; Wan, Raymond; Broeders, Mike; In 't Groen, Stijn L M; van Gestel, Tom J M; van IJcken, Wilfred F J; Cheung, Tom H; van der Ploeg, Ans T; Schaaf, Gerben J; Pijnappel, W W M Pim

2018-06-05

Although skeletal muscle cells can be generated from human induced pluripotent stem cells (iPSCs), transgene-free protocols include only limited options for their purification and expansion. In this study, we found that fluorescence-activated cell sorting-purified myogenic progenitors generated from healthy controls and Pompe disease iPSCs can be robustly expanded as much as 5 × 10 11 -fold. At all steps during expansion, cells could be cryopreserved or differentiated into myotubes with a high fusion index. In vitro, cells were amenable to maturation into striated and contractile myofibers. Insertion of acid α-glucosidase cDNA into the AAVS1 locus in iPSCs using CRISPR/Cas9 prevented glycogen accumulation in myotubes generated from a patient with classic infantile Pompe disease. In vivo, the expression of human-specific nuclear and sarcolemmar antigens indicated that myogenic progenitors engraft into murine muscle to form human myofibers. This protocol is useful for modeling of skeletal muscle disorders and for using patient-derived, gene-corrected cells to develop cell-based strategies. Copyright © 2018 The Author(s). Published by Elsevier Inc. All rights reserved.

Photostick: a method for selective isolation of target cells from culture† †Electronic supplementary information (ESI) available. See DOI: 10.1039/c4sc03676j Click here for additional data file.

PubMed Central

Chien, Miao-Ping; Werley, Christopher A.; Farhi, Samouil L.

2015-01-01

Sorting of target cells from a heterogeneous pool is technically difficult when the selection criterion is complex, e.g. a dynamic response, a morphological feature, or a combination of multiple parameters. At present, mammalian cell selections are typically performed either via static fluorescence (e.g. fluorescence activated cell sorter), via survival (e.g. antibiotic resistance), or via serial operations (flow cytometry, laser capture microdissection). Here we present a simple protocol for selecting cells based on any static or dynamic property that can be identified by video microscopy and image processing. The “photostick” technique uses a cell-impermeant photochemical crosslinker and digital micromirror array-based patterned illumination to immobilize selected cells on the culture dish. Other cells are washed away with mild protease treatment. The crosslinker also labels the selected cells with a fluorescent dye and a biotin for later identification. The photostick protocol preserves cell viability, permits genetic profiling of selected cells, and can be performed with complex functional selection criteria such as neuronal firing patterns. PMID:25705368

Small bowel obstruction: A practical step-by-step evidence-based approach to evaluation, decision making, and management.

PubMed

Azagury, Dan; Liu, Rockson C; Morgan, Ashley; Spain, David A

2015-10-01

The initial goal of evaluating a patient with SBO is to immediately identify strangulation and need for urgent operative intervention, concurrent with rapid resuscitation. This relies on a combination of traditional clinical signs and CT findings. In patients without signs of strangulation, a protocol for administration of Gastrografin immediately in the emergency department efficiently sorts patients into those who will resolve their obstructions and those who will fail nonoperative management.Furthermore, because of the unique ability of Gastrografin to draw water into the bowel lumen, it expedites resolution of partial obstructions, shortening time to removal of nasogastric tube liberalization of diet, and discharge from the hospital. Implementation of such a protocol is a complex, multidisciplinary, and time-consuming endeavor. As such, we cannot over emphasize the importance of clear, open communication with everyone involved.If surgical management is warranted, we encourage an initial laparoscopic approach with open access. Even if this results in immediate conversion to laparotomy after assessment of the intra-abdominal status, we encourage this approach with a goal of 30% conversion rate or higher. This will attest that patients will have been given the highest likelihood of a successful laparoscopic LOA.

Performance evaluation of firefly algorithm with variation in sorting for non-linear benchmark problems

NASA Astrophysics Data System (ADS)

Umbarkar, A. J.; Balande, U. T.; Seth, P. D.

2017-06-01

The field of nature inspired computing and optimization techniques have evolved to solve difficult optimization problems in diverse fields of engineering, science and technology. The firefly attraction process is mimicked in the algorithm for solving optimization problems. In Firefly Algorithm (FA) sorting of fireflies is done by using sorting algorithm. The original FA is proposed with bubble sort for ranking the fireflies. In this paper, the quick sort replaces bubble sort to decrease the time complexity of FA. The dataset used is unconstrained benchmark functions from CEC 2005 [22]. The comparison of FA using bubble sort and FA using quick sort is performed with respect to best, worst, mean, standard deviation, number of comparisons and execution time. The experimental result shows that FA using quick sort requires less number of comparisons but requires more execution time. The increased number of fireflies helps to converge into optimal solution whereas by varying dimension for algorithm performed better at a lower dimension than higher dimension.

Data-driven CT protocol review and management—experience from a large academic hospital.

PubMed

Zhang, Da; Savage, Cristy A; Li, Xinhua; Liu, Bob

2015-03-01

Protocol review plays a critical role in CT quality assurance, but large numbers of protocols and inconsistent protocol names on scanners and in exam records make thorough protocol review formidable. In this investigation, we report on a data-driven cataloging process that can be used to assist in the reviewing and management of CT protocols. We collected lists of scanner protocols, as well as 18 months of recent exam records, for 10 clinical scanners. We developed computer algorithms to automatically deconstruct the protocol names on the scanner and in the exam records into core names and descriptive components. Based on the core names, we were able to group the scanner protocols into a much smaller set of "core protocols," and to easily link exam records with the scanner protocols. We calculated the percentage of usage for each core protocol, from which the most heavily used protocols were identified. From the percentage-of-usage data, we found that, on average, 18, 33, and 49 core protocols per scanner covered 80%, 90%, and 95%, respectively, of all exams. These numbers are one order of magnitude smaller than the typical numbers of protocols that are loaded on a scanner (200-300, as reported in the literature). Duplicated, outdated, and rarely used protocols on the scanners were easily pinpointed in the cataloging process. The data-driven cataloging process can facilitate the task of protocol review. Copyright © 2015 American College of Radiology. Published by Elsevier Inc. All rights reserved.

CFTLB: a novel cross-layer fault tolerant and load balancing protocol for WMN

NASA Astrophysics Data System (ADS)

Krishnaveni, N. N.; Chitra, K.

2017-12-01

Wireless mesh network (WMN) forms a wireless backbone framework for multi-hop transmission among the routers and clients in the extensible coverage area. To improve the throughput of WMNs with multiple gateways (GWs), several issues related to GW selection, load balancing and frequent link failures due to the presence of dynamic obstacles and channel interference should be addressed. This paper presents a novel cross-layer fault tolerant and load balancing (CFTLB) protocol to overcome the issues in WMN. Initially, the neighbour GW is searched and channel load is calculated. The GW having least channel load is selected which is estimated during the arrival of the new node. The proposed algorithm finds the alternate GWs and calculates the channel availability under high loading scenarios. If the current load in the GW is high, another GW is found and channel availability is calculated. Besides, it initiates the channel switching and establishes the communication with the mesh client effectively. The utilisation of hashing technique in proposed CFTLB verifies the status of the packets and achieves better performance in terms of router average throughput, throughput, average channel access time and lower end-to-end delay, communication overhead and average data loss in the channel compared to the existing protocols.

[Treatment of Alcohol Withdrawal Syndrome with Oxazepam or Clomethiazole - A Naturalistic Observational Study].

PubMed

Verthein, Uwe; Kuhn, Silke; Gabriel, Katrin; Mautsch, Ulrich; Reimer, Jens; Behrendt, Klaus

2018-03-01

Whilst internationally benzodiazepines are first choice for treatment of alcohol withdrawal syndrome, Germany has a long tradition with clomethiazole. This study explores effectiveness of clomethiazole versus oxazepam in the treatment of alcohol withdrawal syndrome within an observational, stratified, non-inferiority study in routine care. Main outcome criterion was severity of the alcohol withdrawal syndrome (Alcohol Withdrawal Syndrome [AWS]) Scale in the first five days. Additionally, the association between the detoxification protocol (five vs. ten days) and AWS-Score was examined. 453 patients (74.2 % male, average age 47.1 years [± 9.2]) took part; 249 received oxazepam (55.0 %) and 204 clomethiazole (45.0 %). The average duration of inpatient treatment was 14.0 days (± 6.3) in both groups. The average AWS-score was lower in the oxazepam group compared to the clomethiazole group (50.0 [± 26.5] vs. 56.2 [± 31.5]; p < .05; effect size d = - .25). Patients with a shorter detoxification protocol had a lower AWS sum score compared to patients with a longer protocol (p < .001; d = - .46). In treatment of alcohol withdrawal syndrome in routine care oxazepam yields at least comparable results to clomethiazole. © Georg Thieme Verlag KG Stuttgart · New York.

Nanomedicine for prostate cancer using nanoemulsion: A review.

PubMed

Sasikumar, Aravindsiva; Kamalasanan, Kaladhar

2017-08-28

Prostate cancer (PCa) is a worldwide issue, with burgeoning rise in prevalence, morbidity and mortality. Targeted drug delivery, a long sort solution in this regard using controlled release (CR) - nanocarriers, is still a challenge. There is an emerging criticism that, the challenges are due to less appreciation for the biological barriers and lack of corresponding newer technologies. Over the years, more understanding about the biological barriers has come with the progress in characterization techniques. Correspondingly, there is a change in opinion about approaches in clinical trial that; focus of the end point need to be shifted towards disease stabilization for these explorative technologies. Currently, there is a requirement to overcome these newly identified challenges to develop newer affordable therapeutics. The ongoing clinical protocol for therapy using CR-nanocarriers is intravenous injection followed by local targeting to cancer site. This is the most accepted protocol and new CR-nanocarriers are being developed to suit this protocol. In this review, recent progress in treatment of PCa using CR-nanocarriers is analyzed with respect to newly identified biological barriers and design challenges. Possibilities of exploring nanoemulsion (NE) platform for targeted drug delivery to PCa are examined. Repurposing of drugs and combination therapy using NE platform targeted to PCa can be explored for design and development of affordable nanomedicine. In 20yrs. from now there expected to be numerous affordable nanomedicine technologies available in market exploring these lines. Copyright © 2017 Elsevier B.V. All rights reserved.

Optimization of intra-voxel incoherent motion imaging at 3.0 Tesla for fast liver examination.

PubMed

Leporq, Benjamin; Saint-Jalmes, Hervé; Rabrait, Cecile; Pilleul, Frank; Guillaud, Olivier; Dumortier, Jérôme; Scoazec, Jean-Yves; Beuf, Olivier

2015-05-01

Optimization of multi b-values MR protocol for fast intra-voxel incoherent motion imaging of the liver at 3.0 Tesla. A comparison of four different acquisition protocols were carried out based on estimated IVIM (DSlow , DFast , and f) and ADC-parameters in 25 healthy volunteers. The effects of respiratory gating compared with free breathing acquisition then diffusion gradient scheme (simultaneous or sequential) and finally use of weighted averaging for different b-values were assessed. An optimization study based on Cramer-Rao lower bound theory was then performed to minimize the number of b-values required for a suitable quantification. The duration-optimized protocol was evaluated on 12 patients with chronic liver diseases No significant differences of IVIM parameters were observed between the assessed protocols. Only four b-values (0, 12, 82, and 1310 s.mm(-2) ) were found mandatory to perform a suitable quantification of IVIM parameters. DSlow and DFast significantly decreased between nonadvanced and advanced fibrosis (P < 0.05 and P < 0.01) whereas perfusion fraction and ADC variations were not found to be significant. Results showed that IVIM could be performed in free breathing, with a weighted-averaging procedure, a simultaneous diffusion gradient scheme and only four optimized b-values (0, 10, 80, and 800) reducing scan duration by a factor of nine compared with a nonoptimized protocol. Preliminary results have shown that parameters such as DSlow and DFast based on optimized IVIM protocol can be relevant biomarkers to distinguish between nonadvanced and advanced fibrosis. © 2014 Wiley Periodicals, Inc.

Improving the layout of recycling centres by use of lean production principles.

PubMed

Sundin, Erik; Björkman, Mats; Eklund, Mats; Eklund, Jörgen; Engkvist, Inga-Lill

2011-06-01

There has been increased focus on recycling in Sweden during recent years. This focus can be attributed to external environmental factors such as tougher legislation, but also to the potential gains for raw materials suppliers. Recycling centres are important components in the Swedish total recycling system. Recycling centres are manned facilities for waste collection where visitors can bring, sort and discard worn products as well as large-sized, hazardous, and electrical waste. The aim of this paper was to identify and describe the main flows and layout types at Swedish recycling centres. The aim was also to adapt and apply production theory for designing and managing recycling centre operations. More specifically, this means using lean production principles to help develop guidelines for recycling centre design and efficient control. Empirical data for this research was primarily collected through interviews and questionnaires among both visitors and employees at 16 Swedish recycling centres. Furthermore, adapted observation protocols have been used in order to explore visitor activities. There was also close collaboration with a local recycling centre company, which shared their layout experiences with the researchers in this project. The recycling centres studied had a variety of problems such as queues of visitors, overloading of material and improper sorting. The study shows that in order to decrease the problems, the recycling centres should be designed and managed according to lean production principles, i.e. through choosing more suitable layout choices with visible and linear flows, providing better visitor information, and providing suitable technical equipment. Improvements can be achieved through proper planning of the layout and control of the flow of vehicles, with the result of increased efficiency and capacity, shorter visits, and cleaner waste fractions. The benefits of a lean production mindset include increased visitor capacity, waste flexibility, improved sorting quality, shorter time for visits and improved working conditions. Copyright © 2011 Elsevier Ltd. All rights reserved.

Improved cell therapy protocol for Parkinson’s disease based on differentiation efficiency and safety of hESC-, hiPSC and non-human primate iPSC-derived DA neurons

PubMed Central

Maria, Sundberg; Helle, Bogetofte; Tristan, Lawson; Gaynor, Smith; Arnar, Astradsson; Michele, Moore; Teresia, Osborn; Oliver, Cooper; Roger, Spealman; Penelope, Hallett; Ole, Isacson

2013-01-01

The main motor symptoms of Parkinson’s disease are due to the loss of dopaminergic (DA) neurons in the ventral midbrain (VM). For the future treatment of Parkinson’s disease with cell transplantation it is important to develop efficient differentiation methods for production of human iPSCs and hESCs-derived midbrain-type DA neurons. Here we describe an efficient differentiation and sorting strategy for DA-neurons from both human ES/iPS cells and non-human primate iPSCs. The use of non-human primate iPSCs for neuronal differentiation and autologous transplantation is important for pre-clinical evaluation of safety and efficacy of stem cell-derived DA neurons. The aim of this study was to improve the safety of human- and non-human primate-iPSC (PiPSC)-derived DA neurons. According to our results, NCAM+/CD29low sorting enriched VM DA-neurons from pluripotent stem cell-derived neural cell populations. NCAM+/CD29low DA-neurons were positive for FOXA2/TH and EN1/TH and this cell population had increased expression levels of FOXA2, LMX1A, TH, GIRK2, PITX3, EN1, NURR1 mRNA compared to unsorted neural cell populations. PiPSC-derived NCAM+/CD29low DA-neurons were able to restore motor function of 6-OHDA lesioned rats 16 weeks after transplantation. The transplanted sorted cells also integrated in the rodent brain tissue, with robust TH+/hNCAM+ neuritic innervation of the host striatum. One year after autologous transplantation, the primate iPSC-derived neural cells survived in the striatum of one primate without any immunosuppression. These neural cell grafts contained FOXA2/TH-positive neurons in the graft site. This is an important proof of concept for the feasibility and safety of iPSC-derived cell transplantation therapies in the future. PMID:23666606

Mouse A6-positive hepatic oval cells derived from embryonic stem cells.

PubMed

Yin, Dong-zhi; Cai, Ji-ye; Zheng, Qi-chang; Chen, Zheng-wei; Zhao, Jing-xian; Yuan, You-neng

2014-02-01

Oval cells have a potential to differentiate into a variety of cell lineages including hepatocytes and biliary epithelia. Several models have been established to activate the oval cells by incorporating a variety of toxins and carcinogens, alone or combined with surgical treatment. Those models are obviously not suitable for the study on human hepatic oval cells. It is necessary to establish a new and efficient model to study the human hepatic oval cells. In this study, the hepatocyte growth factor (HGF) and epidermal growth factor (EGF) were used to induce differentiation of mouse embryonic stem (ES) cells into hepatic oval cells. We first confirmed that hepatic oval cells derived from ES cells, which are bipotential, do exist during the course of mouse ES cells' differentiation into hepatic parenchymal cells. RT-PCR and transmission electron microscopy were applied in this study. The ratio of Sca-1+/CD34+ cells sorted by FACS in the induction group was increased from day 4 and reached the maximum on the day 8, whereas that in the control group remained at a low level. The differentiation ratio of Sca-1+/CD34+ cells in the induction group was significantly higher than that in the control group. About 92.48% of the sorted Sca-1+/CD34+ cells on the day 8 were A6 positive. Highly purified A6+/Sca-1+/CD34+ hepatic oval cells derived from ES cells could be obtained by FACS. The differentiation ratio of hepatic oval cells in the induction group (up to 4.46%) was significantly higher than that in the control group. The number of hepatic oval cells could be increased significantly by HGF and EGF. The study also examined the ultrastructures of ES-derived hepatic oval cells' membrane surface by atomic force microscopy. The ES-derived hepatic oval cells cultured and sorted by our protocols may be available for the future clinical application.

Signal voter

DOEpatents

Goodwin, Roy L.

1981-01-01

A voter for providing a single accurate output signal that is derived from the closest two signal levels of three input signals, each of which signals represents a measurement of the same phenomena. By means of the voting circuit, the signals are first sorted by level of amplitude and then ranked as highest, middle or lowest. The highest or lowest signal that is furthest from the middle signal is rejected, while the other highest or lowest signal is selected for processing. The selected high or low signal is then averaged with the middle signal to provide the output signal.

[Rheumatoid arthritis and morbidity among wet spinning factory women workers].

PubMed

Wysocki, Z; Janas, Z; Cichoń, L; Sikorzewski, M; Gregorowicz, H

1977-01-01

Two hundred ninety women employed in the wet spinning mill of the linen plants have been examined. Their average age and duration of employment were respectively 45 and 17,5 years. Examined women worked in specific microclimate including temperature from 24 degrees C to 25.3 degrees C and the moisture of air from 63,5 to 72,5%. Rheumatoid Arthritis in women working in wet spinning factory was the aim of this examination. It has been stated that these surroundings have no influence on that sort of disease.

Treatment of mechanically sorted organic waste by bioreactor landfill: Experimental results and preliminary comparative impact assessment with biostabilization and conventional landfill.

PubMed

Di Maria, Francesco; Micale, Caterina; Sisani, Luciano; Rotondi, Luca

2016-09-01

Treatment and disposal of the mechanically sorted organic fraction (MSOF) of municipal solid waste using a full-scale hybrid bioreactor landfill was experimentally analyzed. A preliminary life cycle assessment was used to compare the hybrid bioreactor landfill with the conventional scheme based on aerobic biostabilization plus landfill. The main findings showed that hybrid bioreactor landfill was able to achieve a dynamic respiration index (DRI)<1000 mgO2/(kgVSh) in 20weeks, on average. Landfill gas (LFG) generation with CH4 concentration >55% v/v started within 140days from MSOF disposal, allowing prompt energy recovery and higher collection efficiency. With the exception of fresh water eutrophication with the bioreactor scenario there was a reduction of the impact categories by about 30% compared to the conventional scheme. Such environmental improvement was mainly a consequence of the reduction of direct and indirect emissions from conventional aerobic biostabilization and of the lower amount of gaseous loses from the bioreactor landfill. Copyright © 2016 Elsevier Ltd. All rights reserved.

Non-Markovian stochastic Schrödinger equations: Generalization to real-valued noise using quantum-measurement theory

NASA Astrophysics Data System (ADS)

Gambetta, Jay; Wiseman, H. M.

2002-07-01

Do stochastic Schrödinger equations, also known as unravelings, have a physical interpretation? In the Markovian limit, where the system on average obeys a master equation, the answer is yes. Markovian stochastic Schrödinger equations generate quantum trajectories for the system state conditioned on continuously monitoring the bath. For a given master equation, there are many different unravelings, corresponding to different sorts of measurement on the bath. In this paper we address the non-Markovian case, and in particular the sort of stochastic Schrödinger equation introduced by Strunz, Diósi, and Gisin [Phys. Rev. Lett. 82, 1801 (1999)]. Using a quantum-measurement theory approach, we rederive their unraveling that involves complex-valued Gaussian noise. We also derive an unraveling involving real-valued Gaussian noise. We show that in the Markovian limit, these two unravelings correspond to heterodyne and homodyne detection, respectively. Although we use quantum-measurement theory to define these unravelings, we conclude that the stochastic evolution of the system state is not a true quantum trajectory, as the identity of the state through time is a fiction.

Selective dispersion of high-purity semiconducting carbon nanotubes using indacenodithiophene-based conjugated polymer

NASA Astrophysics Data System (ADS)

Ji, Dongseob; Lee, Seung-Hoon; Noh, Yong-Young

2018-01-01

The facile sorting of highly pure semiconducting single-walled carbon nanotubes (s-SWNTs) is still one of the challenging issues for the next-generation wearable electronic devices such as various opto-electric devices and field-effect transistors (FETs). Herein, we demonstrate the selective dispersion of high-purity s-SWNTs using indacenodithiophene-co-benzothiadiazole (IDT-BT), which is a state-of-the-art high-mobility conjugated polymer. By the selective wrapping of the IDT-BT copolymer, SWNTs of chiral indices (6, 5), (7, 5), (7, 6), (8, 4), (9, 4), (8, 6), (8, 7), (10, 5), (9, 7), (10, 6), (11, 1), and (13, 3) are sorted. Finally, the networked s-SWNT film formed by spin-coating is applied as an active layer of FETs that exhibited ambipolar characteristics with an average mobility of 2.28 cm2/V s in the p-channel and 2.10 cm2/V s in the n-channel. The ON/OFF ratios in both p- and n-channels are approximately 105, which supports the high purity separation of s-SWNTs wrapped by IDT-BT.

Opposition-Based Memetic Algorithm and Hybrid Approach for Sorting Permutations by Reversals.

PubMed

Soncco-Álvarez, José Luis; Muñoz, Daniel M; Ayala-Rincón, Mauricio

2018-02-21

Sorting unsigned permutations by reversals is a difficult problem; indeed, it was proved to be NP-hard by Caprara (1997). Because of its high complexity, many approximation algorithms to compute the minimal reversal distance were proposed until reaching the nowadays best-known theoretical ratio of 1.375. In this article, two memetic algorithms to compute the reversal distance are proposed. The first one uses the technique of opposition-based learning leading to an opposition-based memetic algorithm; the second one improves the previous algorithm by applying the heuristic of two breakpoint elimination leading to a hybrid approach. Several experiments were performed with one-hundred randomly generated permutations, single benchmark permutations, and biological permutations. Results of the experiments showed that the proposed OBMA and Hybrid-OBMA algorithms achieve the best results for practical cases, that is, for permutations of length up to 120. Also, Hybrid-OBMA showed to improve the results of OBMA for permutations greater than or equal to 60. The applicability of our proposed algorithms was checked processing permutations based on biological data, in which case OBMA gave the best average results for all instances.

Segregation physics of a macroscale granular ratchet

NASA Astrophysics Data System (ADS)

Bhateja, Ashish; Sharma, Ishan; Singh, Jayant K.

2017-05-01

New experiments with multigrain mixtures in a laterally shaken, horizontal channel show complete axial segregation of species. The channel consists of multiple concatenated trapeziums, and superficially resembles microratchets wherein asymmetric geometries and potentials transport, and sort, randomly agitated microscopic particles. However, the physics of our macroscale granular ratchet is fundamentally different, as macroscopic segregation is gravity driven. Our observations are not explained by classical granular segregation theories either. Motivated by the experiments, extensive parallelized discrete element simulations reveal that the macroratchet differentiates grains through hierarchical bidirectional segregation over two different time scales: Grains rapidly sort vertically into horizontal bands spanning the channel's length that, subsequently, slowly separate axially, driven by strikingly gentle, average interfacial pressure gradients acting over long distances. At its maximum, the pressure gradient responsible for axial separation was due to a change in height of about two big grain diameters (d =7 mm) over a meter-long channel. The strong directional segregation achieved by the granular macroratchet has practical importance, while identifying the underlying new physics will further our understanding of granular segregation in industrial and geophysical processes.

Normativity and Desirability in Observational Assessments of Family Interaction.

PubMed

Deal, James E

2018-06-11

Issues of normativity (responding in a typical or average fashion) and desirability (the tendency for raters to endorse positive characteristics rather than neutral or more negative ones) are common in areas of the social sciences that frequently utilize profile correlations to measure dyadic similarity. They have implications for family scholars as well. In the present study, a pre-existing data set was used to make an initial, though limited, investigation into potential confounds of normativity and desirability for macrolevel observational assessments of family interaction. An empirical example is presented using q-sort ratings of family interaction, with variance in observational assessments decomposed into component parts. High levels of both normativity and desirability were found, indicating possible problems in terms of both reliability and validity of assessment. While the results provide an interesting beginning, they are limited due to the use of a q-sort methodology as well as an instrument with limited background and use. These limitations are discussed, as well as alternative interpretations for normativity and desirability and implications for future research. © 2018 Family Process Institute.

Feature extraction using first and second derivative extrema (FSDE) for real-time and hardware-efficient spike sorting.

PubMed

Paraskevopoulou, Sivylla E; Barsakcioglu, Deren Y; Saberi, Mohammed R; Eftekhar, Amir; Constandinou, Timothy G

2013-04-30

Next generation neural interfaces aspire to achieve real-time multi-channel systems by integrating spike sorting on chip to overcome limitations in communication channel capacity. The feasibility of this approach relies on developing highly efficient algorithms for feature extraction and clustering with the potential of low-power hardware implementation. We are proposing a feature extraction method, not requiring any calibration, based on first and second derivative features of the spike waveform. The accuracy and computational complexity of the proposed method are quantified and compared against commonly used feature extraction methods, through simulation across four datasets (with different single units) at multiple noise levels (ranging from 5 to 20% of the signal amplitude). The average classification error is shown to be below 7% with a computational complexity of 2N-3, where N is the number of sample points of each spike. Overall, this method presents a good trade-off between accuracy and computational complexity and is thus particularly well-suited for hardware-efficient implementation. Copyright © 2013 Elsevier B.V. All rights reserved.

Validation of the theoretical domains framework for use in behaviour change and implementation research

PubMed Central

2012-01-01

Background An integrative theoretical framework, developed for cross-disciplinary implementation and other behaviour change research, has been applied across a wide range of clinical situations. This study tests the validity of this framework. Methods Validity was investigated by behavioural experts sorting 112 unique theoretical constructs using closed and open sort tasks. The extent of replication was tested by Discriminant Content Validation and Fuzzy Cluster Analysis. Results There was good support for a refinement of the framework comprising 14 domains of theoretical constructs (average silhouette value 0.29): ‘Knowledge’, ‘Skills’, ‘Social/Professional Role and Identity’, ‘Beliefs about Capabilities’, ‘Optimism’, ‘Beliefs about Consequences’, ‘Reinforcement’, ‘Intentions’, ‘Goals’, ‘Memory, Attention and Decision Processes’, ‘Environmental Context and Resources’, ‘Social Influences’, ‘Emotions’, and ‘Behavioural Regulation’. Conclusions The refined Theoretical Domains Framework has a strengthened empirical base and provides a method for theoretically assessing implementation problems, as well as professional and other health-related behaviours as a basis for intervention development. PMID:22530986

Learning cellular sorting pathways using protein interactions and sequence motifs.

PubMed

Lin, Tien-Ho; Bar-Joseph, Ziv; Murphy, Robert F

2011-11-01

Proper subcellular localization is critical for proteins to perform their roles in cellular functions. Proteins are transported by different cellular sorting pathways, some of which take a protein through several intermediate locations until reaching its final destination. The pathway a protein is transported through is determined by carrier proteins that bind to specific sequence motifs. In this article, we present a new method that integrates protein interaction and sequence motif data to model how proteins are sorted through these sorting pathways. We use a hidden Markov model (HMM) to represent protein sorting pathways. The model is able to determine intermediate sorting states and to assign carrier proteins and motifs to the sorting pathways. In simulation studies, we show that the method can accurately recover an underlying sorting model. Using data for yeast, we show that our model leads to accurate prediction of subcellular localization. We also show that the pathways learned by our model recover many known sorting pathways and correctly assign proteins to the path they utilize. The learned model identified new pathways and their putative carriers and motifs and these may represent novel protein sorting mechanisms. Supplementary results and software implementation are available from http://murphylab.web.cmu.edu/software/2010_RECOMB_pathways/.

Fibro/Adipogenic Progenitors (FAPs): Isolation by FACS and Culture.

PubMed

Low, Marcela; Eisner, Christine; Rossi, Fabio

2017-01-01

Fibro/adipogenic progenitors (FAPs ) are tissue-resident mesenchymal stromal cells (MSCs). Current literature supports a role for these cells in the homeostasis and repair of multiple tissues suggesting that FAPs may have extensive therapeutic potential in the treatment of numerous diseases. In this context, it is crucial to establish efficient and reproducible procedures to purify FAP populations from various tissues. Here, we describe a protocol for the isolation and cell culture of FAPs from murine skeletal muscle using fluorescence -activated cell sorting (FACS), which is particularly useful for experiments where high cell purity is an essential requirement. Identification, isolation, and cell culture of FAPs represent powerful tools that will help us to understand the role of these cells in different conditions and facilitate the development of safe and effective new treatments for diseases.

Real life experimental determination of platinum group metals content in automotive catalytic converters

NASA Astrophysics Data System (ADS)

Yakoumis, I.; Moschovi, A. M.; Giannopoulou, I.; Panias, D.

2018-03-01

The real life experimental protocol for the preparation of spent automobile catalyst samples for elemental analysis is thoroughly described in the following study. Collection, sorting and dismantling, homogenization and sample preparation for X-Ray fluorescence spectroscopy and Atomic Adsorption Spectroscopy combined with Inductive coupled plasma mass spectrometry are discussed in detail for both ceramic and metallic spent catalysts. The concentrations of Platinum Group Metals (PGMs) in spent catalytic converters are presented based on typical consignments of recycled converters (more than 45,000 pieces) from the Greek Market. The conclusions clearly denoted commercial metallic catalytic foil contains higher PGMs loading than ceramic honeycombs. On the other hand, the total PGMs loading in spent ceramic catalytic converters has been found higher than the corresponding value for the metallic ones.

Corneal Stromal Elasticity and Viscoelasticity Assessed by Atomic Force Microscopy after Different Cross Linking Protocols

PubMed Central

Dias, Janice; Diakonis, Vasilios F.; Lorenzo, Michael; Gonzalez, Felipe; Porras, Kevin; Douglas, Simone; Avila, Marcel; Yoo, Sonia H.; Ziebarth, Noël M.

2015-01-01

The purpose of this study was to evaluate elasticity and viscoelasticity in the anterior and deeper stromal regions of the cornea after cross linking with three different protocols using atomic force microscopy (AFM) through indentation. A total of 40 porcine corneas were used in this study and were divided into 4 groups (10 corneas per group): control (no treatment), Dresden (corneal epithelial debridement, riboflavin pretreatment for 30 minutes and a 3mw/cm2 for 30 minutes UVA irradiation), accelerated (corneal epithelial debridement, riboflavin pretreatment for 30 minutes and a 30mw/cm2 for 3 minutes UVA irradiation), and genipin (corneal epithelial debridement and submersion of anterior surface in a 1% genipin solution for 4 hours). Elasticity and viscoelasticity were quantified using AFM through indentation for all corneas, for the anterior stroma and at a depth of 200μm. For the control, Dresden, accelerated, and Genipin groups, respectively, the average Young’s modulus for the anterior stromal region was 0.60±0.58MPa, 1.58 ±1.04MPa, 0.86±0.46MPa, and 1.71±0.51MPa; the average for the 200μm stromal depth was 0.08±0.06MPa, 0.08±0.04MPa, 0.08±0.04MPa, and 0.06±0.01MPa. Corneas crosslinked with the Dresden protocol and genipin were significantly stiffer than controls (p<0.05) in the anterior region only. For the control, Dresden, Accelerated, and Genipin groups, respectively, the average calculated apparent viscosity for the anterior stroma was 88.2±43.7kPa-s, 8.3±7.1kPa-s, 8.1±2.3kPa-s, and 9.5±3.8kPa-s; the average for the 200μm stromal depth was 35.0±3.7kPa-s, 49.6±35.1kPa-s, 42.4±17.6kPa-s, and 41.8±37.6kPa-s. All crosslinking protocols resulted in a decrease in viscosity in the anterior region only (p<0.05). The effects of cross-linking seem to be limited to the anterior corneal stroma and do not extend to the deeper stromal region. Additionally, the Dresden and genipin protocols seem to produce a stiffer anterior corneal stroma when compared to the accelerated protocol. PMID:26093276

The Behavior of TCP and Its Extensions in Space

NASA Technical Reports Server (NTRS)

Wang, Ruhai; Horan, Stephen

2001-01-01

The performance of Transmission Control Protocol (TCP) in space has been examined from the observations of simulation and experimental tests for several years at National Aeronautics and Space Administration (NASA), Department of Defense (DoD) and universities. At New Mexico State University (NMSU), we have been concentrating on studying the performance of two protocol suites: the file transfer protocol (ftp) running over Transmission Control Protocol/Internet Protocol (TCP/IP) stack and the file protocol (fp) running over the Space Communications Protocol Standards (SCPS)-Transport Protocol (TP) developed under the Consultative Committee for Space Data Systems (CCSDS) standards process. SCPS-TP is considered to be TCP's extensions for space communications. This dissertation experimentally studies the behavior of TCP and SCPS-TP by running the protocol suites over both the Space-to-Ground Link Simulator (SGLS) test-bed and realistic satellite link. The study concentrates on comparing protocol behavior by plotting the averaged file transfer times for different experimental configurations and analyzing them using Statistical Analysis System (SAS) based procedures. The effects of different link delays and various Bit-Error-Rates (BERS) on each protocol performance are also studied and linear regression models are built for experiments over SGLS test-bed to reflect the relationships between the file transfer time and various transmission conditions.

Sorting drops and cells with acoustics: acoustic microfluidic fluorescence-activated cell sorter.

PubMed

Schmid, Lothar; Weitz, David A; Franke, Thomas

2014-10-07

We describe a versatile microfluidic fluorescence-activated cell sorter that uses acoustic actuation to sort cells or drops at ultra-high rates. Our acoustic sorter combines the advantages of traditional fluorescence-activated cell (FACS) and droplet sorting (FADS) and is applicable for a multitude of objects. We sort aqueous droplets, at rates as high as several kHz, into two or even more outlet channels. We can also sort cells directly from the medium without prior encapsulation into drops; we demonstrate this by sorting fluorescently labeled mouse melanoma cells in a single phase fluid. Our acoustic microfluidic FACS is compatible with standard cell sorting cytometers, yet, at the same time, enables a rich variety of more sophisticated applications.

Surface acoustic wave actuated cell sorting (SAWACS).

PubMed

Franke, T; Braunmüller, S; Schmid, L; Wixforth, A; Weitz, D A

2010-03-21

We describe a novel microfluidic cell sorter which operates in continuous flow at high sorting rates. The device is based on a surface acoustic wave cell-sorting scheme and combines many advantages of fluorescence activated cell sorting (FACS) and fluorescence activated droplet sorting (FADS) in microfluidic channels. It is fully integrated on a PDMS device, and allows fast electronic control of cell diversion. We direct cells by acoustic streaming excited by a surface acoustic wave which deflects the fluid independently of the contrast in material properties of deflected objects and the continuous phase; thus the device underlying principle works without additional enhancement of the sorting by prior labelling of the cells with responsive markers such as magnetic or polarizable beads. Single cells are sorted directly from bulk media at rates as fast as several kHz without prior encapsulation into liquid droplet compartments as in traditional FACS. We have successfully directed HaCaT cells (human keratinocytes), fibroblasts from mice and MV3 melanoma cells. The low shear forces of this sorting method ensure that cells survive after sorting.

Deterministic generation of remote entanglement with active quantum feedback

DOE PAGES

Martin, Leigh; Motzoi, Felix; Li, Hanhan; ...

2015-12-10

We develop and study protocols for deterministic remote entanglement generation using quantum feedback, without relying on an entangling Hamiltonian. In order to formulate the most effective experimentally feasible protocol, we introduce the notion of average-sense locally optimal feedback protocols, which do not require real-time quantum state estimation, a difficult component of real-time quantum feedback control. We use this notion of optimality to construct two protocols that can deterministically create maximal entanglement: a semiclassical feedback protocol for low-efficiency measurements and a quantum feedback protocol for high-efficiency measurements. The latter reduces to direct feedback in the continuous-time limit, whose dynamics can bemore » modeled by a Wiseman-Milburn feedback master equation, which yields an analytic solution in the limit of unit measurement efficiency. Our formalism can smoothly interpolate between continuous-time and discrete-time descriptions of feedback dynamics and we exploit this feature to derive a superior hybrid protocol for arbitrary nonunit measurement efficiency that switches between quantum and semiclassical protocols. Lastly, we show using simulations incorporating experimental imperfections that deterministic entanglement of remote superconducting qubits may be achieved with current technology using the continuous-time feedback protocol alone.« less

An approach to standardization of urine sediment analysis via suggestion of a common manual protocol.

PubMed

Ko, Dae-Hyun; Ji, Misuk; Kim, Sollip; Cho, Eun-Jung; Lee, Woochang; Yun, Yeo-Min; Chun, Sail; Min, Won-Ki

2016-01-01

The results of urine sediment analysis have been reported semiquantitatively. However, as recent guidelines recommend quantitative reporting of urine sediment, and with the development of automated urine sediment analyzers, there is an increasing need for quantitative analysis of urine sediment. Here, we developed a protocol for urine sediment analysis and quantified the results. Based on questionnaires, various reports, guidelines, and experimental results, we developed a protocol for urine sediment analysis. The results of this new protocol were compared with those obtained with a standardized chamber and an automated sediment analyzer. Reference intervals were also estimated using new protocol. We developed a protocol with centrifugation at 400 g for 5 min, with the average concentration factor of 30. The correlation between quantitative results of urine sediment analysis, the standardized chamber, and the automated sediment analyzer were generally good. The conversion factor derived from the new protocol showed a better fit with the results of manual count than the default conversion factor in the automated sediment analyzer. We developed a protocol for manual urine sediment analysis to quantitatively report the results. This protocol may provide a mean for standardization of urine sediment analysis.

Research of grasping algorithm based on scara industrial robot

NASA Astrophysics Data System (ADS)

Peng, Tao; Zuo, Ping; Yang, Hai

2018-04-01

As the tobacco industry grows, facing the challenge of the international tobacco giant, efficient logistics service is one of the key factors. How to complete the tobacco sorting task of efficient economy is the goal of tobacco sorting and optimization research. Now the cigarette distribution system uses a single line to carry out the single brand sorting task, this article adopts a single line to realize the cigarette sorting task of different brands. Using scara robot special algorithm for sorting and packaging, the optimization scheme significantly enhances the indicators of smoke sorting system. Saving labor productivity, obviously improve production efficiency.

Learning Cellular Sorting Pathways Using Protein Interactions and Sequence Motifs

PubMed Central

Lin, Tien-Ho; Bar-Joseph, Ziv

2011-01-01

Abstract Proper subcellular localization is critical for proteins to perform their roles in cellular functions. Proteins are transported by different cellular sorting pathways, some of which take a protein through several intermediate locations until reaching its final destination. The pathway a protein is transported through is determined by carrier proteins that bind to specific sequence motifs. In this article, we present a new method that integrates protein interaction and sequence motif data to model how proteins are sorted through these sorting pathways. We use a hidden Markov model (HMM) to represent protein sorting pathways. The model is able to determine intermediate sorting states and to assign carrier proteins and motifs to the sorting pathways. In simulation studies, we show that the method can accurately recover an underlying sorting model. Using data for yeast, we show that our model leads to accurate prediction of subcellular localization. We also show that the pathways learned by our model recover many known sorting pathways and correctly assign proteins to the path they utilize. The learned model identified new pathways and their putative carriers and motifs and these may represent novel protein sorting mechanisms. Supplementary results and software implementation are available from http://murphylab.web.cmu.edu/software/2010_RECOMB_pathways/. PMID:21999284

A New Algorithm Using the Non-Dominated Tree to Improve Non-Dominated Sorting.

PubMed

Gustavsson, Patrik; Syberfeldt, Anna

2018-01-01

Non-dominated sorting is a technique often used in evolutionary algorithms to determine the quality of solutions in a population. The most common algorithm is the Fast Non-dominated Sort (FNS). This algorithm, however, has the drawback that its performance deteriorates when the population size grows. The same drawback applies also to other non-dominating sorting algorithms such as the Efficient Non-dominated Sort with Binary Strategy (ENS-BS). An algorithm suggested to overcome this drawback is the Divide-and-Conquer Non-dominated Sort (DCNS) which works well on a limited number of objectives but deteriorates when the number of objectives grows. This article presents a new, more efficient algorithm called the Efficient Non-dominated Sort with Non-Dominated Tree (ENS-NDT). ENS-NDT is an extension of the ENS-BS algorithm and uses a novel Non-Dominated Tree (NDTree) to speed up the non-dominated sorting. ENS-NDT is able to handle large population sizes and a large number of objectives more efficiently than existing algorithms for non-dominated sorting. In the article, it is shown that with ENS-NDT the runtime of multi-objective optimization algorithms such as the Non-Dominated Sorting Genetic Algorithm II (NSGA-II) can be substantially reduced.

Impact of window decrement rate on TCP performance in an adhoc network

NASA Astrophysics Data System (ADS)

Suherman; Hutasuhut, Arief T. W.; Badra, Khaldun; Al-Akaidi, Marwan

2017-09-01

Transmission control protocol (TCP) is a reliable transport protocol handling end to end connection in TCP/IP stack. It works well in copper or optical fibre link, but experiences increasing delay in wireless network. Further, TCP experiences multiple retransmissions due to higher collision probability within wireless network. The situation may get worsen in an ad hoc network. This paper examines the impact half window or window reduction rate to the overall TCP performances. The evaluation using NS-2 simulator shows that the smaller the window decrement rate results the smaller end to end delay. Delay is reduced to 17.05% in average when window decrement rate decreases. Average jitter also decreases 4.15%, while packet loss is not affected.

Municipal solid waste characterization and quantification as a measure towards effective waste management in Ghana.

PubMed

Miezah, Kodwo; Obiri-Danso, Kwasi; Kádár, Zsófia; Fei-Baffoe, Bernard; Mensah, Moses Y

2015-12-01

Reliable national data on waste generation and composition that will inform effective planning on waste management in Ghana is absent. To help obtain this data on a regional basis, selected households in each region were recruited to obtain data on rate of waste generation, physical composition of waste, sorting and separation efficiency and per capita of waste. Results show that rate of waste generation in Ghana was 0.47 kg/person/day, which translates into about 12,710 tons of waste per day per the current population of 27,043,093. Nationally, biodegradable waste (organics and papers) was 0.318 kg/person/day and non-biodegradable or recyclables (metals, glass, textiles, leather and rubbers) was 0.096 kg/person/day. Inert and miscellaneous waste was 0.055 kg/person/day. The average household waste generation rate among the metropolitan cities, except Tamale, was high, 0.72 kg/person/day. Metropolises generated higher waste (average 0.63 kg/person/day) than the municipalities (0.40 kg/person/day) and the least in the districts (0.28 kg/person/day) which are less developed. The waste generation rate also varied across geographical locations, the coastal and forest zones generated higher waste than the northern savanna zone. Waste composition was 61% organics, 14% plastics, 6% inert, 5% miscellaneous, 5% paper, 3% metals, 3% glass, 1% leather and rubber, and 1% textiles. However, organics and plastics, the two major fractions of the household waste varied considerably across the geographical areas. In the coastal zone, the organic waste fraction was highest but decreased through the forest zone towards the northern savanna. However, through the same zones towards the north, plastic waste rather increased in percentage fraction. Households did separate their waste effectively averaging 80%. However, in terms of separating into the bin marked biodegradables, 84% effectiveness was obtained whiles 76% effectiveness for sorting into the bin labeled other waste was achieved. Copyright © 2015 The Authors. Published by Elsevier Ltd.. All rights reserved.

Apples to apples: the origin and magnitude of differences in asbestos cancer risk estimates derived using varying protocols.

PubMed

Berman, D Wayne

2011-08-01

Given that new protocols for assessing asbestos-related cancer risk have recently been published, questions arise concerning how they compare to the "IRIS" protocol currently used by regulators. The newest protocols incorporate findings from 20 additional years of literature. Thus, differences between the IRIS and newer Berman and Crump protocols are examined to evaluate whether these protocols can be reconciled. Risks estimated by applying these protocols to real exposure data from both laboratory and field studies are also compared to assess the relative health protectiveness of each protocol. The reliability of risks estimated using the two protocols are compared by evaluating the degree with which each potentially reproduces the known epidemiology study risks. Results indicate that the IRIS and Berman and Crump protocols can be reconciled; while environment-specific variation within fiber type is apparently due primarily to size effects (not addressed by IRIS), the 10-fold (average) difference between amphibole asbestos risks estimated using each protocol is attributable to an arbitrary selection of the lowest of available mesothelioma potency factors in the IRIS protocol. Thus, the IRIS protocol may substantially underestimate risk when exposure is primarily to amphibole asbestos. Moreover, while the Berman and Crump protocol is more reliable than the IRIS protocol overall (especially for predicting amphibole risk), evidence is presented suggesting a new fiber-size-related adjustment to the Berman and Crump protocol may ultimately succeed in reconciling the entire epidemiology database. However, additional data need to be developed before the performance of the adjusted protocol can be fully validated. © 2011 Society for Risk Analysis.

Analyzing the effect of routing protocols on media access control protocols in radio networks

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

Barrett, C. L.; Drozda, M.; Marathe, A.

2002-01-01

We study the effect of routing protocols on the performance of media access control (MAC) protocols in wireless radio networks. Three well known MAC protocols: 802.11, CSMA, and MACA are considered. Similarly three recently proposed routing protocols: AODV, DSR and LAR scheme 1 are considered. The experimental analysis was carried out using GloMoSim: a tool for simulating wireless networks. The main focus of our experiments was to study how the routing protocols affect the performance of the MAC protocols when the underlying network and traffic parameters are varied. The performance of the protocols was measured w.r.t. five important parameters: (i)more » number of received packets, (ii) average latency of each packet, (iii) throughput (iv) long term fairness and (v) number of control packets at the MAC layer level. Our results show that combinations of routing and MAC protocols yield varying performance under varying network topology and traffic situations. The result has an important implication; no combination of routing protocol and MAC protocol is the best over all situations. Also, the performance analysis of protocols at a given level in the protocol stack needs to be studied not locally in isolation but as a part of the complete protocol stack. A novel aspect of our work is the use of statistical technique, ANOVA (Analysis of Variance) to characterize the effect of routing protocols on MAC protocols. This technique is of independent interest and can be utilized in several other simulation and empirical studies.« less

Stratification in the lunar regolith - A preliminary view

NASA Technical Reports Server (NTRS)

Duke, M. B.; Nagle, J. S.

1975-01-01

Although our knowledge of lunar regolith stratification is incomplete, several categories of thick and thin strata have been identified. Relatively thick units average 2 to 3 cm in thickness, and appear surficially to be massive. On more detailed examination, these units can be uniformly fine-grained, can show internal trends, or can show internal variations which apparently are random. Other thick units contain soil clasts apparently reworked from underlying units. Thin laminae average approximately 1 mm in thickness; lenticular distribution and composition of some thin laminae indicates that they are fillets shed from adjacent rock fragments. Other dark fine-grained well-sorted thin laminae appear to be surficial zones reworked by micrometeorites. Interpretations of stratigraphic succession can be strengthened by the occurrence of characteristic coarse rock fragments and the orientation of large spatter agglutinates, which are commonly found in their original depositional orientation.

Particle Transport and Size Sorting in Bubble Microstreaming Flow

NASA Astrophysics Data System (ADS)

Thameem, Raqeeb; Rallabandi, Bhargav; Wang, Cheng; Hilgenfeldt, Sascha

2014-11-01

Ultrasonic driving of sessile semicylindrical bubbles results in powerful steady streaming flows that are robust over a wide range of driving frequencies. In a microchannel, this flow field pattern can be fine-tuned to achieve size-sensitive sorting and trapping of particles at scales much smaller than the bubble itself; the sorting mechanism has been successfully described based on simple geometrical considerations. We investigate the sorting process in more detail, both experimentally (using new parameter variations that allow greater control over the sorting) and theoretically (incorporating the device geometry as well as the superimposed channel flow into an asymptotic theory). This results in optimized criteria for size sorting and a theoretical description that closely matches the particle behavior close to the bubble, the crucial region for size sorting.

Influence of feed provisioning prior to digesta sampling on precaecal amino acid digestibility in broiler chickens.

PubMed

Siegert, Wolfgang; Ganzer, Christian; Kluth, Holger; Rodehutscord, Markus

2018-06-01

A regression approach was applied to determine the influence of feed provisioning prior to digesta sampling on precaecal (pc) amino acid (AA) digestibility in broiler chickens. Soybean meal was used as an example test ingredient. Five feed-provisioning protocols were investigated, four with restricted provision and one with ad libitum provision. When provision was restricted, feed was provided for 30 min after a withdrawal period of 12 h. Digesta were sampled 1, 2, 4 and 6 h after feeding commenced. A diet containing 300 g maize starch/kg was prepared. Half or all the maize starch was replaced with soybean meal in two other diets. Average pc digestibility of all determined AA in the soybean meal was 86% for the 4 and 6-h protocols and 66% and 60% for the 2 and 1-h protocols, respectively. Average pc AA digestibility of soybean meal was 76% for ad libitum feed provision. Feed provisioning also influenced the determined variance. Variance in digestibility ranked in magnitude 1 h > ad libitum > 2 h > 6 h > 4 h for all AA. Owing to the considerable influence of feed-provisioning protocols found in this study, comparisons of pc AA digestibility between studies applying different protocols prior to digesta sampling must be treated with caution. Digestibility experiments aimed at providing estimates for practical feed formulation should use feed-provisioning procedures similar to those used in practice.

Micro X-ray Fluorescence Study of Late Pre-Hispanic Ceramics from the Western Slopes of the South Central Andes Region in the Arica y Parinacota Region, Chile: A New Methodological Approach

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

Flewett, S.; Saintenoy, T.; Sepulveda, M.

Archeological ceramic paste material typically consists of a mix of a clay matrix and various millimeter and sub-millimeter sized mineral inclusions. Micro X-ray Fluorescence (μXRF) is a standard compositional classification tool, and in this work we propose and demonstrate an improved fluorescence map processing protocol where the mineral inclusions are automatically separated from the clay matrix to allow independent statistical analysis of the two parts. Application of this protocol allowed us to improve enhance the differentiation discrimination between different ceramic shards compared with the standard procedure of comparing working with only the spatially averaged elemental concentrations. Using the new protocol,more » we performed an initial compositional classification of a set of 83 ceramic shards from the western slopes of the south central Andean region in the Arica y Parinacota region of present-day far northern Chile. Comparing the classifications obtained using the new versus the old (average concentrations only) protocols, we found that some samples were erroneously classified with the old protocol. From an archaeological perspective, a very broad and heterogeneous sample set was used in this study due to the fact that this was the first such study to be performed on ceramics from this region. This allowed a general overview to be obtained, however further work on more specific sample sets will be necessary to extract concrete archaeological conclusions.« less

A shortened protocol for assessing cognitive bias in rats.

PubMed

Brydges, Nichola M; Hall, Lynsey

2017-07-15

Reliable measurement of affective state in animals is a significant goal of animal welfare. Such measurements would also improve the validity of pre-clinical mental health research which relies on animal models. However, at present, affective states in animals are inaccessible to direct measurement. In humans, changes in cognitive processing can give reliable indications of emotional state. Therefore, similar techniques are increasingly being used to gain proxy measures of affective states in animals. In particular, the 'cognitive bias' assay has gained popularity in recent years. Major disadvantages of this technique include length of time taken for animals to acquire the task (typically several weeks), negative experiences associated with task training, and issues of motivation. Here we present a shortened cognitive bias protocol using only positive reinforcers which must actively be responded to. The protocol took an average of 4days to complete, and produced similar results to previous, longer methods (minimum 30days). Specifically, rats housed in standard laboratory conditions demonstrated negative cognitive biases when presented with ambiguous stimuli, and took longer to make a decision when faced with an ambiguous stimulus. Compared to previous methods, this protocol is significantly shorter (average 4days vs. minimum 30days), utilises only positive reinforcers to avoid inducing negative affective states, and requires active responses to all cues, avoiding potential confounds of motivational state. We have successfully developed a shortened cognitive bias protocol, suitable for use with laboratory rats. Copyright © 2017 The Author(s). Published by Elsevier B.V. All rights reserved.

Retinal nerve fiber layer measurements by scanning laser polarimetry with enhanced corneal compensation in healthy subjects.

PubMed

Rao, Harsha L; Venkatesh, Chirravuri R; Vidyasagar, Kelli; Yadav, Ravi K; Addepalli, Uday K; Jude, Aarthi; Senthil, Sirisha; Garudadri, Chandra S

2014-12-01

To evaluate the (i) effects of biological (age and axial length) and instrument-related [typical scan score (TSS) and corneal birefringence] parameters on the retinal nerve fiber layer (RNFL) measurements and (ii) repeatability of RNFL measurements with the enhanced corneal compensation (ECC) protocol of scanning laser polarimetry (SLP) in healthy subjects. In a cross-sectional study, 140 eyes of 73 healthy subjects underwent RNFL imaging with the ECC protocol of SLP. Linear mixed modeling methods were used to evaluate the effects of age, axial length, TSS, and corneal birefringence on RNFL measurements. One randomly selected eye of 48 subjects from the cohort underwent 3 serial scans during the same session to determine the repeatability. Age significantly influenced all RNFL measurements. RNFL measurements decreased by 1 µm for every decade increase in age. TSS affected the overall average RNFL measurement (β=-0.62, P=0.003), whereas residual anterior segment retardance affected the superior quadrant measurement (β=1.14, P=0.01). Axial length and corneal birefringence measurements did not influence RNFL measurements. Repeatability, as assessed by the coefficient of variation, ranged between 1.7% for the overall average RNFL measurement and 11.4% for th nerve fiber indicator. Age significantly affected all RNFL measurements with the ECC protocol of SLP, whereas TSS and residual anterior segment retardance affected the overall average and the superior average RNFL measurements, respectively. Axial length and corneal birefringence measurements did not influence any RNFL measurements. RNFL measurements had good intrasession repeatability. These results are important while evaluating the change in structural measurements over time in glaucoma patients.

A single-cell resolution map of mouse hematopoietic stem and progenitor cell differentiation.

PubMed

Nestorowa, Sonia; Hamey, Fiona K; Pijuan Sala, Blanca; Diamanti, Evangelia; Shepherd, Mairi; Laurenti, Elisa; Wilson, Nicola K; Kent, David G; Göttgens, Berthold

2016-08-25

Maintenance of the blood system requires balanced cell fate decisions by hematopoietic stem and progenitor cells (HSPCs). Because cell fate choices are executed at the individual cell level, new single-cell profiling technologies offer exciting possibilities for mapping the dynamic molecular changes underlying HSPC differentiation. Here, we have used single-cell RNA sequencing to profile more than 1600 single HSPCs, and deep sequencing has enabled detection of an average of 6558 protein-coding genes per cell. Index sorting, in combination with broad sorting gates, allowed us to retrospectively assign cells to 12 commonly sorted HSPC phenotypes while also capturing intermediate cells typically excluded by conventional gating. We further show that independently generated single-cell data sets can be projected onto the single-cell resolution expression map to directly compare data from multiple groups and to build and refine new hypotheses. Reconstruction of differentiation trajectories reveals dynamic expression changes associated with early lymphoid, erythroid, and granulocyte-macrophage differentiation. The latter two trajectories were characterized by common upregulation of cell cycle and oxidative phosphorylation transcriptional programs. By using external spike-in controls, we estimate absolute messenger RNA (mRNA) levels per cell, showing for the first time that despite a general reduction in total mRNA, a subset of genes shows higher expression levels in immature stem cells consistent with active maintenance of the stem-cell state. Finally, we report the development of an intuitive Web interface as a new community resource to permit visualization of gene expression in HSPCs at single-cell resolution for any gene of choice. © 2016 by The American Society of Hematology.

Expression analysis of Arabidopsis vacuolar sorting receptor 3 reveals a putative function in guard cells.

PubMed

Avila, Emily L; Brown, Michelle; Pan, Songqin; Desikan, Radhika; Neill, Steven J; Girke, Thomas; Surpin, Marci; Raikhel, Natasha V

2008-01-01

Vacuolar sorting receptors (VSRs) are responsible for the proper targeting of soluble cargo proteins to their destination compartments. The Arabidopsis genome encodes seven VSRs. In this work, the spatio-temporal expression of one of the members of this gene family, AtVSR3, was determined by RT-PCR and promoter::reporter gene fusions. AtVSR3 was expressed specifically in guard cells. Consequently, a reverse genetics approach was taken to determine the function of AtVSR3 by using RNA interference (RNAi) technology. Plants expressing little or no AtVSR3 transcript had a compressed life cycle, bolting approximately 1 week earlier and senescing up to 2 weeks earlier than the wild-type parent line. While the development and distribution of stomata in AtVSR3 RNAi plants appeared normal, stomatal function was altered. The guard cells of mutant plants did not close in response to abscisic acid treatment, and the mean leaf temperatures of the RNAi plants were on average 0.8 degrees C lower than both wild type and another vacuolar sorting receptor mutant, atvsr1-1. Furthermore, the loss of AtVSR3 protein caused the accumulation of nitric oxide and hydrogen peroxide, signalling molecules implicated in the regulation of stomatal opening and closing. Finally, proteomics and western blot analyses of cellular proteins isolated from wild-type and AtVSR3 RNAi leaves showed that phospholipase Dgamma, which may play a role in abscisic acid signalling, accumulated to higher levels in AtVSR3 RNAi guard cells. Thus, AtVSR3 may play an important role in responses to plant stress.

The biodiversity of Aspergillus section Flavi in brazil nuts: from rainforest to consumer.

PubMed

Calderari, Thaiane O; Iamanaka, Beatriz T; Frisvad, Jens C; Pitt, John I; Sartori, Daniele; Pereira, Jose Luiz; Fungaro, Maria Helena P; Taniwaki, Marta H

2013-01-01

A total of 288 brazil nut samples (173 kernel and 115 shell) from the Amazon rainforest region and São Paulo State, Brazil were collected at different stages of brazil nut production. Samples were analysed for: percentages of aflatoxigenic fungal species and potential for aflatoxin production and presence of aflatoxins. Aspergillus nomius was the most common species found (1235 isolates) which amounted to 30% of the total species with potential to produce aflatoxins. This species is of concern since 100% of all isolates produced aflatoxins B(1), B(2), G(1) and G(2). Aspergillus flavus was almost equally common (1212 isolates) although only 46% produced aflatoxins under laboratory conditions, and only aflatoxins B(1) and B(2). Low number of other species with the potential to produce aflatoxins was isolated: Aspergillus arachidicola and Aspergillus bombycis produced B and G aflatoxins whilst Aspergillus pseudotamarii produced only aflatoxin B(1). The total aflatoxin levels found in samples taken from the rainforests was 0.7 μg/kg, from processing plants before and after sorting 8.0 and 0.1 μg/kg respectively, from street markets in the Amazon region 6.3 μg/kg and from supermarkets in São Paulo State 0.2 μg/kg. Processing, which included manual or mechanical sorting and drying at 60°C for 30 to 36 h, eliminated on average more than 98% of total aflatoxins. These results showed that sorting is a very effective way to decrease aflatoxin content in brazil nuts. Copyright © 2012 Elsevier B.V. All rights reserved.

A microfluidic device for automated, high-speed microinjection of Caenorhabditis elegans

PubMed Central

Song, Pengfei; Dong, Xianke; Liu, Xinyu

2016-01-01

The nematode worm Caenorhabditis elegans has been widely used as a model organism in biological studies because of its short and prolific life cycle, relatively simple body structure, significant genetic overlap with human, and facile/inexpensive cultivation. Microinjection, as an established and versatile tool for delivering liquid substances into cellular/organismal objects, plays an important role in C. elegans research. However, the conventional manual procedure of C. elegans microinjection is labor-intensive and time-consuming and thus hinders large-scale C. elegans studies involving microinjection of a large number of C. elegans on a daily basis. In this paper, we report a novel microfluidic device that enables, for the first time, fully automated, high-speed microinjection of C. elegans. The device is automatically regulated by on-chip pneumatic valves and allows rapid loading, immobilization, injection, and downstream sorting of single C. elegans. For demonstration, we performed microinjection experiments on 200 C. elegans worms and demonstrated an average injection speed of 6.6 worm/min (average worm handling time: 9.45 s/worm) and a success rate of 77.5% (post-sorting success rate: 100%), both much higher than the performance of manual operation (speed: 1 worm/4 min and success rate: 30%). We conducted typical viability tests on the injected C. elegans and confirmed that the automated injection system does not impose significant adverse effect on the physiological condition of the injected C. elegans. We believe that the developed microfluidic device holds great potential to become a useful tool for facilitating high-throughput, large-scale worm biology research. PMID:26958099

Determining the amount of waste plastics in the feed of Austrian waste-to-energy facilities

PubMed Central

Schwarzböck, Therese; Van Eygen, Emile; Rechberger, Helmut; Fellner, Johann

2016-01-01

Although thermal recovery of waste plastics is widely practiced in many European countries, reliable information on the amount of waste plastics in the feed of waste-to-energy plants is rare. In most cases the amount of plastics present in commingled waste, such as municipal solid waste, commercial, or industrial waste, is estimated based on a few waste sorting campaigns, which are of limited significance with regard to the characterisation of plastic flows. In the present study, an alternative approach, the so-called Balance Method, is used to determine the total amount of plastics thermally recovered in Austria’s waste incineration facilities in 2014. The results indicate that the plastics content in the waste feed may vary considerably among different plants but also over time. Monthly averages determined range between 8 and 26 wt% of waste plastics. The study reveals an average waste plastics content in the feed of Austria’s waste-to-energy plants of 16.5 wt%, which is considerably above findings from sorting campaigns conducted in Austria. In total, about 385 kt of waste plastics were thermally recovered in all Austrian waste-to-energy plants in 2014, which equals to 45 kg plastics cap-1. In addition, the amount of plastics co-combusted in industrial plants yields a total thermal utilisation rate of 70 kg cap-1 a-1 for Austria. This is significantly above published rates, for example, in Germany reported rates for 2013 are in the range of only 40 kg of waste plastics combusted per capita. PMID:27474393

The importance of particle size in porous titanium and nonporous counterparts for surface energy and its impact on apatite formation.

PubMed

Chen, Xiao-Bo; Li, Yun-Cang; Hodgson, Peter D; Wen, Cuie

2009-07-01

The importance of particle size in titanium (Ti) fabricated by powder metallurgy for the surface energy and its impact on the apatite formation was investigated. Four sorts of Ti powders of different mean particle size were realized through 20min, 2h, 5h and 8h of ball milling, respectively. Each sort of Ti powder was used to fabricate porous Ti and its nonporous counterparts sharing similar surface morphology, grain size and chemical composition, and then alkali-heat treatment was conducted on them. Surface energy was measured on the surfaces of the nonporous Ti counterparts due to the difficulty in measuring the porous surfaces directly. The surface energy increase on the alkali-heat-treated porous and nonporous Ti was observed due to the decrease in the particle size of the Ti powders and the presence of Ti-OH groups brought by the alkali-heat treatment. The apatite-inducing ability of the alkali-heat-treated porous and nonporous Ti with different surface energy values was evaluated in modified simulated body fluid and results indicated that there was a strong correlation between the apatite-inducing ability and the surface energy. The alkali-heat-treated porous and nonporous Ti discs prepared from the powders with an average particle size of 5.89+/-0.76microm possessed the highest surface energy and the best apatite-inducing ability when compared to the samples produced from the powders with the average particle size varying from 19.79+/-0.31 to 10.25+/-0.39microm.

Determining the amount of waste plastics in the feed of Austrian waste-to-energy facilities.

PubMed

Schwarzböck, Therese; Van Eygen, Emile; Rechberger, Helmut; Fellner, Johann

2017-02-01

Although thermal recovery of waste plastics is widely practiced in many European countries, reliable information on the amount of waste plastics in the feed of waste-to-energy plants is rare. In most cases the amount of plastics present in commingled waste, such as municipal solid waste, commercial, or industrial waste, is estimated based on a few waste sorting campaigns, which are of limited significance with regard to the characterisation of plastic flows. In the present study, an alternative approach, the so-called Balance Method, is used to determine the total amount of plastics thermally recovered in Austria's waste incineration facilities in 2014. The results indicate that the plastics content in the waste feed may vary considerably among different plants but also over time. Monthly averages determined range between 8 and 26 wt% of waste plastics. The study reveals an average waste plastics content in the feed of Austria's waste-to-energy plants of 16.5 wt%, which is considerably above findings from sorting campaigns conducted in Austria. In total, about 385 kt of waste plastics were thermally recovered in all Austrian waste-to-energy plants in 2014, which equals to 45 kg plastics cap -1 . In addition, the amount of plastics co-combusted in industrial plants yields a total thermal utilisation rate of 70 kg cap -1  a -1 for Austria. This is significantly above published rates, for example, in Germany reported rates for 2013 are in the range of only 40 kg of waste plastics combusted per capita.

Sortilin 1 Loss-of-Function Protects Against Cholestatic Liver Injury by Attenuating Hepatic Bile Acid Accumulation in Bile Duct Ligated Mice.

PubMed

Li, Jibiao; Woolbright, Benjamin L; Zhao, Wen; Wang, Yifeng; Matye, David; Hagenbuch, Bruno; Jaeschke, Hartmut; Li, Tiangang

2018-01-01

Sortilin 1 (Sort1) is an intracellular trafficking receptor that mediates protein sorting in the endocytic or secretory pathways. Recent studies revealed a role of Sort1 in the regulation of cholesterol and bile acid (BA) metabolism. This study further investigated the role of Sort1 in modulating BA detoxification and cholestatic liver injury in bile duct ligated mice. We found that Sort1 knockout (KO) mice had attenuated liver injury 24 h after bile duct ligation (BDL), which was mainly attributed to less bile infarct formation. Sham-operated Sort1 KO mice had about 20% larger BA pool size than sham-operated wildtype (WT) mice, but 24 h after BDL Sort1 KO mice had significantly attenuated hepatic BA accumulation and smaller BA pool size. After 14 days BDL, Sort1 KO mice showed significantly lower hepatic BA concentration and reduced expression of inflammatory and fibrotic marker genes, but similar degree of liver fibrosis compared with WT mice. Unbiased quantitative proteomics revealed that Sort1 KO mice had increased hepatic BA sulfotransferase 2A1, but unaltered phase-I BA metabolizing cytochrome P450s or phase-III BA efflux transporters. Consistently, Sort1 KO mice showed elevated plasma sulfated taurocholate after BDL. Finally, we found that liver Sort1 was repressed after BDL, which may be due to BA activation of farnesoid x receptor. In conclusion, we report a role of Sort1 in the regulation of hepatic BA detoxification and cholestatic liver injury in mice. The mechanisms underlying increased hepatic BA elimination in Sort1 KO mice after BDL require further investigation. © The Author 2017. Published by Oxford University Press on behalf of the Society of Toxicology. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

NIH Toolbox Cognition Battery (NIHTB-CB): list sorting test to measure working memory.

PubMed

Tulsky, David S; Carlozzi, Noelle; Chiaravalloti, Nancy D; Beaumont, Jennifer L; Kisala, Pamela A; Mungas, Dan; Conway, Kevin; Gershon, Richard

2014-07-01

The List Sorting Working Memory Test was designed to assess working memory (WM) as part of the NIH Toolbox Cognition Battery. List Sorting is a sequencing task requiring children and adults to sort and sequence stimuli that are presented visually and auditorily. Validation data are presented for 268 participants ages 20 to 85 years. A subset of participants (N=89) was retested 7 to 21 days later. As expected, the List Sorting Test had moderately high correlations with other measures of working memory and executive functioning (convergent validity) but a low correlation with a test of receptive vocabulary (discriminant validity). Furthermore, List Sorting demonstrates expected changes over the age span and has excellent test-retest reliability. Collectively, these results provide initial support for the construct validity of the List Sorting Working Memory Measure as a measure of working memory. However, the relationship between the List Sorting Test and general executive function has yet to be determined.

Manual sorting to eliminate aflatoxin from peanuts.

PubMed

Galvez, F C F; Francisco, M L D L; Villarino, B J; Lustre, A O; Resurreccion, A V A

2003-10-01

A manual sorting procedure was developed to eliminate aflatoxin contamination from peanuts. The efficiency of the sorting process in eliminating aflatoxin-contaminated kernels from lots of raw peanuts was verified. The blanching of 20 kg of peanuts at 140 degrees C for 25 min in preheated roasters facilitated the manual sorting of aflatoxin-contaminated kernels after deskinning. The manual sorting of raw materials with initially high aflatoxin contents (300 ppb) resulted in aflatoxin-free peanuts (i.e., peanuts in which no aflatoxin was detected). Verification procedures showed that the sorted sound peanuts contained no aflatoxin or contained low levels (<15 ppb) of aflatoxin. The results obtained confirmed that the sorting process was effective in separating contaminated peanuts whether or nor contamination was extensive. At the commercial level, when roasters were not preheated, the dry blanching of 50 kg of peanuts for 45 to 55 min facilitated the proper deskinning and subsequent manual sorting of aflatoxin-contaminated peanut kernels from sound kernels.

Automated spike sorting algorithm based on Laplacian eigenmaps and k-means clustering.

PubMed

Chah, E; Hok, V; Della-Chiesa, A; Miller, J J H; O'Mara, S M; Reilly, R B

2011-02-01

This study presents a new automatic spike sorting method based on feature extraction by Laplacian eigenmaps combined with k-means clustering. The performance of the proposed method was compared against previously reported algorithms such as principal component analysis (PCA) and amplitude-based feature extraction. Two types of classifier (namely k-means and classification expectation-maximization) were incorporated within the spike sorting algorithms, in order to find a suitable classifier for the feature sets. Simulated data sets and in-vivo tetrode multichannel recordings were employed to assess the performance of the spike sorting algorithms. The results show that the proposed algorithm yields significantly improved performance with mean sorting accuracy of 73% and sorting error of 10% compared to PCA which combined with k-means had a sorting accuracy of 58% and sorting error of 10%.A correction was made to this article on 22 February 2011. The spacing of the title was amended on the abstract page. No changes were made to the article PDF and the print version was unaffected.

A Simple Deep Learning Method for Neuronal Spike Sorting

NASA Astrophysics Data System (ADS)

Yang, Kai; Wu, Haifeng; Zeng, Yu

2017-10-01

Spike sorting is one of key technique to understand brain activity. With the development of modern electrophysiology technology, some recent multi-electrode technologies have been able to record the activity of thousands of neuronal spikes simultaneously. The spike sorting in this case will increase the computational complexity of conventional sorting algorithms. In this paper, we will focus spike sorting on how to reduce the complexity, and introduce a deep learning algorithm, principal component analysis network (PCANet) to spike sorting. The introduced method starts from a conventional model and establish a Toeplitz matrix. Through the column vectors in the matrix, we trains a PCANet, where some eigenvalue vectors of spikes could be extracted. Finally, support vector machine (SVM) is used to sort spikes. In experiments, we choose two groups of simulated data from public databases availably and compare this introduced method with conventional methods. The results indicate that the introduced method indeed has lower complexity with the same sorting errors as the conventional methods.

NIH Toolbox Cognition Battery (NIHTB-CB): The List Sorting Test to Measure Working Memory

PubMed Central

Tulsky, David S.; Carlozzi, Noelle; Chiaravalloti, Nancy D.; Beaumont, Jennifer L.; Kisala, Pamela A.; Mungas, Dan; Conway, Kevin; Gershon, Richard

2015-01-01

The List Sorting Working Memory Test was designed to assess working memory (WM) as part of the NIH Toolbox Cognition Battery. List Sorting is a sequencing task requiring children and adults to sort and sequence stimuli that are presented visually and auditorily. Validation data are presented for 268 participants ages 20 to 85 years. A subset of participants (N=89) was retested 7 to 21 days later. As expected, the List Sorting Test had moderately high correlations with other measures of working memory and executive functioning (convergent validity) but a low correlation with a test of receptive vocabulary (discriminant validity). Furthermore, List Sorting demonstrates expected changes over the age span and has excellent test-retest reliability. Collectively, these results provide initial support the construct validity of the List Sorting Working Memory Measure as a measure of working memory. However, the relation between the List Sorting Test and general executive function has yet to be determined. PMID:24959983

Scoring System for the Management of Acute Gallstone Pancreatitis: Cost Analysis of a Prospective Study.

PubMed

Prigoff, Jake G; Swain, Gary W; Divino, Celia M

2016-05-01

Predicting the presence of a persistent common bile duct (CBD) stone is a difficult and expensive task. The aim of this study is to determine if a previously described protocol-based scoring system is a cost-effective strategy. The protocol includes all patients with gallstone pancreatitis and stratifies them based on laboratory values and imaging to high, medium, and low likelihood of persistent stones. The patient's stratification then dictates the next course of management. A decision analytic model was developed to compare the costs for patients who followed the protocol versus those that did not. Clinical data model inputs were obtained from a prospective study conducted at The Mount Sinai Medical Center to validate the protocol from Oct 2009 to May 2013. The study included all patients presenting with gallstone pancreatitis regardless of disease severity. Seventy-three patients followed the proposed protocol and 32 did not. The protocol group cost an average of $14,962/patient and the non-protocol group cost $17,138/patient for procedural costs. Mean length of stay for protocol and non-protocol patients was 5.6 and 7.7 days, respectively. The proposed protocol is a cost-effective way to determine the course for patients with gallstone pancreatitis, reducing total procedural costs over 12 %.

Compact Modbus TCP/IP protocol for data acquisition systems based on limited hardware resources

NASA Astrophysics Data System (ADS)

Bai, Q.; Jin, B.; Wang, D.; Wang, Y.; Liu, X.

2018-04-01

The Modbus TCP/IP has been a standard industry communication protocol and widely utilized for establishing sensor-cloud platforms on the Internet. However, numerous existing data acquisition systems built on traditional single-chip microcontrollers without sufficient resources cannot support it, because the complete Modbus TCP/IP protocol always works dependent on a full operating system which occupies abundant hardware resources. Hence, a compact Modbus TCP/IP protocol is proposed in this work to make it run efficiently and stably even on a resource-limited hardware platform. Firstly, the Modbus TCP/IP protocol stack is analyzed and the refined protocol suite is rebuilt by streamlining the typical TCP/IP suite. Then, specific implementation of every hierarchical layer is respectively presented in detail according to the protocol structure. Besides, the compact protocol is implemented in a traditional microprocessor to validate the feasibility of the scheme. Finally, the performance of the proposed scenario is assessed. The experimental results demonstrate that message packets match the frame format of Modbus TCP/IP protocol and the average bandwidth reaches to 1.15 Mbps. The compact protocol operates stably even based on a traditional microcontroller with only 4-kB RAM and 12-MHz system clock, and no communication congestion or frequent packet loss occurs.

CSR: Constrained Selfish Routing in Ad-Hoc Networks

NASA Astrophysics Data System (ADS)

Bassem, Christine; Bestavros, Azer

Routing protocols for ad-hoc networks assume that the nodes forming the network are either under a single authority, or else that they would be altruistically forwarding data for other nodes with no expectation of a return. These assumptions are unrealistic since in ad-hoc networks, nodes are likely to be autonomous and rational (selfish), and thus unwilling to help unless they have an incentive to do so. Providing such incentives is an important aspect that should be considered when designing ad-hoc routing protocols. In this paper, we propose a dynamic, decentralized routing protocol for ad-hoc networks that provides incentives in the form of payments to intermediate nodes used to forward data for others. In our Constrained Selfish Routing (CSR) protocol, game-theoretic approaches are used to calculate payments (incentives) that ensure both the truthfulness of participating nodes and the fairness of the CSR protocol. We show through simulations that CSR is an energy efficient protocol and that it provides lower communication overhead in the best and average cases compared to existing approaches.

Regulation of synaptic activity by snapin-mediated endolysosomal transport and sorting

PubMed Central

Di Giovanni, Jerome; Sheng, Zu-Hang

2015-01-01

Recycling synaptic vesicles (SVs) transit through early endosomal sorting stations, which raises a fundamental question: are SVs sorted toward endolysosomal pathways? Here, we used snapin mutants as tools to assess how endolysosomal sorting and trafficking impact presynaptic activity in wild-type and snapin−/− neurons. Snapin acts as a dynein adaptor that mediates the retrograde transport of late endosomes (LEs) and interacts with dysbindin, a subunit of the endosomal sorting complex BLOC-1. Expressing dynein-binding defective snapin mutants induced SV accumulation at presynaptic terminals, mimicking the snapin−/− phenotype. Conversely, over-expressing snapin reduced SV pool size by enhancing SV trafficking to the endolysosomal pathway. Using a SV-targeted Ca2+ sensor, we demonstrate that snapin–dysbindin interaction regulates SV positional priming through BLOC-1/AP-3-dependent sorting. Our study reveals a bipartite regulation of presynaptic activity by endolysosomal trafficking and sorting: LE transport regulates SV pool size, and BLOC-1/AP-3-dependent sorting fine-tunes the Ca2+ sensitivity of SV release. Therefore, our study provides new mechanistic insights into the maintenance and regulation of SV pool size and synchronized SV fusion through snapin-mediated LE trafficking and endosomal sorting. PMID:26108535

Evaluating multicenter DTI data in Huntington's disease on site specific effects: An ex post facto approach.

PubMed

Müller, Hans-Peter; Grön, Georg; Sprengelmeyer, Reiner; Kassubek, Jan; Ludolph, Albert C; Hobbs, Nicola; Cole, James; Roos, Raymund A C; Duerr, Alexandra; Tabrizi, Sarah J; Landwehrmeyer, G Bernhard; Süssmuth, Sigurd D

2013-01-01

Assessment of the feasibility to average diffusion tensor imaging (DTI) metrics of MRI data acquired in the course of a multicenter study. Sixty-one early stage Huntington's disease patients and forty healthy controls were studied using four different MR scanners at four European sites with acquisition protocols as close as possible to a given standard protocol. The potential and feasibility of averaging data acquired at different sites was evaluated quantitatively by region-of-interest (ROI) based statistical comparisons of coefficients of variation (CV) across centers, as well as by testing for significant group-by-center differences on averaged fractional anisotropy (FA) values between patients and controls. In addition, a whole-brain based statistical between-group comparison was performed using FA maps. The ex post facto statistical evaluation of CV and FA-values in a priori defined ROIs showed no differences between sites above chance indicating that data were not systematically biased by center specific factors. Averaging FA-maps from DTI data acquired at different study sites and different MR scanner types does not appear to be systematically biased. A suitable recipe for testing on the possibility to pool multicenter DTI data is provided to permit averaging of DTI-derived metrics to differentiate patients from healthy controls at a larger scale.

Abbreviated MRI Protocols for Detecting Breast Cancer in Women with Dense Breasts.

PubMed

Chen, Shuang-Qing; Huang, Min; Shen, Yu-Ying; Liu, Chen-Lu; Xu, Chuan-Xiao

2017-01-01

To evaluate the validity of two abbreviated protocols (AP) of MRI in breast cancer screening of dense breast tissue. This was a retrospective study in 356 participants with dense breast tissue and negative mammography results. The study was approved by the Nanjing Medical University Ethics Committee. Patients were imaged with a full diagnostic protocol (FDP) of MRI. Two APs (AP-1 consisting of the first post-contrast subtracted [FAST] and maximum-intensity projection [MIP] images, and AP-2 consisting of AP-1 combined with diffusion-weighted imaging [DWI]) and FDP images were analyzed separately, and the sensitivities and specificities of breast cancer detection were calculated. Of the 356 women, 67 lesions were detected in 67 women (18.8%) by standard MR protocol, and histological examination revealed 14 malignant lesions and 53 benign lesions. The average interpretation time of AP-1 and AP-2 were 37 seconds and 54 seconds, respectively, while the average interpretation time of the FDP was 3 minutes and 25 seconds. The sensitivities of the AP-1, AP-2, and FDP were 92.9, 100, and 100%, respectively, and the specificities of the three MR protocols were 86.5, 95.0, and 96.8%, respectively. There was no significant difference among the three MR protocols in the diagnosis of breast cancer ( p > 0.05). However, the specificity of AP-1 was significantly lower than that of AP-2 ( p = 0.031) and FDP ( p = 0.035), while there was no difference between AP-2 and FDP ( p > 0.05). The AP may be efficient in the breast cancer screening of dense breast tissue. FAST and MIP images combined with DWI of MRI are helpful to improve the specificity of breast cancer detection.

Effects of a Straw Phonation Protocol on Acoustic and Perceptual Measures of an SATB Chorus.

PubMed

Manternach, Jeremy N; Daugherty, James F

2017-12-29

Recent scholarship has suggested that semi-occluded vocal tract (SOVT) exercises may increase vocal economy of individuals by reducing vocal effort while maintaining or increasing acoustic output. Choral singers, however, may use different resonance techniques or change voicing behaviors in an effort to hear their own sound in relation to others. One investigation revealed significant increases in a choir's mean spectral energy after participating in a straw phonation protocol. However, that study reported only acoustic measures and did not include choristers' perceptions of the choral sound and their own voicing efficiency. The purpose of this study was to measure the effect of a straw phonation protocol on acoustic (long-term average spectrum) and perceptual (self-report) measures of the choral sound of an intact soprano, alto, tenor, and bass (SATB) choir. This is a quasi-experimental, one-group, pretest-posttest design. An SATB choir (N = 48 singers) performed a Renaissance motet, participated in a 4-minute voicing protocol with a small straw, and then sang the motet a second time. They completed the same procedure later in the rehearsal. Long-term average spectrum results indicated no statistically significant mean changes in spectral energy after the SOVT protocols. Most participants, however, perceived that the choir sounded better (78.26%) and that their own vocal production was more efficient or comfortable (73.91%) following the protocol. Choristers perceived less vocal effort while maintaining vocal output after straw phonation, which may feasibly align with extant solo research. More research may determine whether this result is due specifically to SOVTs. Copyright © 2017 The Voice Foundation. Published by Elsevier Inc. All rights reserved.

Use and efficacy of a nutrition protocol for patients with burns in intensive care.

PubMed

Lown, D

1991-01-01

The University of Michigan Burn Center uses a protocol to standardize the assessment, initiation, and monitoring of nutritional support for patients with burns of greater than 30% total body surface area (TBSA). Six patients with 20% to 80% TBSA burns were followed for 3 weeks to determine the effect of the protocol on the assessment, initiation, monitoring, and adequacy of nutritional support. The protocol calls for resting energy expenditure (REE) measurement within 24 hours of injury, to be repeated 3 times per week, for assessment of caloric requirements. Patients experienced an average delay before first REE measurement of 3 days after burn injury because measurements were unavailable on weekends and surgical days. REE measurements were used to determine caloric requirements and to tailor nutritional support to fluctuating metabolic needs. In four of the six patients a Dobhoff feeding tube (Biosearch Medical Products, Inc., Somerville, N.J.) was placed in the small bowel and enteral nutrition was initiated within 24 hours of admission, as outlined in the protocol. Two patients received concurrent parenteral nutrition because of difficulty in placing the Dobhoff feeding tube when fluoroscopy was not available. The three patients receiving nutrition solely through enteral feeding had achieved 100% of their caloric requirements by day 2, 4, and greater than 7 days after injury, respectively. Overall, the six patients received enterally an average of 75% of their caloric requirements. The major reason for inadequate enteral support was interruption of tube feedings because of tube dislodgment or multiple surgical procedures. The protocol used weekly measurements of total iron-binding capacity and prealbumin level s parameters of nutritional support.(ABSTRACT TRUNCATED AT 250 WORDS)

A fast screening protocol for carotid plaques imaging using 3D multi-contrast MRI without contrast agent.

PubMed

Zhang, Na; Zhang, Lei; Yang, Qi; Pei, Anqi; Tong, Xiaoxin; Chung, Yiu-Cho; Liu, Xin

2017-06-01

To implement a fast (~15min) MRI protocol for carotid plaque screening using 3D multi-contrast MRI sequences without contrast agent on a 3Tesla MRI scanner. 7 healthy volunteers and 25 patients with clinically confirmed transient ischemic attack or suspected cerebrovascular ischemia were included in this study. The proposed protocol, including 3D T1-weighted and T2-weighted SPACE (variable-flip-angle 3D turbo spin echo), and T1-weighted magnetization prepared rapid acquisition gradient echo (MPRAGE) was performed first and was followed by 2D T1-weighted and T2-weighted turbo spin echo, and post-contrast T1-weighted SPACE sequences. Image quality, number of plaques, and vessel wall thicknesses measured at the intersection of the plaques were evaluated and compared between sequences. Average examination time of the proposed protocol was 14.6min. The average image quality scores of 3D T1-weighted, T2-weighted SPACE, and T1-weighted magnetization prepared rapid acquisition gradient echo were 3.69, 3.75, and 3.48, respectively. There was no significant difference in detecting the number of plaques and vulnerable plaques using pre-contrast 3D images with or without post-contrast T1-weighted SPACE. The 3D SPACE and 2D turbo spin echo sequences had excellent agreement (R=0.96 for T1-weighted and 0.98 for T2-weighted, p<0.001) regarding vessel wall thickness measurements. The proposed protocol demonstrated the feasibility of attaining carotid plaque screening within a 15-minute scan, which provided sufficient anatomical coverage and critical diagnostic information. This protocol offers the potential for rapid and reliable screening for carotid plaques without contrast agent. Copyright © 2016. Published by Elsevier Inc.

Phase estimation of coherent states with a noiseless linear amplifier

NASA Astrophysics Data System (ADS)

Assad, Syed M.; Bradshaw, Mark; Lam, Ping Koy

Amplification of quantum states is inevitably accompanied with the introduction of noise at the output. For protocols that are probabilistic with heralded success, noiseless linear amplification in theory may still be possible. When the protocol is successful, it can lead to an output that is a noiselessly amplified copy of the input. When the protocol is unsuccessful, the output state is degraded and is usually discarded. Probabilistic protocols may improve the performance of some quantum information protocols, but not for metrology if the whole statistics is taken into consideration. We calculate the precision limits on estimating the phase of coherent states using a noiseless linear amplifier by computing its quantum Fisher information and we show that on average, the noiseless linear amplifier does not improve the phase estimate. We also discuss the case where abstention from measurement can reduce the cost for estimation.

High-efficiency transformation by biolistics of soybean, common bean and cotton transgenic plants.

PubMed

Rech, Elibio L; Vianna, Giovanni R; Aragão, Francisco J L

2008-01-01

This protocol describes a method for high-frequency recovery of transgenic soybean, bean and cotton plants, by combining resistance to the herbicide imazapyr as a selectable marker, multiple shoot induction from embryonic axes of mature seeds and biolistics techniques. This protocol involves the following stages: plasmid design, preparation of soybean, common bean and cotton apical meristems for bombardment, microparticle-coated DNA bombardment of apical meristems and in vitro culture and selection of transgenic plants. The average frequencies (the total number of fertile transgenic plants divided by the total number of bombarded embryonic axes) of producing germline transgenic soybean and bean and cotton plants using this protocol are 9, 2.7 and 0.55%, respectively. This protocol is suitable for studies of gene function as well as the production of transgenic cultivars carrying different traits for breeding programs. This protocol can be completed in 7-10 months.

Induction, maintenance, and reversal of therapeutic hypothermia with an esophageal heat transfer device.

PubMed

Kulstad, Erik; Metzger, Anja K; Courtney, D Mark; Rees, Jennifer; Shanley, Patrick; Matsuura, Timothy; McKnite, Scott; Lurie, Keith

2013-11-01

To evaluate a novel esophageal heat transfer device for use in inducing, maintaining, and reversing hypothermia. We hypothesized that this device could successfully induce, maintain (within a 1 °C range of goal temperature), and reverse, mild therapeutic hypothermia in a large animal model over a 30-h treatment protocol. Five female Yorkshire swine, weighing a mean of 65 kg (range 61-70) kg each, were anesthetized with inhalational isoflurane via endotracheal intubation and instrumented. The esophageal device was connected to an external chiller and then placed into the esophagus and connected to wall suction. Reduction to goal temperature was achieved by setting the chiller to cooling mode, and a 24h cooling protocol was completed before rewarming and recovering the animals. Histopathologic analysis was scheduled for 3-14 days after protocol completion. Average baseline temperature for the 5 animals was 38.6 °C (range 38.1-39.2 °C). All swine were cooled successfully, with average rate of temperature decrease of 1.3 °C/h (range 1.1-1.9) °C/h. Standard deviation from goal temperature averaged 0.2 °C throughout the steady-state maintenance phase, and no treatment for shivering was necessary during the protocol. Histopathology of esophageal tissue showed no adverse effects from the device. A new esophageal heat transfer device successfully and safely induced, maintained, and reversed therapeutic hypothermia in large swine. Goal temperature was maintained within a narrow range, and thermogenic shivering did not occur. These findings suggest a useful new modality to induce therapeutic hypothermia. Copyright © 2013 The Authors. Published by Elsevier Ireland Ltd.. All rights reserved.

Early Weightbearing Protocol in Operative Fixation of Acute Jones Fractures.

PubMed

Waverly, Brett J; Sorensen, Matthew D; Sorensen, Tyler K

The treatment of Jones fractures has been controversial in terms of nonoperative versus operative management, given the high incidence of nonunion secondary to the delicate blood supply to the proximal fifth metatarsal. We report a retrospective review of a patient cohort treated with an early weightbearing protocol after operative intramedullary fixation in acute Jones fractures. Thirty-one consecutive patients with an acute Jones fracture underwent operative fixation with a single intramedullary solid screw. The postoperative protocol consisted of immediate weightbearing in a controlled ankle motion boot for 2 weeks with a gradual transition to regular shoes at 2 weeks postoperative. At 2 weeks, the patients were allowed to perform low-impact activities such as walking, swimming, biking, or elliptical training. Patients were allowed to return to all activities, as tolerated, regardless of radiographic healing, at 6 weeks postoperatively. Serial postoperative radiographs were taken at 2-week intervals to determine radiographic union. Our patient population consisted of 24 males (77.42%) and 7 females (22.58%), with a mean average age of 37.5 ± 12.59 years and mean average body mass index of 25.7 ± 2.32 kg/m 2 . Fracture union was observed in all 31 patients (100%) at a mean average of 5.7 ± 1.47 (range 4 to 10) weeks. Two (6.5%) patients required hardware removal, with one (3.2%) experiencing sural neuritis. This review of patients undergoing early weightbearing after operative fixation of an acute Jones fracture demonstrated a satisfactory incidence of union compared with traditional postoperative protocols at a mean follow-up duration of 18.58 ± 5.66 months. Copyright © 2017 The American College of Foot and Ankle Surgeons. Published by Elsevier Inc. All rights reserved.

CellSort: a support vector machine tool for optimizing fluorescence-activated cell sorting and reducing experimental effort.

PubMed

Yu, Jessica S; Pertusi, Dante A; Adeniran, Adebola V; Tyo, Keith E J

2017-03-15

High throughput screening by fluorescence activated cell sorting (FACS) is a common task in protein engineering and directed evolution. It can also be a rate-limiting step if high false positive or negative rates necessitate multiple rounds of enrichment. Current FACS software requires the user to define sorting gates by intuition and is practically limited to two dimensions. In cases when multiple rounds of enrichment are required, the software cannot forecast the enrichment effort required. We have developed CellSort, a support vector machine (SVM) algorithm that identifies optimal sorting gates based on machine learning using positive and negative control populations. CellSort can take advantage of more than two dimensions to enhance the ability to distinguish between populations. We also present a Bayesian approach to predict the number of sorting rounds required to enrich a population from a given library size. This Bayesian approach allowed us to determine strategies for biasing the sorting gates in order to reduce the required number of enrichment rounds. This algorithm should be generally useful for improve sorting outcomes and reducing effort when using FACS. Source code available at http://tyolab.northwestern.edu/tools/ . k-tyo@northwestern.edu. Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

Categorizing Variations of Student-Implemented Sorting Algorithms

ERIC Educational Resources Information Center

Taherkhani, Ahmad; Korhonen, Ari; Malmi, Lauri

2012-01-01

In this study, we examined freshmen students' sorting algorithm implementations in data structures and algorithms' course in two phases: at the beginning of the course before the students received any instruction on sorting algorithms, and after taking a lecture on sorting algorithms. The analysis revealed that many students have insufficient…

Review of log sort yards

Treesearch

John Rusty Dramm; Gerry L. Jackson; Jenny Wong

2002-01-01

This report provides a general overview of current log sort yard operations in the United States, including an extensive literature review and information collected during on-site visits to several operations throughout the nation. Log sort yards provide many services in marketing wood and fiber by concentrating, merchandising, processing, sorting, and adding value to...

COST EVALUATION OF AUTOMATED AND MANUAL POST- CONSUMER PLASTIC BOTTLE SORTING SYSTEMS

EPA Science Inventory

This project evaluates, on the basis of performance and cost, two Automated BottleSort® sorting systems for post-consumer commingled plastic containers developed by Magnetic Separation Systems. This study compares the costs to sort mixed bales of post-consumer plastic at these t...

TU-EF-304-04: A Heart Motion Model for Proton Scanned Beam Chest Radiotherapy

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

White, B; Kiely, J Blanco; Lin, L

Purpose: To model fast-moving heart surface motion as a function of cardiac-phase in order to compensate for the lack of cardiac-gating in evaluating accurate dose to coronary structures. Methods: Ten subjects were prospectively imaged with a breath-hold, cardiac-gated MRI protocol to determine heart surface motion. Radial and planar views of the heart were resampled into a 3-dimensional volume representing one heartbeat. A multi-resolution optical flow deformable image registration algorithm determined tissue displacement during the cardiac-cycle. The surface of the heart was modeled as a thin membrane comprised of voxels perpendicular to a pencil beam scanning (PBS) beam. The membrane’s out-of-planemore » spatial displacement was modeled as a harmonic function with Lame’s equations. Model accuracy was assessed with the root mean squared error (RMSE). The model was applied to a cohort of six chest wall irradiation patients with PBS plans generated on phase-sorted 4DCT. Respiratory motion was separated from the cardiac motion with a previously published technique. Volumetric dose painting was simulated and dose accumulated to validate plan robustness (target coverage variation accepted within 2%). Maximum and mean heart surface dose assessed the dosimetric impact of heart and coronary artery motion. Results: Average and maximum heart surface displacements were 2.54±0.35mm and 3.6mm from the end-diastole phase to the end-systole cardiac-phase respectively. An average RMSE of 0.11±0.04 showed the model to be accurate. Observed errors were greatest between the circumflex artery and mitral valve level of the heart anatomy. Heart surface displacements correspond to a 3.6±1.0% and 5.1±2.3% dosimetric impact on the maximum and mean heart surface DVH indicators respectively. Conclusion: Although heart surface motion parallel to beam’s direction was substantial, its maximum dosimetric impact was 5.1±2.3%. Since PBS delivers low doses to coronary structures relative to photon radiotherapy, it is unknown whether this variation would be clinically significant for late effects.« less

SU-E-J-141: Comparison of Dose Calculation On Automatically Generated MRBased ED Maps and Corresponding Patient CT for Clinical Prostate EBRT Plans

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

Schadewaldt, N; Schulz, H; Helle, M

2014-06-01

Purpose: To analyze the effect of computing radiation dose on automatically generated MR-based simulated CT images compared to true patient CTs. Methods: Six prostate cancer patients received a regular planning CT for RT planning as well as a conventional 3D fast-field dual-echo scan on a Philips 3.0T Achieva, adding approximately 2 min of scan time to the clinical protocol. Simulated CTs (simCT) where synthesized by assigning known average CT values to the tissue classes air, water, fat, cortical and cancellous bone. For this, Dixon reconstruction of the nearly out-of-phase (echo 1) and in-phase images (echo 2) allowed for water andmore » fat classification. Model based bone segmentation was performed on a combination of the DIXON images. A subsequent automatic threshold divides into cortical and cancellous bone. For validation, the simCT was registered to the true CT and clinical treatment plans were re-computed on the simCT in pinnacle{sup 3}. To differentiate effects related to the 5 tissue classes and changes in the patient anatomy not compensated by rigid registration, we also calculate the dose on a stratified CT, where HU values are sorted in to the same 5 tissue classes as the simCT. Results: Dose and volume parameters on PTV and risk organs as used for the clinical approval were compared. All deviations are below 1.1%, except the anal sphincter mean dose, which is at most 2.2%, but well below clinical acceptance threshold. Average deviations are below 0.4% for PTV and risk organs and 1.3% for the anal sphincter. The deviations of the stratifiedCT are in the same range as for the simCT. All plans would have passed clinical acceptance thresholds on the simulated CT images. Conclusion: This study demonstrated the clinical usability of MR based dose calculation with the presented Dixon acquisition and subsequent fully automatic image processing. N. Schadewaldt, H. Schulz, M. Helle and S. Renisch are employed by Phlips Technologie Innovative Techonologies, a subsidiary of Royal Philips NV.« less

Who needs inpatient detox? Development and implementation of a hospitalist protocol for the evaluation of patients for alcohol detoxification.

PubMed

Stephens, John R; Liles, E Allen; Dancel, Ria; Gilchrist, Michael; Kirsch, Jonathan; DeWalt, Darren A

2014-04-01

Clinicians caring for patients seeking alcohol detoxification face many challenges, including lack of evidence-based guidelines for treatment and high recidivism rates. To develop a standardized protocol for determining which alcohol dependent patients seeking detoxification need inpatient versus outpatient treatment, and to study the protocol's implementation. Review of best evidence by ad hoc task force and subsequent creation of standardized protocol. Prospective observational evaluation of initial protocol implementation. Patients presenting for alcohol detoxification. Development and implementation of a protocol for evaluation and treatment of patients requesting alcohol detoxification. Number of admissions per month with primary alcohol related diagnosis (DRG), 30-day readmission rate, and length of stay, all measured before and after protocol implementation. We identified one randomized clinical trial and three cohort studies to inform the choice of inpatient versus outpatient detoxification, along with one prior protocol in this population, and combined that data with clinical experience to create an institutional protocol. After implementation, the average number of alcohol related admissions was 15.9 per month, compared with 18.9 per month before implementation (p = 0.037). There was no difference in readmission rate or length of stay. Creation and utilization of a protocol led to standardization of care for patients requesting detoxification from alcohol. Initial evaluation of protocol implementation showed a decrease in number of admissions.

Periodically Relieving Ischial Sitting Load to Decrease the Risk of Pressure Ulcers

PubMed Central

Makhsous, Mohsen; Rowles, Diane M.; Rymer, William Z.; Bankard, James; Nam, Ellis K.; Chen, David; Lin, Fang

2010-01-01

Objective To investigate the relieving effect on interface pressure of an alternate sitting protocol involving a sitting posture that reduces ischial support. Design Repeated measures in 2 protocols on 3 groups of subjects. Setting Laboratory. Participants Twenty able-bodied persons, 20 persons with paraplegia, and 20 persons with tetraplegia. Interventions Two 1-hour protocols were used: alternate and normal plus pushup. In the alternate protocol, sitting posture was alternated every 10 minutes between normal (sitting upright with ischial support) and with partially removed ischial support (WO-BPS) postures; in the normal plus pushup protocol, sitting was in normal posture with pushups (lifting the subject off the seat) performed every 20 minutes. Main Outcome Measure Interface pressure on seat and backrest. Results In WO-BPS posture, the concentrated interface pressure observed around the ischia in normal posture was significantly repositioned to the thighs. By cyclically repositioning the interface pressure, the alternate protocol was superior to the normal plus pushup protocol in terms of a significantly lower average interface pressure over the buttocks. Conclusions A sitting protocol periodically reducing the ischial support helps lower the sitting load on the buttocks, especially the area close to ischial tuberosities. PMID:17601466

Transferable residues from dog fur and plasma cholinesterase inhibition in dogs treated with a flea control dip containing chlorpyrifos.

PubMed Central

Boone, J S; Tyler, J W; Chambers, J E

2001-01-01

We studied chlorpyrifos, an insecticide present in a commercial dip for treating ectoparasites in dogs, to estimate the amount of transferable residues that children could obtain from their treated pets. Although the chlorpyrifos dip is no longer supported by the manufacturer, the methodology described herein can help determine transferable residues from other flea control insecticide formulations. Twelve dogs of different breeds and weights were dipped using the recommended guidelines with a commercial, nonprescription chlorpyrifos flea dip for 4 consecutive treatments at 3-week intervals (nonshampoo protocol) and another 12 dogs were dipped with shampooing between dips (shampoo protocol). The samples collected at 4 hr and 7, 14, and 21 days after treatment in the nonshampoo protocol averaged 971, 157, 70, and 26 microg chlorpyrifos, respectively; in the shampoo protocol the samples averaged 459, 49, 15, and 10 microg, respectively. The highest single sample was about 7,000 microg collected at 4 hr. The pretreatment specific activities in the plasma of the dogs were about 75 nmol/min/mg protein for butyrylcholinesterase (BChE), and 9 nmol/min/mg protein for acetylcholinesterase (AChE). BChE was inhibited 50-75% throughout the study, and AChE was inhibited 11-18% in the nonshampoo protocol; inhibition was not as great in the shampoo protocol. There was no correlation (p

Application of visible spectroscopy in waste sorting

NASA Astrophysics Data System (ADS)

Spiga, Philippe; Bourely, Antoine

2011-10-01

Today, waste recycling, (bottles, papers...), is a mechanical operation: the waste are crushed, fused and agglomerated in order to obtain new manufactured products (e.g. new bottles, clothes ...). The plastics recycling is the main application in the color sorting process. The colorless plastics recovered are more valuable than the colored plastics. Other emergent applications are in the paper sorting, where the main goal is to sort dyed paper from white papers. Up to now, Pellenc Selective Technologies has manufactured color sorting machines based on RGB cameras. Three dimensions (red, green and blue) are no longer sufficient to detect low quantities of dye in the considered waste. In order to increase the efficiency of the color detection, a new sorting machine, based on visible spectroscopy, has been developed. This paper presents the principles of the two approaches and their difference in terms of sorting performance, making visible spectroscopy a clear winner.

MetaSort untangles metagenome assembly by reducing microbial community complexity

PubMed Central

Ji, Peifeng; Zhang, Yanming; Wang, Jinfeng; Zhao, Fangqing

2017-01-01

Most current approaches to analyse metagenomic data rely on reference genomes. Novel microbial communities extend far beyond the coverage of reference databases and de novo metagenome assembly from complex microbial communities remains a great challenge. Here we present a novel experimental and bioinformatic framework, metaSort, for effective construction of bacterial genomes from metagenomic samples. MetaSort provides a sorted mini-metagenome approach based on flow cytometry and single-cell sequencing methodologies, and employs new computational algorithms to efficiently recover high-quality genomes from the sorted mini-metagenome by the complementary of the original metagenome. Through extensive evaluations, we demonstrated that metaSort has an excellent and unbiased performance on genome recovery and assembly. Furthermore, we applied metaSort to an unexplored microflora colonized on the surface of marine kelp and successfully recovered 75 high-quality genomes at one time. This approach will greatly improve access to microbial genomes from complex or novel communities. PMID:28112173

Ubiquitin-dependent sorting of integral membrane proteins for degradation in lysosomes

PubMed Central

Piper, Robert C.

2007-01-01

Summary The pathways that deliver newly synthesized proteins that reside in lysosomes are well understood by comparison with our knowledge of how integral membrane proteins are sorted and delivered to the lysosome for degradation. Many membrane proteins are sorted to lysosomes following ubiquitination, which provides a sorting signal that can operate for sorting at the TGN (trans-Golgi network), at the plasma membrane or at the endosome for delivery into lumenal vesicles. Candidate multicomponent machines that can potentially move ubiquitinated integral membrane cargo proteins have been identified, but much work is still required to ascertain which of these candidates directly recognizes ubiquitinated cargo and what they do with cargo after recognition. In the case of the machinery required for sorting into the lumenal vesicles of endosomes, other functions have also been determined including a link between sorting and movement of endosomes along microtubules. PMID:17689064

Is it time to revisit the log-sort yard?

Treesearch

John Dramm; Gerry Jackson

2000-01-01

Log-sort yards provide better utilization and marketing with improved value recovery of currently available timber resources in North America. Log-sort yards provide many services in marketing wood and fiber by concentrating, merchandising, manufacturing, sorting, and adding value to logs. Such operations supply forest products firms with desired raw materials, which...

Word Sorts for General Music Classes

ERIC Educational Resources Information Center

Cardany, Audrey Berger

2015-01-01

Word sorts are standard practice for aiding children in acquiring skills in English language arts. When included in the general music classroom, word sorts may aid students in acquiring a working knowledge of music vocabulary. The author shares a word sort activity drawn from vocabulary in John Lithgow's children's book "Never Play…

The main factors influencing canine demodicosis treatment outcome and determination of optimal therapy.

PubMed

Arsenović, Milica; Pezo, Lato; Vasić, Nebojša; Ćirić, Rodoljub; Stefanović, Milan

2015-07-01

The main idea of this research was to evaluate the efficacy of canine demodicosis conventional treatments using mathematical analyses. All available papers published between 1980 and 2014 were used in this study. One hundred six clinical trials enrolling 3414 cases of generalized demodicosis in dogs are studied. Dogs entered in the analysis were only the ones in which the disease occurred naturally, excluding the studies in which transplantation of Demodex canis mites was done from other animals. In conventional acaricide treatments, sorted according to active substances (moxidectin, amitraz, doramectin, ivermectin, and milbemycin oxime), the way of application (spot-on, dips, orally, or subcutaneous), concentration, and interval of application were used as input parameters in mathematical modeling. Data of interest were the treatment outcome, the number of dogs that went into remission, the number of animals not responding to treatment microscopically, the average duration of therapy, the follow-up period, the number of patients with disease recurrence, the number of adverse effects, and the number of animals with side effects. Dogs lost to follow-up or when the treatment was discontinued, due to various reasons not in connection with the therapy protocol, were not considered. Statistical and mathematical analyses were applied for prediction of the drugs' effectiveness. Developed mathematical models showed satisfactorily r (2), higher than 0.87. Good evidence for recommending the use of milbemycin oxime PO (0.5 mg/kg, daily) and moxidectin spot-on (Advocate®, Bayer) weekly is found. A bit less effective therapies were based on ivermectin PO (0.5 mg/kg, daily), moxidectin PO (0.35 mg/kg, daily), and amitraz dips (0.05 % solution, weekly), respectively. It is important to keep in mind that Advocate® is recommended by the manufacturer for use in milder cases.

A highly efficient protocol for micropropagation of Begonia tuberous.

PubMed

Duong, Tan Nhut; Nguyen, Thanh Hai; Mai, Xuan Phan

2010-01-01

A protocol for micropropagation of begonia was established utilizing a thin cell layer (TCL) system. This system has been employed to produce several thousand shoots per sample. Explant size and position, and plant growth regulators (PGRs) contribute to the tissue morphogenesis. By optimizing the size of the tissue and applying an improved selection procedure, shoots were elongated in 8 weeks of culture, with an average number of 210 +/- 9.7 shoots per segment. This system has facilitated a number of studies using TCL as a model for micropropagation and will enable the large-scale production of begonia. On an average, the best treatment would allow production of about 10,000 plantlets by the micropropagation of the axillary buds of one plant with five petioles, within a period of 8 months.

Fetal shielding combined with state of the art CT dose reduction strategies during maternal chest CT.

PubMed

Chatterson, Leslie C; Leswick, David A; Fladeland, Derek A; Hunt, Megan M; Webster, Stephen; Lim, Hyun

2014-07-01

Custom bismuth-antimony shields were previously shown to reduce fetal dose by 53% on an 8DR (detector row) CT scanner without dynamic adaptive section collimation (DASC), automatic tube current modulation (ATCM) or adaptive statistical iterative reconstruction (ASiR). The purpose of this study is to compare the effective maternal and average fetal organ dose reduction both with and without bismuth-antimony shields on a 64DR CT scanner using DASC, ATCM and ASiR during maternal CTPA. A phantom with gravid prosthesis and a bismuth-antimony shield were used. Thermoluminescent dosimeters (TLDs) measured fetal radiation dose. The average fetal organ dose and effective maternal dose were determined using 100 kVp, scanning from the lung apices to the diaphragm utilizing DASC, ATCM and ASiR on a 64DR CT scanner with and without shielding in the first and third trimester. Isolated assessment of DASC was done via comparing a new 8DR scan without DASC to a similar scan on the 64DR with DASC. Average third trimester unshielded fetal dose was reduced from 0.22 mGy ± 0.02 on the 8DR to 0.13 mGy ± 0.03 with the conservative 64DR protocol that included 30% ASiR, DASC and ATCM (42% reduction, P<0.01). Use of a shield further reduced average third trimester fetal dose to 0.04 mGy ± 0.01 (69% reduction, P<0.01). The average fetal organ dose reduction attributable to DASC alone was modest (6% reduction from 0.17 mGy ± 0.02 to 0.16 mGy ± 0.02, P=0.014). First trimester fetal organ dose on the 8DR protocol was 0.07 mGy ± 0.03. This was reduced to 0.05 mGy ± 0.03 on the 64DR protocol without shielding (30% reduction, P=0.009). Shields further reduced this dose to below accurately detectable levels. Effective maternal dose was reduced from 4.0 mSv on the 8DR to 2.5 mSv on the 64DR scanner using the conservative protocol (38% dose reduction). ASiR, ATCM and DASC combined significantly reduce effective maternal and fetal organ dose during CTPA. Shields continue to be an effective means of fetal dose reduction. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

T2-weighted four dimensional magnetic resonance imaging with result-driven phase sorting

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

Liu, Yilin; Yin, Fang-Fang; Cai, Jing, E-mail: jing.cai@duke.edu

2015-08-15

Purpose: T2-weighted MRI provides excellent tumor-to-tissue contrast for target volume delineation in radiation therapy treatment planning. This study aims at developing a novel T2-weighted retrospective four dimensional magnetic resonance imaging (4D-MRI) phase sorting technique for imaging organ/tumor respiratory motion. Methods: A 2D fast T2-weighted half-Fourier acquisition single-shot turbo spin-echo MR sequence was used for image acquisition of 4D-MRI, with a frame rate of 2–3 frames/s. Respiratory motion was measured using an external breathing monitoring device. A phase sorting method was developed to sort the images by their corresponding respiratory phases. Besides, a result-driven strategy was applied to effectively utilize redundantmore » images in the case when multiple images were allocated to a bin. This strategy, selecting the image with minimal amplitude error, will generate the most representative 4D-MRI. Since we are using a different image acquisition mode for 4D imaging (the sequential image acquisition scheme) with the conventionally used cine or helical image acquisition scheme, the 4D dataset sufficient condition was not obviously and directly predictable. An important challenge of the proposed technique was to determine the number of repeated scans (N{sub R}) required to obtain sufficient phase information at each slice position. To tackle this challenge, the authors first conducted computer simulations using real-time position management respiratory signals of the 29 cancer patients under an IRB-approved retrospective study to derive the relationships between N{sub R} and the following factors: number of slices (N{sub S}), number of 4D-MRI respiratory bins (N{sub B}), and starting phase at image acquisition (P{sub 0}). To validate the authors’ technique, 4D-MRI acquisition and reconstruction were simulated on a 4D digital extended cardiac-torso (XCAT) human phantom using simulation derived parameters. Twelve healthy volunteers were involved in an IRB-approved study to investigate the feasibility of this technique. Results: 4D data acquisition completeness (C{sub p}) increases as NR increases in an inverse-exponential fashion (C{sub p} = 100 − 99 × exp(−0.18 × N{sub R}), when N{sub B} = 6, fitted using 29 patients’ data). The N{sub R} required for 4D-MRI reconstruction (defined as achieving 95% completeness, C{sub p} = 95%, N{sub R} = N{sub R,95}) is proportional to N{sub B} (N{sub R,95} ∼ 2.86 × N{sub B}, r = 1.0), but independent of N{sub S} and P{sub 0}. Simulated XCAT 4D-MRI showed a clear pattern of respiratory motion. Tumor motion trajectories measured on 4D-MRI were comparable to the average input signal, with a mean relative amplitude error of 2.7% ± 2.9%. Reconstructed 4D-MRI for healthy volunteers illustrated clear respiratory motion on three orthogonal planes, with minimal image artifacts. The artifacts were presumably caused by breathing irregularity and incompleteness of data acquisition (95% acquired only). The mean relative amplitude error between critical structure trajectory and average breathing curve for 12 healthy volunteers is 2.5 ± 0.3 mm in superior–inferior direction. Conclusions: A novel T2-weighted retrospective phase sorting 4D-MRI technique has been developed and successfully applied on digital phantom and healthy volunteers.« less

Hydrodynamic sorting and transport of terrestrially derived organic carbon in sediments of the Mississippi and Atchafalaya Rivers

NASA Astrophysics Data System (ADS)

Bianchi, Thomas S.; Galler, John J.; Allison, Mead A.

2007-06-01

Over the course of two years, four cruises were conducted at varying levels of discharge in the lower Mississippi and Atchafalaya Rivers (MR and AR) where grab samples were collected from sand- and mud-dominated sediments. The tetramethylammonium hydroxide (TMAH) thermochemolysis method was used to determine sources of terrestrially derived organic carbon (OC) in these two sediment types, to examine the effects of hydrodynamic sorting on lignin sources in river sediments. Average lignin concentrations in the lower MR were 1.4 ± 1.1 mg gOC -1 at English Turn (ET) and 10.4 ± 27.4 mg gOC -1 at Venice. Using these concentrations, annual lignin fluxes to the Gulf of Mexico, from tidal and estuarine mud remobilization at ET and Venice, were 3.1 ± 2.5 × 10 5 kg and 11.4 ± 30.0 × 10 5 kg, respectively. Much of the lignin-derived materials in muddy sediments appeared to be derived from non-woody grass-like sources - which should decay more quickly than the woody materials typically found in the sandy deposits. The average total OC% (1.93 ± 0.47) of English Turn sands yields an annual flux of 0.34 ± 0.09 × 10 9 kg. Lignin flux in the English Turn sands (3.6 ± 2.6 mg gC -1) using the numbers above would be 12.2 ± 9.4 × 10 5 kg. The extensive amounts of sand-sized woody materials (coffee-grinds) found in the sandy sediments in both the AR and MR are likely derived from woody plant materials. This is the first time it has been demonstrated that sandy sediments in the MR provide an equally important pathway (compared to muds) for the transport of terrestrially derived organic matter to the northern Gulf of Mexico. Using the AR average %OC in sand (1.16 ± 0.72), we estimated an annual flux of OC to the shelf of 0.13 ± 0.07 × 10 9 kg. Lignin flux for AR sands was estimated to be 12.4 ± 12.1 × 10 5 kg. Despite the high error associated with these numbers, we observe for the first time that the flux of lignin in sandy sediments in the AR to the northern Gulf of Mexico is comparable to that found in the MR. These results further support the likelihood of grain-size related hydrodynamic sorting of terrestrially derived organic carbon in the lower Mississippi and Atchafalaya Rivers, suggesting that there is a distinct sandy sediment organic fraction contributed by major rivers to the global carbon cycle.

Brainlab: A Python Toolkit to Aid in the Design, Simulation, and Analysis of Spiking Neural Networks with the NeoCortical Simulator.

PubMed

Drewes, Rich; Zou, Quan; Goodman, Philip H

2009-01-01

Neuroscience modeling experiments often involve multiple complex neural network and cell model variants, complex input stimuli and input protocols, followed by complex data analysis. Coordinating all this complexity becomes a central difficulty for the experimenter. The Python programming language, along with its extensive library packages, has emerged as a leading "glue" tool for managing all sorts of complex programmatic tasks. This paper describes a toolkit called Brainlab, written in Python, that leverages Python's strengths for the task of managing the general complexity of neuroscience modeling experiments. Brainlab was also designed to overcome the major difficulties of working with the NCS (NeoCortical Simulator) environment in particular. Brainlab is an integrated model-building, experimentation, and data analysis environment for the powerful parallel spiking neural network simulator system NCS.

Brainlab: A Python Toolkit to Aid in the Design, Simulation, and Analysis of Spiking Neural Networks with the NeoCortical Simulator

PubMed Central

Drewes, Rich; Zou, Quan; Goodman, Philip H.

2008-01-01

Neuroscience modeling experiments often involve multiple complex neural network and cell model variants, complex input stimuli and input protocols, followed by complex data analysis. Coordinating all this complexity becomes a central difficulty for the experimenter. The Python programming language, along with its extensive library packages, has emerged as a leading “glue” tool for managing all sorts of complex programmatic tasks. This paper describes a toolkit called Brainlab, written in Python, that leverages Python's strengths for the task of managing the general complexity of neuroscience modeling experiments. Brainlab was also designed to overcome the major difficulties of working with the NCS (NeoCortical Simulator) environment in particular. Brainlab is an integrated model-building, experimentation, and data analysis environment for the powerful parallel spiking neural network simulator system NCS. PMID:19506707

Proteolipidic Composition of Exosomes Changes during Reticulocyte Maturation*

PubMed Central

Carayon, Kévin; Chaoui, Karima; Ronzier, Elsa; Lazar, Ikrame; Bertrand-Michel, Justine; Roques, Véronique; Balor, Stéphanie; Terce, François; Lopez, André; Salomé, Laurence; Joly, Etienne

2011-01-01

During the orchestrated process leading to mature erythrocytes, reticulocytes must synthesize large amounts of hemoglobin, while eliminating numerous cellular components. Exosomes are small secreted vesicles that play an important role in this process of specific elimination. To understand the mechanisms of proteolipidic sorting leading to their biogenesis, we have explored changes in the composition of exosomes released by reticulocytes during their differentiation, in parallel to their physical properties. By combining proteomic and lipidomic approaches, we found dramatic alterations in the composition of the exosomes retrieved over the course of a 7-day in vitro differentiation protocol. Our data support a previously proposed model, whereby in reticulocytes the biogenesis of exosomes involves several distinct mechanisms for the preferential recruitment of particular proteins and lipids and suggest that the respective prominence of those pathways changes over the course of the differentiation process. PMID:21828046

The Giardia genome project database.

PubMed

McArthur, A G; Morrison, H G; Nixon, J E; Passamaneck, N Q; Kim, U; Hinkle, G; Crocker, M K; Holder, M E; Farr, R; Reich, C I; Olsen, G E; Aley, S B; Adam, R D; Gillin, F D; Sogin, M L

2000-08-15

The Giardia genome project database provides an online resource for Giardia lamblia (WB strain, clone C6) genome sequence information. The database includes edited single-pass reads, the results of BLASTX searches, and details of progress towards sequencing the entire 12 million-bp Giardia genome. Pre-sorted BLASTX results can be retrieved based on keyword searches and BLAST searches of the high throughput Giardia data can be initiated from the web site or through NCBI. Descriptions of the genomic DNA libraries, project protocols and summary statistics are also available. Although the Giardia genome project is ongoing, new sequences are made available on a bi-monthly basis to ensure that researchers have access to information that may assist them in the search for genes and their biological function. The current URL of the Giardia genome project database is www.mbl.edu/Giardia.

Average waiting time in FDDI networks with local priorities

NASA Technical Reports Server (NTRS)

Gercek, Gokhan

1994-01-01

A method is introduced to compute the average queuing delay experienced by different priority group messages in an FDDI node. It is assumed that no FDDI MAC layer priorities are used. Instead, a priority structure is introduced to the messages at a higher protocol layer (e.g. network layer) locally. Such a method was planned to be used in Space Station Freedom FDDI network. Conservation of the average waiting time is used as the key concept in computing average queuing delays. It is shown that local priority assignments are feasable specially when the traffic distribution is asymmetric in the FDDI network.

Cardiac-Specific Conversion Factors to Estimate Radiation Effective Dose From Dose-Length Product in Computed Tomography.

PubMed

Trattner, Sigal; Halliburton, Sandra; Thompson, Carla M; Xu, Yanping; Chelliah, Anjali; Jambawalikar, Sachin R; Peng, Boyu; Peters, M Robert; Jacobs, Jill E; Ghesani, Munir; Jang, James J; Al-Khalidi, Hussein; Einstein, Andrew J

2018-01-01

This study sought to determine updated conversion factors (k-factors) that would enable accurate estimation of radiation effective dose (ED) for coronary computed tomography angiography (CTA) and calcium scoring performed on 12 contemporary scanner models and current clinical cardiac protocols and to compare these methods to the standard chest k-factor of 0.014 mSv·mGy -1 cm -1 . Accurate estimation of ED from cardiac CT scans is essential to meaningfully compare the benefits and risks of different cardiac imaging strategies and optimize test and protocol selection. Presently, ED from cardiac CT is generally estimated by multiplying a scanner-reported parameter, the dose-length product, by a k-factor which was determined for noncardiac chest CT, using single-slice scanners and a superseded definition of ED. Metal-oxide-semiconductor field-effect transistor radiation detectors were positioned in organs of anthropomorphic phantoms, which were scanned using all cardiac protocols, 120 clinical protocols in total, on 12 CT scanners representing the spectrum of scanners from 5 manufacturers (GE, Hitachi, Philips, Siemens, Toshiba). Organ doses were determined for each protocol, and ED was calculated as defined in International Commission on Radiological Protection Publication 103. Effective doses and scanner-reported dose-length products were used to determine k-factors for each scanner model and protocol. k-Factors averaged 0.026 mSv·mGy -1 cm -1 (95% confidence interval: 0.0258 to 0.0266) and ranged between 0.020 and 0.035 mSv·mGy -1 cm -1 . The standard chest k-factor underestimates ED by an average of 46%, ranging from 30% to 60%, depending on scanner, mode, and tube potential. Factors were higher for prospective axial versus retrospective helical scan modes, calcium scoring versus coronary CTA, and higher (100 to 120 kV) versus lower (80 kV) tube potential and varied among scanner models (range of average k-factors: 0.0229 to 0.0277 mSv·mGy -1 cm -1 ). Cardiac k-factors for all scanners and protocols are considerably higher than the k-factor currently used to estimate ED of cardiac CT studies, suggesting that radiation doses from cardiac CT have been significantly and systematically underestimated. Using cardiac-specific factors can more accurately inform the benefit-risk calculus of cardiac-imaging strategies. Copyright © 2018 The Authors. Published by Elsevier Inc. All rights reserved.

Effects of a meaningful, a discriminative, and a meaningless stimulus on equivalence class formation.

PubMed

Fields, Lanny; Arntzen, Erik; Nartey, Richard K; Eilifsen, Christoffer

2012-03-01

Thirty college students attempted to form three 3-node 5-member equivalence classes under the simultaneous protocol. After concurrent training of AB, BC, CD, and DE relations, all probes used to assess the emergence of symmetrical, transitive, and equivalence relations were presented for two test blocks. When the A-E stimuli were all abstract shapes, none of 10 participants formed classes. When the A, B, D, and E stimuli were abstract shapes and the C stimuli were meaningful pictures, 8 of 10 participants formed classes. This high yield may reflect the expansion of existing classes that consist of the associates of the meaningful stimuli, rather than the formation of the ABCDE classes, per se. When the A-E stimuli were abstract shapes and the C stimuli became S(D)s prior to class formation, 5 out of 10 participants formed classes. Thus, the discriminative functions served by the meaningful stimuli can account for some of the enhancement of class formation produced by the inclusion of a meaningful stimulus as a class member. A sorting task, which provided a secondary measure of class formation, indicated the formation of all three classes when the emergent relations probes indicated the same outcome. In contrast, the sorting test indicated "partial" class formation when the emergent relations test indicated no class formation. Finally, the effects of nodal distance on the relatedness of stimuli in the equivalence classes were not influenced by the functions served by the C stimuli in the equivalence classes.

Effects of a Meaningful, a Discriminative, and a Meaningless Stimulus on Equivalence Class Formation

PubMed Central

Fields, Lanny; Arntzen, Erik; Nartey, Richard K; Eilifsen, Christoffer

2012-01-01

Thirty college students attempted to form three 3-node 5-member equivalence classes under the simultaneous protocol. After concurrent training of AB, BC, CD, and DE relations, all probes used to assess the emergence of symmetrical, transitive, and equivalence relations were presented for two test blocks. When the A–E stimuli were all abstract shapes, none of 10 participants formed classes. When the A, B, D, and E stimuli were abstract shapes and the C stimuli were meaningful pictures, 8 of 10 participants formed classes. This high yield may reflect the expansion of existing classes that consist of the associates of the meaningful stimuli, rather than the formation of the ABCDE classes, per se. When the A–E stimuli were abstract shapes and the C stimuli became SDs prior to class formation, 5 out of 10 participants formed classes. Thus, the discriminative functions served by the meaningful stimuli can account for some of the enhancement of class formation produced by the inclusion of a meaningful stimulus as a class member. A sorting task, which provided a secondary measure of class formation, indicated the formation of all three classes when the emergent relations probes indicated the same outcome. In contrast, the sorting test indicated “partial” class formation when the emergent relations test indicated no class formation. Finally, the effects of nodal distance on the relatedness of stimuli in the equivalence classes were not influenced by the functions served by the C stimuli in the equivalence classes. PMID:22389524

Sorting out Ideas about Function

ERIC Educational Resources Information Center

Hillen, Amy F.; Malik, LuAnn

2013-01-01

Card sorting has the potential to provide opportunities for exploration of a variety of topics and levels. In a card-sorting task, each participant is presented with a set of cards--each of which depicts a relationship--and is asked to sort the cards into categories that make sense to him or her. The concept of function is critical to…

Gender Sorting across K-12 Schools in the United States

ERIC Educational Resources Information Center

Long, Mark C.; Conger, Dylan

2013-01-01

This article documents evidence of nonrandom gender sorting across K-12 schools in the United States. The sorting exists among coed schools and at all grade levels, and it is highest in the secondary school grades. We observe some gender sorting across school sectors and types: for instance, males are slightly underrepresented in private schools…

Lazarus's BASIC ID: Making Initial Client Assessments Using Q-Sorts.

ERIC Educational Resources Information Center

Miller, Mark J.

1987-01-01

Presents overview of Lazarus's multimodal therapy model and the Q-sort, an observer-evaluation scoring instrument. Outlines feasibility of integrating Q-sort within multimodal model. Describes both a preliminary attempt using expert raters to categorize Q-sort cards within the model and a case study on how to assess client by incorporating Q-sort…

Machine Vision System for Color Sorting Wood Edge-Glued Panel Parts

Treesearch

Qiang Lu; S. Srikanteswara; W. King; T. Drayer; Richard Conners; D. Earl Kline; Philip A. Araman

1997-01-01

This paper describes an automatic color sorting system for hardwood edge-glued panel parts. The color sorting system simultaneously examines both faces of a panel part and then determines which face has the "better" color given specified color uniformity and priority defined by management. The real-time color sorting system software and hardware are briefly...

Flankers Facilitate 3-Year-Olds' Performance in a Card-Sorting Task

ERIC Educational Resources Information Center

Jordan, Patricia L.; Morton, J. Bruce

2008-01-01

Three-year-old children often act inflexibly in card-sorting tasks by continuing to sort by an old rule after being asked to switch and sort by a new rule. This inflexibility has been variously attributed to age-related constraints on higher order rule use, object redescription, and attention shifting. In 2 experiments, flankers that were…

My eSorts and Digital Extensions of Word Study

ERIC Educational Resources Information Center

Zucker, Tricia A.; Invernizzi, Marcia

2008-01-01

"My eSorts" is a strategy for helping children learn to read and spell in a socially motivated context. It is based on developmental spelling research and the word study approach to teaching phonics and spelling. "eSorting" employs digital desktop publishing tools that allow children to author their own electronic word sorts and then share these…

Continuous sorting of Brownian particles using coupled photophoresis and asymmetric potential cycling.

PubMed

Ng, Tuck Wah; Neild, Adrian; Heeraman, Pascal

2008-03-15

Feasible sorters need to function rapidly and permit the input and delivery of particles continuously. Here, we describe a scheme that incorporates (i) restricted spatial input location and (ii) orthogonal sort and movement direction features. Sorting is achieved using an asymmetric potential that is cycled on and off, whereas movement is accomplished using photophoresis. Simulations with 0.2 and 0.5 microm diameter spherical particles indicate that sorting can commence quickly from a continuous stream. Procedures to optimize the sorting scheme are also described.

Application of Raman spectroscopy to identification and sorting of post-consumer plastics for recycling

DOEpatents

Sommer, Edward J.; Rich, John T.

2001-01-01

A high accuracy rapid system for sorting a plurality of waste products by polymer type. The invention involves the application of Raman spectroscopy and complex identification techniques to identify and sort post-consumer plastics for recycling. The invention reads information unique to the molecular structure of the materials to be sorted to identify their chemical compositions and uses rapid high volume sorting techniques to sort them into product streams at commercially viable throughput rates. The system employs a laser diode (20) for irradiating the material sample (10), a spectrograph (50) is used to determine the Raman spectrum of the material sample (10) and a microprocessor based controller (70) is employed to identify the polymer type of the material sample (10).

Reproductive performance of lactating dairy cows managed for first service using timed artificial insemination with or without detection of estrus using an activity-monitoring system.

PubMed

Fricke, P M; Giordano, J O; Valenza, A; Lopes, G; Amundson, M C; Carvalho, P D

2014-05-01

Lactating dairy cows (n=1,025) on a commercial dairy farm were randomly assigned at 10 ± 3 d in milk (DIM) to 1 of 3 treatments for submitting cows to first artificial insemination (AI) and were fitted with activity-monitoring tags (Heatime; SCR Engineers Ltd., Netanya, Israel) at 24 ± 3 DIM. Cows (n=339) in treatment 1 were inseminated based on increased activity from the end of the voluntary waiting period (50 DIM) until submission to an Ovsynch protocol; cows without increased activity from 21 to 65 DIM began an Ovsynch protocol at 65 ± 3 DIM, whereas cows without increased activity from 21 to 50 DIM but not from 51 to 79 DIM began an Ovsynch protocol at 79 ± 3 DIM. Cows (n=340) in treatment 2 were inseminated based on activity after the second PGF2α injection of a Presynch-Ovsynch protocol at 50 DIM, and cows without increased activity began an Ovsynch protocol at 65 ± 3 DIM. Cows (n=346) in treatment 3 were monitored for activity after the second PGF2α injection of a Presynch-Ovsynch protocol, but all cows received timed AI (TAI) at 75 ± 3 DIM after completing the Presynch-Ovsynch protocol. The activity-monitoring system detected increased activity in 56, 69, and 70% of cows in treatments 1, 2, and 3, respectively. Treatment-2 cows had the fewest average days to first AI (62.5), treatment-3 cows had the most average days to first AI (74.9), and treatment-1 cows had intermediate average days to first AI (67.4). Treatment-1 and -2 cows in which inseminations occurred as a combination between increased activity and TAI had fewer overall pregnancies per AI (P/AI) 35 d after AI (32% for both treatments) compared with treatment-3 cows, all of which received TAI after completing the Presynch-Ovsynch protocol (40%). Based on survival analysis, although the rate at which cows were inseminated differed among treatments, treatment did not affect the proportion of cows pregnant by 300 DIM. Thus, use of an activity-monitoring system to inseminate cows based on activity reduced days to first AI, whereas cows receiving 100% TAI after completing a Presynch-Ovsynch protocol had more P/AI. The trade-off between AI service rate and P/AI in the rate at which cows became pregnant was supported by an economic analysis in which the net present value ($/cow per year) differed by only $4 to $8 among treatments. We conclude that a variety of strategies using a combination of AI based on increased activity using an activity-monitoring system and synchronization of ovulation and TAI can be used to submit cows for first AI. Copyright © 2014 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Development of a safe and pragmatic awake craniotomy program at Maine Medical Center.

PubMed

Rughani, Anand I; Rintel, Theodor; Desai, Rajiv; Cushing, Deborah A; Florman, Jeffrey E

2011-01-01

Awake craniotomy offers an excellent means of performing intraoperative mapping and optimizing surgical resection of brain tumors. Awake craniotomy relies on a strong collaboration between anesthesiologists, neurosurgeons, and operating room staff. The authors recently introduced awake craniotomy for tumor resection at the Maine Medical Center and propose that it can be performed safely, effectively, and efficiently in a high-volume community hospital. We describe a practical approach to performing awake craniotomy involving streamlined anesthetic protocols and simplified intraoperative testing parameters in a carefully selected group of patients. Our first 25 patients are retrospectively reviewed with particular attention to the anesthetic protocol, the extent of resection, the operative time, post-operative complications, the length of hospitalization, and their functional status at follow-up. The authors established an anesthetic protocol based primarily on midazolam, fentanyl, propofol, and local anesthetic. The authors note that all but one patient was able to tolerate the awake procedure. Gross total resection was achieved in nearly 80% of patients with a glial tumor. Operative time was short, averaging 159 minutes of entire anesthesia care. Length of stay averaged 3.7 days. Persistent new post-operative deficits were noted in 2 of 25 patients. There was no substantial difference in total hospital charges for patients undergoing awake craniotomy when compared to a matched historical control. With attention focused on patient selection and a streamlined anesthetic protocol, the authors were able to successfully implement an awake craniotomy protocol in a community setting with satisfying results, including low operative morbidity, short operative times, low anesthetic complications, and excellent patient tolerance.

Full dose reduction potential of statistical iterative reconstruction for head CT protocols in a predominantly pediatric population

PubMed Central

Mirro, Amy E.; Brady, Samuel L.; Kaufman, Robert. A.

2016-01-01

Purpose To implement the maximum level of statistical iterative reconstruction that can be used to establish dose-reduced head CT protocols in a primarily pediatric population. Methods Select head examinations (brain, orbits, sinus, maxilla and temporal bones) were investigated. Dose-reduced head protocols using an adaptive statistical iterative reconstruction (ASiR) were compared for image quality with the original filtered back projection (FBP) reconstructed protocols in phantom using the following metrics: image noise frequency (change in perceived appearance of noise texture), image noise magnitude, contrast-to-noise ratio (CNR), and spatial resolution. Dose reduction estimates were based on computed tomography dose index (CTDIvol) values. Patient CTDIvol and image noise magnitude were assessed in 737 pre and post dose reduced examinations. Results Image noise texture was acceptable up to 60% ASiR for Soft reconstruction kernel (at both 100 and 120 kVp), and up to 40% ASiR for Standard reconstruction kernel. Implementation of 40% and 60% ASiR led to an average reduction in CTDIvol of 43% for brain, 41% for orbits, 30% maxilla, 43% for sinus, and 42% for temporal bone protocols for patients between 1 month and 26 years, while maintaining an average noise magnitude difference of 0.1% (range: −3% to 5%), improving CNR of low contrast soft tissue targets, and improving spatial resolution of high contrast bony anatomy, as compared to FBP. Conclusion The methodology in this study demonstrates a methodology for maximizing patient dose reduction and maintaining image quality using statistical iterative reconstruction for a primarily pediatric population undergoing head CT examination. PMID:27056425

SU-F-P-13: NRG Oncology Medical Physics Manpower Survey Quantifying Support Demands for Multi Institutional Clinical Trials

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

Monroe, J; Case Western Reserve University; Boparai, K

Purpose: A survey was taken by NRG Oncology to assess Full Time Equivalent (FTE) contributions to multi institutional clinical trials by medical physicists.No current quantification of physicists’ efforts in FTE units associated with clinical trials is available. The complexity of multi-institutional trials increases with new technologies and techniques. Proper staffing may directly impact the quality of trial data and outcomes. The demands on physics time supporting clinical trials needs to be assessed. Methods: The NRG Oncology Medical Physicist Subcommittee created a sixteen question survey to obtain this FTE data. IROC Houston distributed the survey to their list of 1802 contactmore » physicists. Results: After three weeks, 363 responded (20.1% response). 187 (51.5%) institutions reporting external beam participation were processed. There was a wide range in number of protocols active and supported at each institution. Of the 187 clinics, 134 (71.7%) participate in 0 to 10 trials, 28 (15%) in 11 to 20 trials, 10 (5.3%) in 21 to 30 trials, 9 (4.8%) had 40 to 75 trials. On average, physicist spent 2.7 hours (SD: 6.0) per week supervising or interacting with clinical trial staff. 1.25 hours (SD: 3.37), 1.83 hours (SD: 4.13), and 0.64 hours(SD: 1.13) per week were spent on patient simulation, reviewing treatment plans, and maintaining a DICOM server, respectively. For all protocol credentialing activities, physicist spent an average of 37.05 hours (SD: 96.94) yearly. To support dosimetrists, clinicians, and therapists, physicist spend on average 2.07 hours (SD: 3.52) per week just reading protocols. Physicist attended clinical trial meetings for on average 1.13 hours (SD: 1.85) per month. Conclusion: Responding physicists spend a nontrivial amount of time: 8.8 hours per week (0.22 FTE) supporting, on average, 9 active multi-institutional clinical trials.« less

HLRW management during MR reactor decommissioning in NRC 'Kurchatov Institute'

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

Chesnokov, Alexander; Ivanov, Oleg; Kolyadin, Vyacheslav

2013-07-01

A program of decommissioning of MR research reactor in the Kurchatov institute started in 2008. The decommissioning work presumed a preliminary stage, which included: removal of spent fuel from near reactor storage; removal of spent fuel assemble of metal liquid loop channel from a core; identification, sorting and disposal of radioactive objects from gateway of the reactor; identification, sorting and disposal of radioactive objects from cells of HLRW storage of the Kurchatov institute for radwaste creating form the decommissioning of MR. All these works were performed by a remote controlled means with use of a remote identification methods of highmore » radioactive objects. A distribution of activity along high radiated objects was measured by a collimated radiometer installed on the robot Brokk-90, a gamma image of the object was registered by gamma-visor. Spectrum of gamma radiation was measured by a gamma locator and semiconductor detector system. For identification of a presence of uranium isotopes in the HLRW a technique, based on the registration of characteristic radiation of U, was developed. For fragmentation of high radiated objects was used a cold cutting technique and dust suppression system was applied for reduction of volume activity of aerosols in air. The management of HLRW was performed by remote controlled robots Brokk-180 and Brokk-330. They executed sorting, cutting and parking of high radiated part of contaminated equipment. The use of these techniques allowed to reduce individual and collective doses of personal performed the decommissioning. The average individual dose of the personnel was 1,9 mSv/year in 2011, and the collective dose is estimated by 0,0605 man x Sv/year. Use of the remote control machines enables reducing the number of working personal (20 men) and doses. X-ray spectrometric methods enable determination of a presence of the U in high radiated objects and special cans and separation of them for further spent fuel inspection. The sorting of radwaste enabled shipping of the LLRW and ILRW to special repositories and keeping of the HLRW for decay in the Kurchatov institute repository. (authors)« less

Atypical birefringence pattern and the diagnostic ability of scanning laser polarimetry with enhanced corneal compensation in glaucoma.

PubMed

Rao, Harsha L; Yadav, Ravi K; Begum, Viquar U; Addepalli, Uday K; Senthil, Sirisha; Choudhari, Nikhil S; Garudadri, Chandra S

2015-03-01

To evaluate the effect of typical scan score (TSS), when within the acceptable limits, on the diagnostic performance of retinal nerve fibre layer (RNFL) parameters with the enhanced corneal compensation (ECC) protocol of scanning laser polarimetry (SLP) in glaucoma. In a cross-sectional study, 203 eyes of 160 glaucoma patients and 140 eyes of 104 control subjects underwent RNFL imaging with the ECC protocol of SLP. TSS was used to quantify atypical birefringence pattern (ABP) images. Influence of TSS on the diagnostic ability of SLP parameters was evaluated by receiver operating characteristic (ROC) regression models after adjusting for the effect of disease severity [based on mean deviation (MD)] on standard automated perimetry). Diagnostic abilities of all RNFL parameters of SLP increased when the TSS values were higher. This effect was statistically significant for TSNIT (coefficient: 0.08, p<0.001) and inferior average parameters (coefficient: 0.06, p=0.002) but not for nerve fibre indicator (NFI, coefficient: 0.03, p=0.21). In early glaucoma (MD of -5 dB), predicted area under ROC curve (AUC) for TSNIT average parameter improved from 0.642 at a TSS of 90 to 0.845 at a TSS of 100. In advanced glaucoma (MD of -15 dB), AUC for TSNIT average improved from 0.832 at a TSS of 90 to 0.947 at 100. Diagnostic performances of TSNIT and inferior average RNFL parameters with ECC protocol of SLP were significantly influenced by TSS even when the TSS values were within the acceptable limits. Diagnostic ability of NFI was unaffected by TSS values. © 2014 Acta Ophthalmologica Scandinavica Foundation. Published by John Wiley & Sons Ltd.

The use of WaveLight® Contoura to create a uniform cornea: the LYRA Protocol. Part 3: the results of 50 treated eyes.

PubMed

Motwani, Manoj

2017-01-01

To demonstrate how using the Wavelight Contoura measured astigmatism and axis eliminates corneal astigmatism and creates uniformly shaped corneas. A retrospective analysis was conducted of the first 50 eyes to have bilateral full WaveLight ® Contoura LASIK correction of measured astigmatism and axis (vs conventional manifest refraction), using the Layer Yolked Reduction of Astigmatism Protocol in all cases. All patients had astigmatism corrected, and had at least 1 week of follow-up. Accuracy to desired refractive goal was assessed by postoperative refraction, aberration reduction via calculation of polynomials, and postoperative visions were analyzed as a secondary goal. The average difference of astigmatic power from manifest to measured was 0.5462D (with a range of 0-1.69D), and the average difference of axis was 14.94° (with a range of 0°-89°). Forty-seven of 50 eyes had a goal of plano, 3 had a monovision goal. Astigmatism was fully eliminated from all but 2 eyes, and 1 eye had regression with astigmatism. Of the eyes with plano as the goal, 80.85% were 20/15 or better, and 100% were 20/20 or better. Polynomial analysis postoperatively showed that at 6.5 mm, the average C3 was reduced by 86.5% and the average C5 by 85.14%. Using WaveLight ® Contoura measured astigmatism and axis removes higher order aberrations and allows for the creation of a more uniform cornea with accurate removal of astigmatism, and reduction of aberration polynomials. WaveLight ® Contoura successfully links the refractive correction layer and aberration repair layer using the Layer Yolked Reduction of Astigmatism Protocol to demonstrate how aberration removal can affect refractive correction.

Efficient and high yield isolation of myoblasts from skeletal muscle.

PubMed

Shahini, Aref; Vydiam, Kalyan; Choudhury, Debanik; Rajabian, Nika; Nguyen, Thy; Lei, Pedro; Andreadis, Stelios T

2018-05-24

Skeletal muscle (SkM) regeneration relies on the activity of myogenic progenitors that reside beneath the basal lamina of myofibers. Here, we describe a protocol for the isolation of the SkM progenitors from young and old mice by exploiting their outgrowth potential from SkM explants on matrigel coated dishes in the presence of high serum, chicken embryo extract and basic fibroblast growth factor. Compared to other protocols, this method yields a higher number of myoblasts (10-20 million) by enabling the outgrowth of these cells from tissue fragments. The majority of outgrowth cells (~90%) were positive for myogenic markers such as α7-integrin, MyoD, and Desmin. The myogenic cell population could be purified to 98% with one round of pre-plating on collagen coated dishes, where differential attachment of fibroblasts and other non-myogenic progenitors separates them from myoblasts. Moreover, the combination of high serum medium and matrigel coating provided a proliferation advantage to myogenic cells, which expanded rapidly (~24 h population doubling), while non-myogenic cells diminished over time, thereby eliminating the need for further purification steps such as FACS sorting. Finally, myogenic progenitors gave rise to multinucleated myotubes that exhibited sarcomeres and spontaneous beating in the culture dish. Copyright © 2018 The Authors. Published by Elsevier B.V. All rights reserved.

Ratiometric fluorescence-imaging assays of plant membrane traffic using polyproteins.

PubMed

Samalova, Marketa; Fricker, Mark; Moore, Ian

2006-12-01

Fluorescent protein markers are widely used to report plant membrane traffic; however, effective protocols to quantify fluorescence or marker expression are lacking. Here the 20 residue self-cleaving 2A peptide from Foot and Mouth Disease Virus was used to construct polyproteins that expressed a trafficked marker in fixed stoichiometry with a reference protein in a different cellular compartment. Various pairs of compartments were simultaneously targeted. Together with a bespoke image analysis tool, these constructs allowed biosynthetic membrane traffic to be assayed with markedly improved sensitivity, dynamic range and statistical significance using protocols compatible with the common plant transfection and transgenic systems. As marker and effector expression could be monitored in populations or individual cells, saturation phenomena could be avoided and stochastic or epigenetic influences could be controlled. Surprisingly, mutational analysis of the ratiometric assay constructs revealed that the 2A peptide was dispensable for efficient cleavage of polyproteins carrying a single internal signal peptide, whereas the signal peptide was essential. In contrast, a construct bearing two signal peptide/anchors required 2A for efficient separation and stability, but 2A caused the amino-terminal moiety of such fusions to be mis-sorted to the vacuole. A model to account for the behaviour of 2A in these and other studies in plants is proposed.

Source-to-sensation level ratio of transmitted biosonar pulses in an echolocating false killer whale.

PubMed

Supin, Alexander Ya; Nachtigall, Paul E; Breese, Marlee

2006-07-01

Transmitted biosonar pulses, and the brain auditory evoked potentials (AEPs) associated with those pulses, were synchronously recorded in a false killer whale Pseudorca crassidens trained to accept suction-cup EEG electrodes and to detect targets by echolocation. AEP amplitude was investigated as a function of the transmitted biosonar pulse source level. For that, a few thousand of the individual AEP records were sorted according to the spontaneously varied amplitude of synchronously recorded biosonar pulses. In each of the sorting bins (in 5-dB steps) AEP records were averaged to extract AEP from noise; AEP amplitude was plotted as a function of the biosonar pulse source level. For comparison, AEPs were recorded to external (in free field) sound pulses of a waveform and spectrum similar to those of the biosonar pulses; amplitude of these AEPs was plotted as a function of sound pressure level. A comparison of these two functions has shown that, depending on the presence or absence of a target, the sensitivity of the whale's hearing to its own transmitted biosonar pulses was 30 to 45 dB lower than might be expected in a free acoustic field.

A parameterization method and application in breast tomosynthesis dosimetry

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

Li, Xinhua; Zhang, Da; Liu, Bob

2013-09-15

Purpose: To present a parameterization method based on singular value decomposition (SVD), and to provide analytical parameterization of the mean glandular dose (MGD) conversion factors from eight references for evaluating breast tomosynthesis dose in the Mammography Quality Standards Act (MQSA) protocol and in the UK, European, and IAEA dosimetry protocols.Methods: MGD conversion factor is usually listed in lookup tables for the factors such as beam quality, breast thickness, breast glandularity, and projection angle. The authors analyzed multiple sets of MGD conversion factors from the Hologic Selenia Dimensions quality control manual and seven previous papers. Each data set was parameterized usingmore » a one- to three-dimensional polynomial function of 2–16 terms. Variable substitution was used to improve accuracy. A least-squares fit was conducted using the SVD.Results: The differences between the originally tabulated MGD conversion factors and the results computed using the parameterization algorithms were (a) 0.08%–0.18% on average and 1.31% maximum for the Selenia Dimensions quality control manual, (b) 0.09%–0.66% on average and 2.97% maximum for the published data by Dance et al. [Phys. Med. Biol. 35, 1211–1219 (1990); ibid. 45, 3225–3240 (2000); ibid. 54, 4361–4372 (2009); ibid. 56, 453–471 (2011)], (c) 0.74%–0.99% on average and 3.94% maximum for the published data by Sechopoulos et al. [Med. Phys. 34, 221–232 (2007); J. Appl. Clin. Med. Phys. 9, 161–171 (2008)], and (d) 0.66%–1.33% on average and 2.72% maximum for the published data by Feng and Sechopoulos [Radiology 263, 35–42 (2012)], excluding one sample in (d) that does not follow the trends in the published data table.Conclusions: A flexible parameterization method is presented in this paper, and was applied to breast tomosynthesis dosimetry. The resultant data offer easy and accurate computations of MGD conversion factors for evaluating mean glandular breast dose in the MQSA protocol and in the UK, European, and IAEA dosimetry protocols. Microsoft Excel™ spreadsheets are provided for the convenience of readers.« less

'Fast cast' and 'needle Tenotomy' protocols with the Ponseti method to improve clubfoot management in Bangladesh.

PubMed

Evans, Angela; Chowdhury, Mamun; Rana, Sohel; Rahman, Shariar; Mahboob, Abu Hena

2017-01-01

The management of congenital talipes equino varus ( clubfoot deformity ) has been transformed in the last 20 years as surgical correction has been replaced by the non-surgical Ponseti method. The Ponseti method, consists of corrective serial casting followed by maintenance bracing, and has been repeatedly demonstrated to give best results - regarded as the 'gold standard' treatment for paediatric clubfoot. To develop the study protocol Level 2 evidence was used to modify the corrective casting phase of the Ponseti method in children aged up to 12 months. Using Level 4 evidence, the percutaneous Achilles tenotomy (PAT) was performed using a 19-gauge needle instead of a scalpel blade, a technique found to reduce bleeding and scarring. A total of 123 children participated in this study; 88 male, 35 female. Both feet were affected in 67 cases, left only in 22 cases, right only in 34 cases. Typical clubfeet were found in 112/123 cases, six atypical, five syndromic. The average age at first cast was 51 days (13-240 days).The average number of casts applied was five (2-10 casts). The average number of days between the first cast and brace was 37.8 days (10-122 days), including 21 days in a post-PAT cast. Hence, average time of corrective casts was 17 days.Parents preferred the reduced casting time, and were less concerned about unseen skin wounds.PAT was performed in 103/123 cases, using the needle technique. All post tenotomy casts were in situ for three weeks. Minor complications occurred in seven cases - four cases had skin lesions, three cases disrupted casting phase. At another site, 452 PAT were performed using the needle technique. The 'fast cast' protocol Ponseti casting was successfully used in infants aged less than 8 months. Extended manual manipulation of two minutes was the essential modification. Parents preferred the faster treatment phase, and ability to closer observe the foot and skin. The treating physiotherapists preferred the 'fast cast' protocol, achieving better correction with less complication. The needle technique for PAT is a further improvement for the Ponseti method.

Unsupervised neural spike sorting for high-density microelectrode arrays with convolutive independent component analysis.

PubMed

Leibig, Christian; Wachtler, Thomas; Zeck, Günther

2016-09-15

Unsupervised identification of action potentials in multi-channel extracellular recordings, in particular from high-density microelectrode arrays with thousands of sensors, is an unresolved problem. While independent component analysis (ICA) achieves rapid unsupervised sorting, it ignores the convolutive structure of extracellular data, thus limiting the unmixing to a subset of neurons. Here we present a spike sorting algorithm based on convolutive ICA (cICA) to retrieve a larger number of accurately sorted neurons than with instantaneous ICA while accounting for signal overlaps. Spike sorting was applied to datasets with varying signal-to-noise ratios (SNR: 3-12) and 27% spike overlaps, sampled at either 11.5 or 23kHz on 4365 electrodes. We demonstrate how the instantaneity assumption in ICA-based algorithms has to be relaxed in order to improve the spike sorting performance for high-density microelectrode array recordings. Reformulating the convolutive mixture as an instantaneous mixture by modeling several delayed samples jointly is necessary to increase signal-to-noise ratio. Our results emphasize that different cICA algorithms are not equivalent. Spike sorting performance was assessed with ground-truth data generated from experimentally derived templates. The presented spike sorter was able to extract ≈90% of the true spike trains with an error rate below 2%. It was superior to two alternative (c)ICA methods (≈80% accurately sorted neurons) and comparable to a supervised sorting. Our new algorithm represents a fast solution to overcome the current bottleneck in spike sorting of large datasets generated by simultaneous recording with thousands of electrodes. Copyright © 2016 Elsevier B.V. All rights reserved.

Evaluation of a shortened QIAsymphony DNA extraction protocol for stool samples using a multiplex real-time PCR for the detection of enteric pathogens.

PubMed

van Zanten, E; Wisselink, G J; Stoll, S; Alvarez, R; Kooistra-Smid, A M D

2011-02-01

A shortened DNA extraction protocol for the QIAsymphony SP was evaluated by quantitative and qualitative comparison of real-time PCR results of 150 co-extracted stool samples. The average ∆Cycle threshold value for positive pathogenic targets was 0.28 Ct. A consensus of 96.91%, with a correlation coefficient of 0.9880 was recorded. Copyright © 2010 Elsevier B.V. All rights reserved.

Automatic Color Sorting of Hardwood Edge-Glued Panel Parts

Treesearch

D. Earl Kline; Richard Conners; Qiang Lu; Philip A. Araman

1997-01-01

This paper describes an automatic color sorting system for red oak edge-glued panel parts. The color sorting system simultaneously examines both faces of a panel part and then determines which face has the "best" color, and sorts the part into one of a number of color classes at plant production speeds. Initial test results show that the system generated over...

Two Types of Perseveration in the Dimension Change Card Sort Task

ERIC Educational Resources Information Center

Hanania, Rima

2010-01-01

In the Dimension Change Card Sort (DCCS) task, 3-year-olds can sort cards well by one dimension but have difficulty in switching to sort the same cards by another dimension when asked; that is, they perseverate on the first relevant information. What is the information that children perseverate on? Using a new version of the DCCS, the experiments…

Cell-Free Reconstitution of Multivesicular Body Formation and Receptor Sorting

PubMed Central

Sun, Wei; Vida, Thomas A.; Sirisaengtaksin, Natalie; Merrill, Samuel A.; Hanson, Phyllis I.; Bean, Andrew J.

2010-01-01

The number of surface membrane proteins and their residence time on the plasma membrane are critical determinants of cellular responses to cues that can control plasticity, growth and differentiation. After internalization, the ultimate fate of many plasma membrane proteins is dependent on whether they are sorted for internalization into the lumenal vesicles of multivesicular bodies (MVBs), an obligate step prior to lysosomal degradation. To help to elucidate the mechanisms underlying MVB sorting, we have developed a novel cell-free assay that reconstitutes the sorting of a prototypical membrane protein, the epidermal growth factor receptor, with which we have probed some of its molecular requirements. The sorting event measured is dependent on cytosol, ATP, time, temperature and an intact proton gradient. Depletion of Hrs inhibited biochemical and morphological measures of sorting that were rescued by inclusion of recombinant Hrs in the assay. Moreover, depletion of signal-transducing adaptor molecule (STAM), or addition of mutated ATPase-deficient Vps4, also inhibited sorting. This assay reconstitutes the maturation of late endosomes, including the formation of internal vesicles and the sorting of a membrane protein, and allows biochemical investigation of this process. PMID:20214752

Low power and high accuracy spike sorting microprocessor with on-line interpolation and re-alignment in 90 nm CMOS process.

PubMed

Chen, Tung-Chien; Ma, Tsung-Chuan; Chen, Yun-Yu; Chen, Liang-Gee

2012-01-01

Accurate spike sorting is an important issue for neuroscientific and neuroprosthetic applications. The sorting of spikes depends on the features extracted from the neural waveforms, and a better sorting performance usually comes with a higher sampling rate (SR). However for the long duration experiments on free-moving subjects, the miniaturized and wireless neural recording ICs are the current trend, and the compromise on sorting accuracy is usually made by a lower SR for the lower power consumption. In this paper, we implement an on-chip spike sorting processor with integrated interpolation hardware in order to improve the performance in terms of power versus accuracy. According to the fabrication results in 90nm process, if the interpolation is appropriately performed during the spike sorting, the system operated at the SR of 12.5 k samples per second (sps) can outperform the one not having interpolation at 25 ksps on both accuracy and power.

Plutonium isotopes in the Hungarian environment.

PubMed

Varga, Beata; Tarján, Sandor; Vajda, Nora

2008-04-01

More than 50 soil samples were analysed from different parts of the country, the activity concentration of 239+240Pu was in the range of 0.01-0.84 Bq/kg dry soil with the average of 0.10 Bq/kg. 238Pu could be detected only in few moss samples and 238Pu/239+240Pu ratio determines the origin of plutonium. 241Pu was determined by liquid scintillation spectrometry. The activity concentration of this isotope in the soil is between 0.04 and 3.74 Bq/kg with the average of 0.82 Bq/kg, while in the moss is also similar 0.01-2.07 Bq/kg fresh mass with the average of 0.43 Bq/kg. Significant difference could not be observed between the different types of soils occurring in the country, but the results could be sorted according to the sampling carried out on undisturbed or cultivated area. The isotope ratios 241Pu/239+240Pu prove that the origin of the plutonium in Hungary is the global fallout determined by the atmospheric nuclear weapon tests.

Average current is better than peak current as therapeutic dosage for biphasic waveforms in a ventricular fibrillation pig model of cardiac arrest.

PubMed

Chen, Bihua; Yu, Tao; Ristagno, Giuseppe; Quan, Weilun; Li, Yongqin

2014-10-01

Defibrillation current has been shown to be a clinically more relevant dosing unit than energy. However, the effects of average and peak current in determining shock outcome are still undetermined. The aim of this study was to investigate the relationship between average current, peak current and defibrillation success when different biphasic waveforms were employed. Ventricular fibrillation (VF) was electrically induced in 22 domestic male pigs. Animals were then randomized to receive defibrillation using one of two different biphasic waveforms. A grouped up-and-down defibrillation threshold-testing protocol was used to maintain the average success rate of 50% in the neighborhood. In 14 animals (Study A), defibrillations were accomplished with either biphasic truncated exponential (BTE) or rectilinear biphasic waveforms. In eight animals (Study B), shocks were delivered using two BTE waveforms that had identical peak current but different waveform durations. Both average and peak currents were associated with defibrillation success when BTE and rectilinear waveforms were investigated. However, when pathway impedance was less than 90Ω for the BTE waveform, bivariate correlation coefficient was 0.36 (p=0.001) for the average current, but only 0.21 (p=0.06) for the peak current in Study A. In Study B, a high defibrillation success (67.9% vs. 38.8%, p<0.001) was observed when the waveform delivered more average current (14.9±2.1A vs. 13.5±1.7A, p<0.001) while keeping the peak current unchanged. In this porcine model of VF, average current was better than peak current to be an adequate parameter to describe the therapeutic dosage when biphasic defibrillation waveforms were used. The institutional protocol number: P0805. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

Petrology and provenance of Upper Cretaceous Sandstone, southern San Rafael Mountains, Santa Barbara County, California

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

Toyne, C.D.

1987-05-01

Petrologic analysis of 24 medium to coarse-grained sandstone samples, collected from a 2950-m submarine fan complex of late Campanian-early Maestrichtian age exposed within Mono Creek Canyon, reveal commonly calcite cemented, poorly sorted, subangular biotic arkoses. Framework averages 86.0%. Matrix - primarily detrital quartz, feldspar, and lithic fragments finer than 0.03 mm and mechanically and chemically altered phyllosilicates and labile aphanites - averages 8.9%. Calcite cement averages 4.2%. Porosity averages 0.9%. Gazzi-Dickinson point counts of 400 framework grains per slide yield modal averages of Q/sub 37.7/ F/sub 49.8/ L/sub 12.5/; Qm/sub 27.4/ F/sub 49.8/ Lt/sub 22.8/; Qm/sub 35.6/ P/sub 43.7/ K/submore » 20.7/; and Qp/sub 49.4/ Lv/sub 22.1/ Ls/sub 28.5/. P/F averages 0.68, Lv/L averages 0.45, Qp/Q averages 0.27, and detrital phyllosilicate, predominantly biotite, averages 5.7% of total framework. Neither primary nor secondary parameters vary systematically with stratigraphic position. Miscellaneous constituents average 1.3% of framework and include epidote, garnet, amphibole, pyroxene, zircon, and tourmaline as well as carbonaceous blebs, opaque minerals, and unidentifiable lithic fragments. Separate analysis of 100 medium sized quartz grains per slide indicates a mean population of 63.0% non-undulatory monocrystalline quartz, 9.1% undulatory monocrystalline quartz, 10.1% polycrystalline quartz of 2 to 3 crystals, and 17.9% polycrystalline quartz composed of more than 3 crystals. Modal data, plotted upon provenance discrimination diagrams, indicate a plutonic provenance transitional between a dissected magmatic arc and uplifted basement terrane. Paleocurrent data, neglecting possible clockwise rotation, indicate sediment transport from the north.« less

Four-dimensional MRI using an internal respiratory surrogate derived by dimensionality reduction

NASA Astrophysics Data System (ADS)

Uh, Jinsoo; Ayaz Khan, M.; Hua, Chiaho

2016-11-01

This study aimed to develop a practical and accurate 4-dimensional (4D) magnetic resonance imaging (MRI) method using a non-navigator, image-based internal respiratory surrogate derived by dimensionality reduction (DR). The use of DR has been previously suggested but not implemented for reconstructing 4D MRI, despite its practical advantages. We compared multiple image-acquisition schemes and refined a retrospective-sorting process to optimally implement a DR-derived surrogate. The comparison included an unconventional scheme that acquires paired slices alternately to mitigate the internal surrogate’s dependency on a specific slice location. We introduced ‘target-oriented sorting’, as opposed to conventional binning, to quantify the coherence in retrospectively sorted images, thereby determining the minimal scan time needed for sufficient coherence. This study focused on evaluating the proposed method using digital phantoms which provided unequivocal gold standard. The evaluation indicated that the DR-based respiratory surrogate is highly accurate: the error in amplitude percentile of the surrogate signal was less than 5% with the optimal scheme. Acquiring alternating paired slices was superior to the conventional scheme of acquiring individual slices; the advantage of the unconventional scheme was more pronounced when a substantial phase shift occurred across slice locations. The analysis of coherence across sorted images confirmed the advantage of higher sampling efficiencies in non-navigator respiratory surrogates. We determined that a scan time of 20 s per imaging slice was sufficient to achieve a mean coherence error of less than 1% for the tested respiratory patterns. The clinical applicability of the proposed 4D MRI has been demonstrated with volunteers and patients. The diaphragm motion in 4D MRI was consistent with that in dynamic 2D imaging which was regarded as the gold standard (difference within 1.8 mm on average).

Evaluating multicenter DTI data in Huntington's disease on site specific effects: An ex post facto approach☆

PubMed Central

Müller, Hans-Peter; Grön, Georg; Sprengelmeyer, Reiner; Kassubek, Jan; Ludolph, Albert C.; Hobbs, Nicola; Cole, James; Roos, Raymund A.C.; Duerr, Alexandra; Tabrizi, Sarah J.; Landwehrmeyer, G. Bernhard; Süssmuth, Sigurd D.

2013-01-01

Purpose Assessment of the feasibility to average diffusion tensor imaging (DTI) metrics of MRI data acquired in the course of a multicenter study. Materials and methods Sixty-one early stage Huntington's disease patients and forty healthy controls were studied using four different MR scanners at four European sites with acquisition protocols as close as possible to a given standard protocol. The potential and feasibility of averaging data acquired at different sites was evaluated quantitatively by region-of-interest (ROI) based statistical comparisons of coefficients of variation (CV) across centers, as well as by testing for significant group-by-center differences on averaged fractional anisotropy (FA) values between patients and controls. In addition, a whole-brain based statistical between-group comparison was performed using FA maps. Results The ex post facto statistical evaluation of CV and FA-values in a priori defined ROIs showed no differences between sites above chance indicating that data were not systematically biased by center specific factors. Conclusion Averaging FA-maps from DTI data acquired at different study sites and different MR scanner types does not appear to be systematically biased. A suitable recipe for testing on the possibility to pool multicenter DTI data is provided to permit averaging of DTI-derived metrics to differentiate patients from healthy controls at a larger scale. PMID:24179771

SU-F-J-117: Impact of Motion Artifacts On Image Quality and Accuracy of Tumor Motion Reconstruction in 4D CT-On-Rails and MV-CBCT Scans: A Phantom Study

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

Lin, T; Ma, C

Purpose: To compare and quantify respiratory motion artifacts in images from free breathing 4D-CT-on-Rails(CTOR) and those from MV-Cone-beam-CT(MVCB) and facilitate respiratory motion guided radiation therapy. Methods: 4D-CTOR: Siemens Somatom CT-on-Rails system with Anzai belt loaded with pressure sensor load cells. 4D scans were performed in helical mode, pitch 0.1, gantry rotation time 0.5s, 1.5mm slice thickness, 120kVp, 400 mAs. Normal and fast breathing (>12rpm) scanning protocols were investigated. Helical scan, AIP(average intensity projection) and MIP(maximum intensity projection) were generated from 4D-CTOR scans with amplitude sorting into 10 phases.MVCB: Siemens Artiste diamond view(1MV)MVCB was performed with 5MU thorax protocol with 60more » second of full rotation.Phantom: Anzai AZ-733V respiratory phantom. The settings were set to normal and resp. modes with repetition rates at 15 rpm and 10 rpm. Surgical clips, acrylic, wooden, rubber and lung density, total six mock-ups were scanned and compared in this study.Signal-to-noise ratio(SNR), contrast-to-noise ratio(CNR) and reconstructed motion volume were compared to different respiratory setups for the mock-ups. Results: Reconstructed motion volume was compared to the real object volume for the six test mock-ups. It shows that free breathing helical in all instances underestimates the object excursions largest to −67.4% and least −6.3%. Under normal breathing settings, MIP can predict very precise motion volume with minimum 0.4% and largest −13.9%. MVCB shows underestimate of the motion volume with −1.11% minimum and −18.0% maximum. With fast breathing, AIP provides bad representation of the object motion; however, the MIP can predict the motion volume with −2.0% to −11.4% underestimate. Conclusion: Respiratory motion guided radiation therapy requires good motion recording. This study shows that regular CTOR helical scans provides bad guidance, 4D CTOR AIP cannot represent the fast breathing pattern, MIP can represent the best motion volume, MVCBCT can only be used for normal breathing with acceptable uncertainties.« less

Algorithm Sorts Groups Of Data

NASA Technical Reports Server (NTRS)

Evans, J. D.

1987-01-01

For efficient sorting, algorithm finds set containing minimum or maximum most significant data. Sets of data sorted as desired. Sorting process simplified by reduction of each multielement set of data to single representative number. First, each set of data expressed as polynomial with suitably chosen base, using elements of set as coefficients. Most significant element placed in term containing largest exponent. Base selected by examining range in value of data elements. Resulting series summed to yield single representative number. Numbers easily sorted, and each such number converted back to original set of data by successive division. Program written in BASIC.

The morphology and migration of transverse bars off the west-central Florida coast

USGS Publications Warehouse

Gelfenbaum, G.; Brooks, G.R.

2003-01-01

A series of migrating shore-normal sandbars with wavelengths of 75-120 m and heights up to 2 m have been identified off the northern tip of Anna Maria Island, a barrier island on the west-central Florida coast. Similar features have been described elsewhere since the 1930s and termed 'transverse bars'. The transverse bars identified off Anna Maria Island are found for about 3 km along the coast and extend 4 km offshore, well outside the normal surf-zone width. No cusps or any other associated beach expression is evident despite the fact that the bars come to within about 75 m of the beach. Sediments on the crests of the bars are a well-sorted fine quartz sand, whereas sediments in the troughs are a poorly sorted coarse carbonate shell hash. Historical aerial photographs and repeated high-resolution bathymetric surveys provide a means of quantifying the migration of the transverse bars. Analyses of orthorectified aerial photographs from the early 1940s through the mid 1990s clearly show movement or migration taking place in the bar field. In the 40-yr period from 1951 to 1991, the southern edge of the bar field moved 200-350 m to the south, with an average long-term migration rate of 8 m/yr. Repeated bathymetric surveys over an 8-month period give an average short-term migration rate of 21 m/yr to the south. Wave and current measurements suggest that southerly winds associated with the passage of cold fronts drive near-bed currents to the south that are strong enough to initiate sediment transport and cause the southerly migration of the transverse bars.

Performance comparison analysis library communication cluster system using merge sort

NASA Astrophysics Data System (ADS)

Wulandari, D. A. R.; Ramadhan, M. E.

2018-04-01

Begins by using a single processor, to increase the speed of computing time, the use of multi-processor was introduced. The second paradigm is known as parallel computing, example cluster. The cluster must have the communication potocol for processing, one of it is message passing Interface (MPI). MPI have many library, both of them OPENMPI and MPICH2. Performance of the cluster machine depend on suitable between performance characters of library communication and characters of the problem so this study aims to analyze the comparative performances libraries in handling parallel computing process. The case study in this research are MPICH2 and OpenMPI. This case research execute sorting’s problem to know the performance of cluster system. The sorting problem use mergesort method. The research method is by implementing OpenMPI and MPICH2 on a Linux-based cluster by using five computer virtual then analyze the performance of the system by different scenario tests and three parameters for to know the performance of MPICH2 and OpenMPI. These performances are execution time, speedup and efficiency. The results of this study showed that the addition of each data size makes OpenMPI and MPICH2 have an average speed-up and efficiency tend to increase but at a large data size decreases. increased data size doesn’t necessarily increased speed up and efficiency but only execution time example in 100000 data size. OpenMPI has a execution time greater than MPICH2 example in 1000 data size average execution time with MPICH2 is 0,009721 and OpenMPI is 0,003895 OpenMPI can customize communication needs.

Relationship between molecular connectivity and carcinogenic activity: a confirmation with a new software program based on graph theory.

PubMed Central

Malacarne, D; Pesenti, R; Paolucci, M; Parodi, S

1993-01-01

For a database of 826 chemicals tested for carcinogenicity, we fragmented the structural formula of the chemicals into all possible contiguous-atom fragments with size between two and eight (nonhydrogen) atoms. The fragmentation was obtained using a new software program based on graph theory. We used 80% of the chemicals as a training set and 20% as a test set. The two sets were obtained by random sorting. From the training sets, an average (8 computer runs with independently sorted chemicals) of 315 different fragments were significantly (p < 0.125) associated with carcinogenicity or lack thereof. Even using this relatively low level of statistical significance, 23% of the molecules of the test sets lacked significant fragments. For 77% of the molecules of the test sets, we used the presence of significant fragments to predict carcinogenicity. The average level of accuracy of the predictions in the test sets was 67.5%. Chemicals containing only positive fragments were predicted with an accuracy of 78.7%. The level of accuracy was around 60% for chemicals characterized by contradictory fragments or only negative fragments. In a parallel manner, we performed eight paired runs in which carcinogenicity was attributed randomly to the molecules of the training sets. The fragments generated by these pseudo-training sets were devoid of any predictivity in the corresponding test sets. Using an independent software program, we confirmed (for the complex biological endpoint of carcinogenicity) the validity of a structure-activity relationship approach of the type proposed by Klopman and Rosenkranz with their CASE program. Images Figure 1. Figure 2. Figure 3. Figure 4. Figure 5. Figure 6. PMID:8275991

Cell-type-specific profiling of protein-DNA interactions without cell isolation using targeted DamID with next-generation sequencing.

PubMed

Marshall, Owen J; Southall, Tony D; Cheetham, Seth W; Brand, Andrea H

2016-09-01

This protocol is an extension to: Nat. Protoc. 2, 1467-1478 (2007); doi:10.1038/nprot.2007.148; published online 7 June 2007The ability to profile transcription and chromatin binding in a cell-type-specific manner is a powerful aid to understanding cell-fate specification and cellular function in multicellular organisms. We recently developed targeted DamID (TaDa) to enable genome-wide, cell-type-specific profiling of DNA- and chromatin-binding proteins in vivo without cell isolation. As a protocol extension, this article describes substantial modifications to an existing protocol, and it offers additional applications. TaDa builds upon DamID, a technique for detecting genome-wide DNA-binding profiles of proteins, by coupling it with the GAL4 system in Drosophila to enable both temporal and spatial resolution. TaDa ensures that Dam-fusion proteins are expressed at very low levels, thus avoiding toxicity and potential artifacts from overexpression. The modifications to the core DamID technique presented here also increase the speed of sample processing and throughput, and adapt the method to next-generation sequencing technology. TaDa is robust, reproducible and highly sensitive. Compared with other methods for cell-type-specific profiling, the technique requires no cell-sorting, cross-linking or antisera, and binding profiles can be generated from as few as 10,000 total induced cells. By profiling the genome-wide binding of RNA polymerase II (Pol II), TaDa can also identify transcribed genes in a cell-type-specific manner. Here we describe a detailed protocol for carrying out TaDa experiments and preparing the material for next-generation sequencing. Although we developed TaDa in Drosophila, it should be easily adapted to other organisms with an inducible expression system. Once transgenic animals are obtained, the entire experimental procedure-from collecting tissue samples to generating sequencing libraries-can be accomplished within 5 d.

What is in your cup of tea? DNA Verity Test to characterize black and green commercial teas

PubMed Central

Comparone, Maria; Di Maio, Antonietta; Del Guacchio, Emanuele; Menale, Bruno; Troisi, Jacopo; Aliberti, Francesco

2017-01-01

In this study, we used several molecular techniques to develop a fast and reliable protocol (DNA Verity Test, DVT) for the characterization and confirmation of the species or taxa present in herbal infusions. As a model plant for this protocol, Camellia sinensis, a traditional tea plant, was selected due to the following reasons: its historical popularity as a (healthy) beverage, its high selling value, the importation of barely recognizable raw product (i.e., crushed), and the scarcity of studies concerning adulterants or contamination. The DNA Verity Test includes both the sequencing of DNA barcoding markers and genotyping of labeled-PCR DNA barcoding fragments for each sample analyzed. This protocol (DVT) was successively applied to verify the authenticity of 32 commercial teas (simple or admixture), and the main results can be summarized as follows: (1) the DVT protocol is suitable to detect adulteration in tea matrices (contaminations or absence of certified ingredients), and the method can be exported for the study of other similar systems; (2) based on the BLAST analysis of the sequences of rbcL+matK±rps7-trnV(GAC) chloroplast markers, C. sinensis can be taxonomically characterized; (3) rps7-trnV(GAC) can be employed to discriminate C. sinensis from C. pubicosta; (4) ITS2 is not an ideal DNA barcode for tea samples, reflecting potential incomplete lineage sorting and hybridization/introgression phenomena in C. sinensis taxa; (5) the genotyping approach is an easy, inexpensive and rapid pre-screening method to detect anomalies in the tea templates using the trnH(GUG)-psbA barcoding marker; (6) two herbal companies provided no authentic products with a contaminant or without some of the listed ingredients; and (7) the leaf matrices present in some teabags could be constituted using an admixture of different C. sinensis haplotypes and/or allied species (C. pubicosta). PMID:28542606

Chip-based droplet sorting

DOEpatents

Beer, Neil Reginald; Lee, Abraham; Hatch, Andrew

2014-07-01

A non-contact system for sorting monodisperse water-in-oil emulsion droplets in a microfluidic device based on the droplet's contents and their interaction with an applied electromagnetic field or by identification and sorting.

A QR code identification technology in package auto-sorting system

NASA Astrophysics Data System (ADS)

di, Yi-Juan; Shi, Jian-Ping; Mao, Guo-Yong

2017-07-01

Traditional manual sorting operation is not suitable for the development of Chinese logistics. For better sorting packages, a QR code recognition technology is proposed to identify the QR code label on the packages in package auto-sorting system. The experimental results compared with other algorithms in literatures demonstrate that the proposed method is valid and its performance is superior to other algorithms.

When Seeing Is Knowing: The Role of Visual Cues in the Dissociation between Children's Rule Knowledge and Rule Use

ERIC Educational Resources Information Center

Buss, Aaron T.; Spencer, John P.

2012-01-01

The Dimensional Change Card Sort (DCCS) task requires children to switch from sorting cards based on shape or color to sorting based on the other dimension. Typically, 3-year-olds perseverate, whereas 4-year-olds flexibly sort by different dimensions. Zelazo and colleagues (1996, Cognitive Development, 11, 37-63) asked children questions about the…

Technology to sort lumber by color and grain for furniture parts

Treesearch

D. Earl Kline; Richard Conners; Philip A. Araman

2000-01-01

This paper describes an automatic color and grain sorting system for wood edge-glued panel parts. The color sorting system simultaneously examines both faces of a panel part and then determines which face has the "best" color, and sorts the part into one of a number of color classes at plant production speeds. In-plant test results show that the system...

BayesMotif: de novo protein sorting motif discovery from impure datasets.

PubMed

Hu, Jianjun; Zhang, Fan

2010-01-18

Protein sorting is the process that newly synthesized proteins are transported to their target locations within or outside of the cell. This process is precisely regulated by protein sorting signals in different forms. A major category of sorting signals are amino acid sub-sequences usually located at the N-terminals or C-terminals of protein sequences. Genome-wide experimental identification of protein sorting signals is extremely time-consuming and costly. Effective computational algorithms for de novo discovery of protein sorting signals is needed to improve the understanding of protein sorting mechanisms. We formulated the protein sorting motif discovery problem as a classification problem and proposed a Bayesian classifier based algorithm (BayesMotif) for de novo identification of a common type of protein sorting motifs in which a highly conserved anchor is present along with a less conserved motif regions. A false positive removal procedure is developed to iteratively remove sequences that are unlikely to contain true motifs so that the algorithm can identify motifs from impure input sequences. Experiments on both implanted motif datasets and real-world datasets showed that the enhanced BayesMotif algorithm can identify anchored sorting motifs from pure or impure protein sequence dataset. It also shows that the false positive removal procedure can help to identify true motifs even when there is only 20% of the input sequences containing true motif instances. We proposed BayesMotif, a novel Bayesian classification based algorithm for de novo discovery of a special category of anchored protein sorting motifs from impure datasets. Compared to conventional motif discovery algorithms such as MEME, our algorithm can find less-conserved motifs with short highly conserved anchors. Our algorithm also has the advantage of easy incorporation of additional meta-sequence features such as hydrophobicity or charge of the motifs which may help to overcome the limitations of PWM (position weight matrix) motif model.

Sorted bedforms developed on sandy lobes fed by small ephemeral streams (Catalan continental shelf)

NASA Astrophysics Data System (ADS)

Durán, R.; Guillén, J.; Muñoz, A.; Guerrero, Q.

2016-12-01

The morphology and sedimentological characteristics of sorted bedforms identified in the Catalan continental shelf (NW Mediterranean Sea) have been characterized using multibeam echosounder data and sediment samples collected in 2013 within the FORMED project. Bathymetric data was compared with previous data gathered in 2004 within the ESPACE project to assess the decadal stability of these bedforms. The sorted bedforms were observed on the inner shelf at water depths from 10 to 40 m, along a coastal stretch of more than 3 km. They are associated with elongated patches of low backscatter, corresponding to fine sand. The fine-grained sediment patches are located off small bays fed by short, intermittent streams, extending down to 40 m water depth. The sorted bedforms exhibit elongated shapes with subtle relief (up to 1 m) and are oriented nearly perpendicular to the shoreline. In cross-section, the sorted bedforms display lateral symmetry in bathymetric relief and backscatter, with high backscatter corresponding to poorly sorted coarse sand (median size of 0.55-0.96 mm) centered on the bathymetric depression, and low backscatter consisting of well-sorted fine to medium sand (median sized of 0.22-0.35 mm) on the crest. The local input of well-sorted fine sand supplied by ephemeral streams over the coarse sand domain of the infralittoral prograding wedge contributes to the bed sediment heterogeneity (mixture of sediment), which is further reorganized into sorted bedforms. The sorted bedforms are better developed in deeper waters (20-40 m) than near the shoreline, probably due to stronger wave forcing in the shallower shelf that prevents the maintenance of these morphologies. At a decadal time scale, the morphological evolution of these bedforms indicates that they are persistent features, showing small changes in their boundaries, which is in agreement with previous observations and numerical simulations that highlighted the persistence and long-term stability of sorted bedforms at water depths greater than 15-20 m over annual or even decadal timescales.

Knowledge about the research and ethics committee at Makerere University, Kampala.

PubMed

Ibingira, B R; Ochieng, J

2013-12-01

All research involving human participants should be reviewed by a competent and independent institutional research and ethics committee. Research conducted at Makerere University College of Health Sciences should be subjected to a rigorous review process by the ethics committee in order to protect human participants' interests, rights and welfare. To evaluate researchers' knowledge about the functions and ethical review process of the College of Health Sciences research and ethics committee. A cross sectional study. 135 researchers consented to participate in the study, but 70 questionnaires were answered giving a 52% response. Age ranged between 30 to 61 years, majority of participants 30-39 years. Most of the respondents do agree that the REC functions include Protocol review 86%, protection of research participants 84.3%, and monitoring of ongoing research. During ethical review, the RECpays special attention to scientific design [79.7%] and ethical issues [75.3%], but less to the budget and literature review. More than 97% of the respondents believe that the REC is either average or very good, while 2.8% rank it below average. Respondents knew the major functions of the committee including protection of the rights and welfare of research participants, protocol review and monitoring of on going research, and the elements of protocol review that are given more attention include ;scientific design and ethical issues. Overall performance of the REC was ranked as average by respondents. The committee should limit delays in approval and effectively handle all functions of the committee.

Benchmarking a quantum teleportation protocol in superconducting circuits using tomography and an entanglement witness.

PubMed

Baur, M; Fedorov, A; Steffen, L; Filipp, S; da Silva, M P; Wallraff, A

2012-01-27

Teleportation of a quantum state may be used for distributing entanglement between distant qubits in quantum communication and for quantum computation. Here we demonstrate the implementation of a teleportation protocol, up to the single-shot measurement step, with superconducting qubits coupled to a microwave resonator. Using full quantum state tomography and evaluating an entanglement witness, we show that the protocol generates a genuine tripartite entangled state of all three qubits. Calculating the projection of the measured density matrix onto the basis states of two qubits allows us to reconstruct the teleported state. Repeating this procedure for a complete set of input states we find an average output state fidelity of 86%.

Further developments in generating type-safe messaging

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

Neswold, R.; King, C.; /Fermilab

2011-11-01

At ICALEPCS 09, we introduced a source code generator that allows processes to communicate safely using data types native to each host language. In this paper, we discuss further development that has occurred since the conference in Kobe, Japan, including the addition of three more client languages, an optimization in network packet size and the addition of a new protocol data type. The protocol compiler is continuing to prove itself as an easy and robust way to get applications written in different languages hosted on different computer architectures to communicate. We have two active Erlang projects that are using themore » protocol compiler to access ACNET data at high data rates. We also used the protocol compiler output to deliver ACNET data to an iPhone/iPad application. Since it takes an average of two weeks to support a new language, we're willing to expand the protocol compiler to support new languages that our community uses.« less

Response of lactating dairy cows to degree of steam-flaked barley grain in low-forage diets.

PubMed

Safaei, Kh; Ghorbani, G R; Alikhani, M; Sadeghi-Sefidmazgi, A; Yang, W Z

2017-10-01

This study was conducted to investigate the effects of processing method (grinding vs. steam flaking) and increasing densities of steam-flaked barley grain on dry matter intake (DMI), rumen pH and fermentation characteristics, digestibility of dry matter in the total digestive tract (DDTT), and milk production of dairy cows. Eight multiparous mid-lactation Holstein cows averaging 103 ± 24 DIM, 44.5 ± 4.7 kg milk/day and weighing 611 ± 43 kg at the start of the experiment were used in a replicated 4 × 4 Latin square design with 21-day periods. Cows were fed diets consisting of (DM basis) 23.8% corn silage, 13.5% chopped alfalfa hay and 62.7% concentrate. The dietary treatments were either ground barley (GB) using a hammer mill or steam-flaked barley (SFB) - varying density at 390, 340 or 290 g/l. Processing method (GB vs. SFB) did not affect DMI (23.6 kg/day on average), DDTT (71.0% on average), milk yield (43.4 kg/day on average), milk components, rumen pH and molar proportions of acetate, propionate, butyrate and sorting activity. Ruminal isovalerate concentration tended (p = 0.06) to be higher for cows fed GB than those fed SFB-based diets. Decreasing the density of SFB from 390, 340 to 290 g/l tended to linearly increase DMI (p = 0.09), decrease total solids percentage of milk (p = 0.10) and linearly decreased milk urea nitrogen (12.8, 12.4 and 12.1 mg/dl; p = 0.04); also, the sorting index (SI) of the particles retained on the 19.0-mm sieve without affecting the SI of the particles retained on 8.0-mm, 1.18-mm or passed through 1.18-mm sieve (p = 0.05). These results indicated the limited effects of processing method (grinding vs. steam flaking) and densities of SFB (390, 290 or 290 g/l) on cows' performance and feed utilization for dairy cows fed low-forage diets. Therefore, both processing methods could be recommended under current feeding conditions of dairy cows. Journal of Animal Physiology and Animal Nutrition © 2016 Blackwell Verlag GmbH.

Sedation protocol with fasting and shorter sleep leads to magnetic resonance imaging success.

PubMed

Kimiya, Takahisa; Sekiguchi, Shinichiro; Yagihashi, Tatsuhiko; Arai, Mie; Takahashi, Hirotaka; Takahashi, Takao

2017-10-01

Young children undergoing magnetic resonance imaging (MRI) require sedation. In June 2013, Tokyo Metropolitan Ohtsuka Hospital (TMOH) introduced an oral sedation protocol for young children undergoing MRI; the protocol included instructions on fasting before sedation, and recommended a shorter duration of sleep the night before MRI. We compared the MRI success rate before and after the introduction of this protocol. The eligible subjects were children under 3 years old who underwent MRI by appointment at TMOH between October 2012 and March 2014, under sedation with triclofos sodium. All those who underwent MRI in or after June 2013 were enrolled prospectively as a post-protocol group. All patients who underwent MRI before June 2013 were enrolled retrospectively as a pre-protocol group, with data collected from chart review. Seventy-four patients were enrolled in the post-protocol group, and 42 in the pre-protocol group. The MRI success rate was significantly higher in the post-protocol group than in the pre-protocol group (98.7% vs 88.1%), as was the rate of on-time starting of MRI (86.5% vs 71.4%). The post-protocol group woke up earlier on the day of examination (6:18 a.m. vs 6:43 a.m.), resulting in a significantly longer time between awakening and the beginning of sedation (289.8 min vs 265.9 min), and a significantly shorter average duration of sleep on the previous night (504.8 min vs 532.3 min). Implementation of a hospital-wide sedation protocol for young children undergoing MRI significantly improved the MRI success rate. © 2017 Japan Pediatric Society.

Put your hands up! Gesturing improves preschoolers' executive function.

PubMed

Rhoads, Candace L; Miller, Patricia H; Jaeger, Gina O

2018-09-01

This study addressed the causal direction of a previously reported relation between preschoolers' gesturing and their executive functioning on the Dimensional Change Card Sort (DCCS) sorting-switch task. Gesturing the relevant dimension for sorting was induced in a Gesture group through instructions, imitation, and prompts. In contrast, the Control group was instructed to "think hard" when sorting. Preschoolers (N = 50) performed two DCCS tasks: (a) sort by size and then spatial orientation of two objects and (b) sort by shape and then proximity of the two objects. An examination of performance over trials permitted a fine-grained depiction of patterns of younger and older children in the Gesture and Control conditions. After the relevant dimension was switched, the Gesture group had more accurate sorts than the Control group, particularly among younger children on the second task. Moreover, the amount of gesturing predicted the number of correct sorts among younger children on the second task. The overall association between gesturing and sorting was not reflected at the level of individual trials, perhaps indicating covert gestural representation on some trials or the triggering of a relevant verbal representation by the gesturing. The delayed benefit of gesturing, until the second task, in the younger children may indicate a utilization deficiency. Results are discussed in terms of theories of gesturing and thought. The findings open up a new avenue of research and theorizing about the possible role of gesturing in emerging executive function. Copyright © 2018 Elsevier Inc. All rights reserved.

Comparison of GnRH agonist, GnRH antagonist, and GnRH antagonist mild protocol of controlled ovarian hyperstimulation in good prognosis patients.

PubMed

Stimpfel, Martin; Vrtacnik-Bokal, Eda; Pozlep, Barbara; Virant-Klun, Irma

2015-01-01

The reports on how to stimulate the ovaries for oocyte retrieval in good prognosis patients are contradictory and often favor one type of controlled ovarian hyperstimulation (COH). For this reason, we retrospectively analyzed data from IVF/ICSI cycles carried out at our IVF Unit in good prognosis patients (aged <38 years, first and second attempts of IVF/ICSI, more than 3 oocytes retrieved) to elucidate which type of COH is optimal at our condition. The included patients were undergoing COH using GnRH agonist, GnRH antagonist or GnRH antagonist mild protocol in combination with gonadotrophins. We found significant differences in the average number of retrieved oocytes, immature oocytes, fertilized oocytes, embryos, transferred embryos, embryos frozen per cycle, and cycles with embryo freezing between studied COH protocols. Although there were no differences in live birth rate (LBR), miscarriages, and ectopic pregnancies between compared protocols, pregnancy rate was significantly higher in GnRH antagonist mild protocol in comparison with both GnRH antagonist and GnRH agonist protocols and cumulative LBR per cycle was significantly higher in GnRH antagonist mild protocol in comparison to GnRH agonist protocol. Our data show that GnRH antagonist mild protocol of COH could be the best method of choice in good prognosis patients.

Perseveration and the Status of 3-Year-Olds' Knowledge in a Card-Sorting Task: Evidence from Studies Involving Congruent Flankers

ERIC Educational Resources Information Center

Jordan, Patricia L.; Morton, J. Bruce

2012-01-01

Infants and young children often perseverate despite apparent knowledge of the correct response. Two Experiments addressed questions concerning the status of such knowledge in the context of a card-sorting task. In Experiment 1, three groups of 3-year-olds sorted bivalent cards one way and then were instructed to switch and sort the same cards…

Optimizing the NASA Technical Report Server

NASA Technical Reports Server (NTRS)

Nelson, Michael L.; Maa, Ming-Hokng

1996-01-01

The NASA Technical Report Server (NTRS), a World Wide Web report distribution NASA technical publications service, is modified for performance enhancement, greater protocol support, and human interface optimization. Results include: Parallel database queries, significantly decreasing user access times by an average factor of 2.3; access from clients behind firewalls and/ or proxies which truncate excessively long Uniform Resource Locators (URLs); access to non-Wide Area Information Server (WAIS) databases and compatibility with the 239-50.3 protocol; and a streamlined user interface.

Activation of epidermal growth factor receptor mediates receptor axon sorting and extension in the developing olfactory system of the moth Manduca sexta.

PubMed

Gibson, Nicholas J; Tolbert, Leslie P

2006-04-10

During development of the adult olfactory system of the moth Manduca sexta, olfactory receptor neurons extend axons from the olfactory epithelium in the antenna into the brain. As they arrive at the brain, interactions with centrally derived glial cells cause axons to sort and fasciculate with other axons destined to innervate the same glomeruli. Here we report studies indicating that activation of the epidermal growth factor receptor (EGFR) is involved in axon ingrowth and targeting. Blocking the EGFR kinase domain pharmacologically leads to stalling of many axons in the sorting zone and nerve layer as well as abnormal axonal fasciculation in the sorting zone. We also find that neuroglian, an IgCAM known to activate the EGFR through homophilic interactions in other systems, is transiently present on olfactory receptor neuron axons and on glia during the critical stages of the sorting process. The neuroglian is resistant to extraction with Triton X-100 in the sorting zone and nerve layer, possibly indicating its stabilization by homophilic binding in these regions. Our results suggest a mechanism whereby neuroglian molecules on axons and possibly sorting zone glia bind homophilically, leading to activation of EGFRs, with subsequent effects on axon sorting, pathfinding, and extension, and glomerulus development. Copyright 2006 Wiley-Liss, Inc.

Activation of EGF Receptor Mediates Receptor Axon Sorting and Extension in the Developing Olfactory System of the Moth Manduca sexta

PubMed Central

Gibson, Nicholas J.; Tolbert, Leslie P.

2008-01-01

During development of the adult olfactory system of the moth Manduca sexta, olfactory receptor neurons extend axons from the olfactory epithelium in the antenna into the brain. As they arrive at the brain, interactions with centrally-derived glial cells cause axons to sort and fasciculate with other axons destined to innervate the same glomeruli. Here we report studies that indicate that activation of the epidermal growth factor receptor (EGFR) is involved in axon ingrowth and targeting. Blocking the EGFR kinase domain pharmacologically leads to stalling of many axons in the sorting zone and nerve layer, as well as abnormal axonal fasciculation in the sorting zone. We also find that neuroglian, an IgCAM known to activate the EGFR through homophilic interactions in other systems, is transiently present on olfactory receptor neuron axons and on glia during the critical stages of the sorting process. The neuroglian is resistant to extraction with Triton X-100 in the sorting zone and nerve layer, possibly indicating its stabilization by homophilic binding in these regions. Our results suggest a mechanism whereby neuroglian molecules on axons and possibly sorting zone glia bind homophilically, leading to activation of EGFRs with subsequent effects on axon sorting, pathfinding, and extension, and glomerulus development. PMID:16498681

Sorted bedform pattern evolution: Persistence, destruction and self-organized intermittency

NASA Astrophysics Data System (ADS)

Goldstein, Evan B.; Murray, A. Brad; Coco, Giovanni

2011-12-01

We investigate the long-term evolution of inner continental shelf sorted bedform patterns. Numerical modeling suggests that a range of behaviors are possible, from pattern persistence to spatial-temporal intermittency. Sorted bedform persistence results from a robust sorting feedback that operates when the seabed features a sufficient concentration of coarse material. In the absence of storm events, pattern maturation processes such as defect dynamics and pattern migration tend to cause the burial of coarse material and excavation of fine material, leading to the fining of the active layer. Vertical sorting occurs until a critical state of active layer coarseness is reached. This critical state results in the local cessation of the sorting feedback, leading to a self-organized spatially intermittent pattern, a hallmark of observed sorted bedforms. Bedforms in shallow conditions and those subject to high wave climates may be temporally intermittent features as a result of increased wave orbital velocity during storms. Erosion, or deposition of bimodal sediment, similarly leads to a spatially intermittent pattern, with individual coarse domains exhibiting temporal intermittence. Recurring storm events cause coarsening of the seabed (strengthening the sorting feedback) and the development of large wavelength patterns. Cessation of storm events leads to the superposition of storm (large wavelength) and inter-storm (small wavelength) patterns and spatial heterogeneity of pattern modes.

A Sequence of Sorting Strategies.

ERIC Educational Resources Information Center

Duncan, David R.; Litwiller, Bonnie H.

1984-01-01

Describes eight increasingly sophisticated and efficient sorting algorithms including linear insertion, binary insertion, shellsort, bubble exchange, shakersort, quick sort, straight selection, and tree selection. Provides challenges for the reader and the student to program these efficiently. (JM)

UBE4B Protein Couples Ubiquitination and Sorting Machineries to Enable Epidermal Growth Factor Receptor (EGFR) Degradation*

PubMed Central

Sirisaengtaksin, Natalie; Gireud, Monica; Yan, Qing; Kubota, Yoshihisa; Meza, Denisse; Waymire, Jack C.; Zage, Peter E.; Bean, Andrew J.

2014-01-01

The signaling of plasma membrane proteins is tuned by internalization and sorting in the endocytic pathway prior to recycling or degradation in lysosomes. Ubiquitin modification allows recognition and association of cargo with endosomally associated protein complexes, enabling sorting of proteins to be degraded from those to be recycled. The mechanism that provides coordination between the cellular machineries that mediate ubiquitination and endosomal sorting is unknown. We report that the ubiquitin ligase UBE4B is recruited to endosomes in response to epidermal growth factor receptor (EGFR) activation by binding to Hrs, a key component of endosomal sorting complex required for transport (ESCRT) 0. We identify the EGFR as a substrate for UBE4B, establish UBE4B as a regulator of EGFR degradation, and describe a mechanism by which UBE4B regulates endosomal sorting, affecting cellular levels of the EGFR and its downstream signaling. We propose a model in which the coordinated action of UBE4B, ESCRT-0, and the deubiquitinating enzyme USP8 enable the endosomal sorting and lysosomal degradation of the EGFR. PMID:24344129

An Abbreviated Protocol for High-Risk Screening Breast MRI Saves Time and Resources.

PubMed

Harvey, Susan C; Di Carlo, Phillip A; Lee, Bonmyong; Obadina, Eniola; Sippo, Dorothy; Mullen, Lisa

2016-04-01

To review the ability of an abbreviated, high-risk, screening, breast MRI protocol to detect cancer and save resources. High-risk screening breast MR images were reviewed, from both an abbreviated protocol and a full diagnostic protocol. Differences in cancer detection, scanner utilization, interpretation times, and need for additional imaging were recorded in an integrated data form, and reviewed and compared. A total of 568 MRI cases were reviewed, with the abbreviated and full protocols. No difference was found in the number of cancers detected. Scan times were decreased by 18.8 minutes per case, for a total of 10,678 minutes (178 hours). Interpretation time, on average, was 1.55 minutes for the abbreviated protocol, compared with 6.43 minutes for the full protocol. Review of the full protocol led to a significant change in the final BI-RADS(®) assessment in 12 of 568 (2.1%) cases. Abbreviated MRI is as effective as full-protocol MRI for demonstration of cancers in the high-risk screening setting, with only 12 (2.1%) cases recommended for additional MRI evaluation. The efficiency and resource savings of an abbreviated protocol would be significant, and would allow for opportunities to provide MRI for additional patients, as well as improved radiologist time management and workflow, with the potential to add real-time MRI interpretation or double reading. Copyright © 2016 American College of Radiology. Published by Elsevier Inc. All rights reserved.

An Abbreviated Protocol for High-Risk Screening Breast MRI Saves Time and Resources.

PubMed

Harvey, Susan C; Di Carlo, Phillip A; Lee, Bonmyong; Obadina, Eniola; Sippo, Dorothy; Mullen, Lisa

2016-11-01

To review the ability of an abbreviated, high-risk, screening, breast MRI protocol to detect cancer and save resources. High-risk screening breast MR images were reviewed, from both an abbreviated protocol and a full diagnostic protocol. Differences in cancer detection, scanner utilization, interpretation times, and need for additional imaging were recorded in an integrated data form, and reviewed and compared. A total of 568 MRI cases were reviewed, with the abbreviated and full protocols. No difference was found in the number of cancers detected. Scan times were decreased by 18.8 minutes per case, for a total of 10,678 minutes (178 hours). Interpretation time, on average, was 1.55 minutes for the abbreviated protocol, compared with 6.43 minutes for the full protocol. Review of the full protocol led to a significant change in the final BI-RADS ® assessment in 12 of 568 (2.1%) cases. Abbreviated MRI is as effective as full-protocol MRI for demonstration of cancers in the high-risk screening setting, with only 12 (2.1 %) cases recommended for additional MRI evaluation. The efficiency and resource savings of an abbreviated protocol would be significant, and would allow for opportunities to provide MRI for additional patients, as well as improved radiologist time management and workflow, with the potential to add real-time MRI interpretation or double reading. Copyright © 2016 American College of Radiology. Published by Elsevier Inc. All rights reserved.

Is ExacTrac x-ray system an alternative to CBCT for positioning patients with head and neck cancers?

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

Clemente, Stefania; Chiumento, Costanza; Fiorentino, Alba

Purpose: To evaluate the usefulness of a six-degrees-of freedom (6D) correction using ExacTrac robotics system in patients with head-and-neck (HN) cancer receiving radiation therapy.Methods: Local setup accuracy was analyzed for 12 patients undergoing intensity-modulated radiation therapy (IMRT). Patient position was imaged daily upon two different protocols, cone-beam computed tomography (CBCT), and ExacTrac (ET) images correction. Setup data from either approach were compared in terms of both residual errors after correction and punctual displacement of selected regions of interest (Mandible, C2, and C6 vertebral bodies).Results: On average, both protocols achieved reasonably low residual errors after initial correction. The observed differences inmore » shift vectors between the two protocols showed that CBCT tends to weight more C2 and C6 at the expense of the mandible, while ET tends to average more differences among the different ROIs.Conclusions: CBCT, even without 6D correction capabilities, seems preferable to ET for better consistent alignment and the capability to see soft tissues. Therefore, in our experience, CBCT represents a benchmark for positioning head and neck cancer patients.« less

Efficacy of an accelerated recovery protocol for Oxford unicompartmental knee arthroplasty--a randomised controlled trial.

PubMed

Reilly, K A; Beard, D J; Barker, K L; Dodd, C A F; Price, A J; Murray, D W

2005-10-01

Unicompartmental knee arthroplasty (UKA) is appropriate for one in four patients with osteoarthritic knees. This study was performed to compare the safety, effectiveness and economic viability of a new accelerated protocol with current standard care in a state healthcare system. A single blind RCT design was used. Eligible patients were screened for NSAID tolerance, social circumstances and geographical location before allocation to an accelerated recovery group (A) or standard care group (S). Primary outcome was the Oxford Knee Assessment at 6 months post operation, compared using independent Mann-Whitney U-tests. A simple difference in costs incurred was calculated. The study power was sufficient to avoid type 2 errors. Forty-one patients were included. The average stay for Group A was 1.5 days. Group S averaged 4.3 days. No significant difference in outcomes was found between groups. The new protocol achieved cost savings of 27% and significantly reduced hospital bed occupancy. In addition, patient satisfaction was assessed as greater with the accelerated discharge than with the routine discharge time. The strict inclusion criteria meant that 75% of eligible patients were excluded. However, a large percentage of these were due to the distances patients lived from the hospital.

Statistical Characteristics of Single Sort of Grape Bulgarian Wines

NASA Astrophysics Data System (ADS)

Boyadzhiev, D.

2008-10-01

The aim of this paper is to evaluate the differences in the values of the 8 basic physicochemical indices of single sort of grape Bulgarian wines (white and red ones), obligatory for the standardization of ready production in the winery. Statistically significant differences in the values of various sorts and vintages are established and possibilities for identifying the sort and the vintage on the base of these indices by applying discriminant analysis are discussed.

Measurement of Lipid Accumulation in Chlorella vulgaris via Flow Cytometry and Liquid-State ¹H NMR Spectroscopy for Development of an NMR-Traceable Flow Cytometry Protocol

PubMed Central

Bono Jr., Michael S.; Garcia, Ravi D.; Sri-Jayantha, Dylan V.; Ahner, Beth A.; Kirby, Brian J.

2015-01-01

In this study, we cultured Chlorella vulgaris cells with a range of lipid contents, induced via nitrogen starvation, and characterized them via flow cytometry, with BODIPY 505/515 as a fluorescent lipid label, and liquid-state 1H NMR spectroscopy. In doing so, we demonstrate the utility of calibrating flow cytometric measurements of algal lipid content using triacylglyceride (TAG, also known as triacylglycerol or triglyceride) content per cell as measured via quantitative 1H NMR. Ensemble-averaged fluorescence of BODIPY-labeled cells was highly correlated with average TAG content per cell measured by bulk NMR, with a linear regression yielding a linear fit with r 2 = 0.9974. This correlation compares favorably to previous calibrations of flow cytometry protocols to lipid content measured via extraction, and calibration by NMR avoids the time and complexity that is generally required for lipid quantitation via extraction. Flow cytometry calibrated to a direct measurement of TAG content can be used to investigate the distribution of lipid contents for cells within a culture. Our flow cytometry measurements showed that Chlorella vulgaris cells subjected to nitrogen limitation exhibited higher mean lipid content but a wider distribution of lipid content that overlapped the relatively narrow distribution of lipid content for replete cells, suggesting that nitrogen limitation induces lipid accumulation in only a subset of cells. Calibration of flow cytometry protocols using direct in situ measurement of TAG content via NMR will facilitate rapid development of more precise flow cytometry protocols, enabling investigation of algal lipid accumulation for development of more productive algal biofuel feedstocks and cultivation protocols. PMID:26267664

Improved Detection of Norovirus and Hepatitis A Virus in Surface Water by Applying Pre-PCR Processing.

PubMed

Borgmästars, Emmy; Jazi, Mehrdad Mousavi; Persson, Sofia; Jansson, Linda; Rådström, Peter; Simonsson, Magnus; Hedman, Johannes; Eriksson, Ronnie

2017-12-01

Quantitative reverse transcriptase polymerase chain reaction (RT-qPCR) detection of waterborne RNA viruses generally requires concentration of large water volumes due to low virus levels. A common approach is to use dead-end ultrafiltration followed by precipitation with polyethylene glycol. However, this procedure often leads to the co-concentration of PCR inhibitors that impairs the limit of detection and causes false-negative results. Here, we applied the concept of pre-PCR processing to optimize RT-qPCR detection of norovirus genogroup I (GI), genogroup II (GII), and hepatitis A virus (HAV) in challenging water matrices. The RT-qPCR assay was improved by screening for an inhibitor-tolerant master mix and modifying the primers with twisted intercalating nucleic acid molecules. Additionally, a modified protocol based on chaotropic lysis buffer and magnetic silica bead nucleic acid extraction was developed for complex water matrices. A validation of the modified extraction protocol on surface and drinking waters was performed. At least a 26-fold improvement was seen in the most complex surface water studied. The modified protocol resulted in average recoveries of 33, 13, 8, and 4% for mengovirus, norovirus GI, GII, and HAV, respectively. The modified protocol also improved the limit of detection for norovirus GI and HAV. RT-qPCR inhibition with C q shifts of 1.6, 2.8, and 3.5 for norovirus GI, GII, and HAV, respectively, obtained for the standard nucleic acid extraction were completely eliminated by the modified protocol. The standard nucleic acid extraction method worked well on drinking water with no RT-qPCR inhibition observed and average recoveries of 80, 124, 89, and 32% for mengovirus, norovirus GI, GII, and HAV, respectively.

Cost Analysis of the Addition of Hyperacute Magnetic Resonance Imaging for Selection of Patients for Endovascular Stroke Therapy.

PubMed

John, Seby; Thompson, Nicolas R; Lesko, Terry; Papesh, Nancy; Obuchowski, Nancy; Tomic, Dan; Wisco, Dolora; Khawaja, Zeshaun; Uchino, Ken; Man, Shumei; Cheng-Ching, Esteban; Toth, Gabor; Masaryk, Thomas; Ruggieri, Paul; Modic, Michael; Hussain, Muhammad Shazam

2017-10-01

Patient selection is important to determine the best candidates for endovascular stroke therapy. In application of a hyperacute magnetic resonance imaging (MRI) protocol for patient selection, we have shown decreased utilization with improved outcomes. A cost analysis comparing the pre- and post-MRI protocol time periods was performed to determine if the previous findings translated into cost opportunities. We retrospectively identified individuals considered for endovascular stroke therapy from January 2008 to August 2012 who were ≤8 h from stroke symptoms onset. Patients prior to April 30, 2010 were selected based on results of the computed tomography/computed tomography angiography alone (pre-hyperacute), whereas patients after April 30, 2010 were selected based on results of MRI (post-hyperacute MRI). Demographic, outcome, and financial information was collected. Log-transformed average daily direct costs were regressed on time period. The regression model included demographic and clinical covariates as potential confounders. Multiple imputation was used to account for missing data. We identified 267 patients in our database (88 patients in pre-hyperacute MRI period, 179 in hyperacute MRI protocol period). Patient length of stay was not significantly different in the hyperacute MRI protocol period as compared to the pre-hyperacute MRI period (10.6 vs. 9.9 days, p < 0.42). The median of average daily direct costs was reduced by 24.5% (95% confidence interval 14.1-33.7%, p < 0.001). Use of the hyperacute MRI protocol translated into reduced costs, in addition to reduced utilization and better outcomes. MRI selection of patients is an effective strategy, both for patients and hospital systems.

Comparison of breathing gated CT images generated using a 5DCT technique and a commercial clinical protocol in a porcine model

PubMed Central

O’Connell, Dylan P.; Thomas, David H.; Dou, Tai H.; Lamb, James M.; Feingold, Franklin; Low, Daniel A.; Fuld, Matthew K.; Sieren, Jered P.; Sloan, Chelsea M.; Shirk, Melissa A.; Hoffman, Eric A.; Hofmann, Christian

2015-01-01

Purpose: To demonstrate that a “5DCT” technique which utilizes fast helical acquisition yields the same respiratory-gated images as a commercial technique for regular, mechanically produced breathing cycles. Methods: Respiratory-gated images of an anesthetized, mechanically ventilated pig were generated using a Siemens low-pitch helical protocol and 5DCT for a range of breathing rates and amplitudes and with standard and low dose imaging protocols. 5DCT reconstructions were independently evaluated by measuring the distances between tissue positions predicted by a 5D motion model and those measured using deformable registration, as well by reconstructing the originally acquired scans. Discrepancies between the 5DCT and commercial reconstructions were measured using landmark correspondences. Results: The mean distance between model predicted tissue positions and deformably registered tissue positions over the nine datasets was 0.65 ± 0.28 mm. Reconstructions of the original scans were on average accurate to 0.78 ± 0.57 mm. Mean landmark displacement between the commercial and 5DCT images was 1.76 ± 1.25 mm while the maximum lung tissue motion over the breathing cycle had a mean value of 27.2 ± 4.6 mm. An image composed of the average of 30 deformably registered images acquired with a low dose protocol had 6 HU image noise (single standard deviation) in the heart versus 31 HU for the commercial images. Conclusions: An end to end evaluation of the 5DCT technique was conducted through landmark based comparison to breathing gated images acquired with a commercial protocol under highly regular ventilation. The techniques were found to agree to within 2 mm for most respiratory phases and most points in the lung. PMID:26133604

Thermal/optical methods for elemental carbon quantification in soils and urban dusts: equivalence of different analysis protocols.

PubMed

Han, Yongming; Chen, Antony; Cao, Junji; Fung, Kochy; Ho, Fai; Yan, Beizhan; Zhan, Changlin; Liu, Suixin; Wei, Chong; An, Zhisheng

2013-01-01

Quantifying elemental carbon (EC) content in geological samples is challenging due to interferences of crustal, salt, and organic material. Thermal/optical analysis, combined with acid pretreatment, represents a feasible approach. However, the consistency of various thermal/optical analysis protocols for this type of samples has never been examined. In this study, urban street dust and soil samples from Baoji, China were pretreated with acids and analyzed with four thermal/optical protocols to investigate how analytical conditions and optical correction affect EC measurement. The EC values measured with reflectance correction (ECR) were found always higher and less sensitive to temperature program than the EC values measured with transmittance correction (ECT). A high-temperature method with extended heating times (STN120) showed the highest ECT/ECR ratio (0.86) while a low-temperature protocol (IMPROVE-550), with heating time adjusted for sample loading, showed the lowest (0.53). STN ECT was higher than IMPROVE ECT, in contrast to results from aerosol samples. A higher peak inert-mode temperature and extended heating times can elevate ECT/ECR ratios for pretreated geological samples by promoting pyrolyzed organic carbon (PyOC) removal over EC under trace levels of oxygen. Considering that PyOC within filter increases ECR while decreases ECT from the actual EC levels, simultaneous ECR and ECT measurements would constrain the range of EC loading and provide information on method performance. Further testing with standard reference materials of common environmental matrices supports the findings. Char and soot fractions of EC can be further separated using the IMPROVE protocol. The char/soot ratio was lower in street dusts (2.2 on average) than in soils (5.2 on average), most likely reflecting motor vehicle emissions. The soot concentrations agreed with EC from CTO-375, a pure thermal method.

Measurement of lipid accumulation in Chlorella vulgaris via flow cytometry and liquid-state ¹H NMR spectroscopy for development of an NMR-traceable flow cytometry protocol.

PubMed

Bono, Michael S; Garcia, Ravi D; Sri-Jayantha, Dylan V; Ahner, Beth A; Kirby, Brian J

2015-01-01

In this study, we cultured Chlorella vulgaris cells with a range of lipid contents, induced via nitrogen starvation, and characterized them via flow cytometry, with BODIPY 505/515 as a fluorescent lipid label, and liquid-state 1H NMR spectroscopy. In doing so, we demonstrate the utility of calibrating flow cytometric measurements of algal lipid content using triacylglyceride (TAG, also known as triacylglycerol or triglyceride) content per cell as measured via quantitative 1H NMR. Ensemble-averaged fluorescence of BODIPY-labeled cells was highly correlated with average TAG content per cell measured by bulk NMR, with a linear regression yielding a linear fit with r2 = 0.9974. This correlation compares favorably to previous calibrations of flow cytometry protocols to lipid content measured via extraction, and calibration by NMR avoids the time and complexity that is generally required for lipid quantitation via extraction. Flow cytometry calibrated to a direct measurement of TAG content can be used to investigate the distribution of lipid contents for cells within a culture. Our flow cytometry measurements showed that Chlorella vulgaris cells subjected to nitrogen limitation exhibited higher mean lipid content but a wider distribution of lipid content that overlapped the relatively narrow distribution of lipid content for replete cells, suggesting that nitrogen limitation induces lipid accumulation in only a subset of cells. Calibration of flow cytometry protocols using direct in situ measurement of TAG content via NMR will facilitate rapid development of more precise flow cytometry protocols, enabling investigation of algal lipid accumulation for development of more productive algal biofuel feedstocks and cultivation protocols.

Cloning of Plasmodium falciparum by single-cell sorting

PubMed Central

Miao, Jun; Li, Xiaolian; Cui, Liwang

2010-01-01

Malaria parasite cloning is traditionally carried out mainly by using the limiting dilution method, which is laborious, imprecise, and unable to distinguish multiply-infected RBCs. In this study, we used a parasite engineered to express green fluorescent protein (GFP) to evaluate a single-cell sorting method for rapidly cloning Plasmodium falciparum. By dividing a two dimensional scattergram from a cell sorter into 17 gates, we determined the parameters for isolating singly-infected erythrocytes and sorted them into individual cultures. Pre-gating of the engineered parasites for GFP allowed the isolation of almost 100% GFP-positive clones. Compared with the limiting dilution method, the number of parasite clones obtained by single-cell sorting was much higher. Molecular analyses showed that parasite isolates obtained by single-cell sorting were highly homogenous. This highly efficient single-cell sorting method should prove very useful for cloning both P. falciparum laboratory populations from genetic manipulation experiments and clinical samples. PMID:20435038

PhySortR: a fast, flexible tool for sorting phylogenetic trees in R.

PubMed

Stephens, Timothy G; Bhattacharya, Debashish; Ragan, Mark A; Chan, Cheong Xin

2016-01-01

A frequent bottleneck in interpreting phylogenomic output is the need to screen often thousands of trees for features of interest, particularly robust clades of specific taxa, as evidence of monophyletic relationship and/or reticulated evolution. Here we present PhySortR, a fast, flexible R package for classifying phylogenetic trees. Unlike existing utilities, PhySortR allows for identification of both exclusive and non-exclusive clades uniting the target taxa based on tip labels (i.e., leaves) on a tree, with customisable options to assess clades within the context of the whole tree. Using simulated and empirical datasets, we demonstrate the potential and scalability of PhySortR in analysis of thousands of phylogenetic trees without a priori assumption of tree-rooting, and in yielding readily interpretable trees that unambiguously satisfy the query. PhySortR is a command-line tool that is freely available and easily automatable.

Sortilin 1 knockout alters basal adipose glucose metabolism but not diet-induced obesity in mice.

PubMed

Li, Jibiao; Matye, David J; Wang, Yifeng; Li, Tiangang

2017-04-01

Sortilin 1 (Sort1) is a trafficking receptor that has been implicated in the regulation of plasma cholesterol in humans and mice. Here, we use metabolomics and hyperinsulinemic-euglycemic clamp approaches to obtain further understanding of the in vivo effects of Sort1 deletion on diet-induced obesity as well as on adipose lipid and glucose metabolism. Results show that Sort1 knockout (KO) does not affect Western diet-induced obesity nor adipose fatty acid and ceramide concentrations. Under the basal fasting state, chow-fed Sort1 KO mice have decreased adipose glycolytic metabolites, but Sort1 deletion does not affect insulin-stimulated tissue glucose uptake during the insulin clamp. These results suggest that Sort1 loss-of-function in vivo does not affect obesity development, but differentially modulates adipose glucose metabolism under fasting and insulin-stimulated states. © 2017 Federation of European Biochemical Societies.

Standard practice for cell sorting in a BSL-3 facility.

PubMed

Perfetto, Stephen P; Ambrozak, David R; Nguyen, Richard; Roederer, Mario; Koup, Richard A; Holmes, Kevin L

2011-01-01

Over the past decade, there has been a rapid growth in the number of BSL-3 and BSL-4 laboratories in the USA and an increase in demand for infectious cell sorting in BSL-3 laboratories. In 2007, the International Society for Advancement of Cytometry (ISAC) Biosafety Committee published standards for the sorting of unfixed cells and is an important resource for biosafety procedures when performing infectious cell sorting. Following a careful risk assessment, if it is determined that a cell sorter must be located within a BSL-3 laboratory, there are a variety of factors to be considered prior to the establishment of the laboratory. This chapter outlines procedures for infectious cell sorting in a BSL-3 environment to facilitate the establishment and safe operation of a BSL-3 cell sorting laboratory. Subjects covered include containment verification, remote operation, disinfection, personal protective equipment (PPE), and instrument-specific modifications for enhanced aerosol evacuation.

Standard Practice for Cell Sorting in a BSL-3 Facility

PubMed Central

Perfetto, Stephen P.; Ambrozak, David R.; Nguyen, Richard; Roederer, Mario; Koup, Richard A.; Holmes, Kevin L.

2016-01-01

Over the past decade, there has been a rapid growth in the number of BSL-3 and BSL-4 laboratories in the USA and an increase in demand for infectious cell sorting in BSL-3 laboratories. In 2007, the International Society for Advancement of Cytometry (ISAC) Biosafety Committee published standards for the sorting of unfixed cells and is an important resource for biosafety procedures when performing infectious cell sorting. Following a careful risk assessment, if it is determined that a cell sorter must be located within a BSL-3 laboratory, there are a variety of factors to be considered prior to the establishment of the laboratory. This chapter outlines procedures for infectious cell sorting in a BSL-3 environment to facilitate the establishment and safe operation of a BSL-3 cell sorting laboratory. Subjects covered include containment verification, remote operation, disinfection, personal protective equipment (PPE), and instrument-specific modifications for enhanced aerosol evacuation. PMID:21116997

Data parallel sorting for particle simulation

NASA Technical Reports Server (NTRS)

Dagum, Leonardo

1992-01-01

Sorting on a parallel architecture is a communications intensive event which can incur a high penalty in applications where it is required. In the case of particle simulation, only integer sorting is necessary, and sequential implementations easily attain the minimum performance bound of O (N) for N particles. Parallel implementations, however, have to cope with the parallel sorting problem which, in addition to incurring a heavy communications cost, can make the minimun performance bound difficult to attain. This paper demonstrates how the sorting problem in a particle simulation can be reduced to a merging problem, and describes an efficient data parallel algorithm to solve this merging problem in a particle simulation. The new algorithm is shown to be optimal under conditions usual for particle simulation, and its fieldwise implementation on the Connection Machine is analyzed in detail. The new algorithm is about four times faster than a fieldwise implementation of radix sort on the Connection Machine.

The interactive electrode localization utility: software for automatic sorting and labeling of intracranial subdural electrodes

PubMed Central

Tang, Wei; Peled, Noam; Vallejo, Deborah I.; Borzello, Mia; Dougherty, Darin D.; Eskandar, Emad N.; Widge, Alik S.; Cash, Sydney S.; Stufflebeam, Steven M.

2018-01-01

Purpose Existing methods for sorting, labeling, registering, and across-subject localization of electrodes in intracranial encephalography (iEEG) may involve laborious work requiring manual inspection of radiological images. Methods We describe a new open-source software package, the interactive electrode localization utility which presents a full pipeline for the registration, localization, and labeling of iEEG electrodes from CT and MR images. In addition, we describe a method to automatically sort and label electrodes from subdural grids of known geometry. Results We validated our software against manual inspection methods in twelve subjects undergoing iEEG for medically intractable epilepsy. Our algorithm for sorting and labeling performed correct identification on 96% of the electrodes. Conclusions The sorting and labeling methods we describe offer nearly perfect performance and the software package we have distributed may simplify the process of registering, sorting, labeling, and localizing subdural iEEG grid electrodes by manual inspection. PMID:27915398

Synthesis and screening of one-bead-one-compound cyclic peptide libraries.

PubMed

Qian, Ziqing; Upadhyaya, Punit; Pei, Dehua

2015-01-01

Cyclic peptides have been a rich source of biologically active molecules. Herein we present a method for the combinatorial synthesis and screening of large one-bead-one-compound (OBOC) libraries of cyclic peptides against biological targets such as proteins. Up to ten million different cyclic peptides are rapidly synthesized on TentaGel microbeads by the split-and-pool synthesis method and subjected to a multistage screening protocol which includes magnetic sorting, on-bead enzyme-linked and fluorescence-based assays, and in-solution binding analysis of cyclic peptides selectively released from single beads by fluorescence anisotropy. Finally, the most active hit(s) is identified by the partial Edman degradation-mass spectrometry (PED-MS) method. This method allows a single researcher to synthesize and screen up to ten million cyclic peptides and identify the most active ligand(s) in ~1 month, without the time-consuming and expensive hit resynthesis or the use of any special equipment.

Issues to be resolved in Torrents—Future Revolutionised File Sharing

NASA Astrophysics Data System (ADS)

Thanekar, Sachin Arun

2010-11-01

Torrenting is a highly popular peer to peer file sharing activity that allows participants to send and receive files from other computers. As it is an advantageous technique as compare to traditional client server file sharing in terms of time, cost and speed, some drawbaks are also there. Content unavailability, lack of anonymity, leechers, cheaters and download speed consistency are the major problems to sort out. Efforts are needed to resolve these problems and to make this better application. Legal issues are also one of the measure factors of consideration. BitTorrent metafiles themselves do not store copyrighted data. Whether the publishers of BitTorrent metafiles violate copyrights by linking to copyrighted material is controversial. Various countries have taken legal action against websites that host BitTorrent trackers. Eg. Supernova.org, Torrentspy. Efforts are also needed to make such a useful protocol legal.

Mothers With Physical Disability: Child Care Adaptations at Home

PubMed Central

Smith, Diane L.; Iezzoni, Lisa I.

2016-01-01

OBJECTIVE. This study describes how women with physical disability experience caregiving for a new infant and how they adapt their home environment and care tasks. METHOD. In 2013, we conducted 2-hr telephone interviews with 22 women with significant physical disability who had delivered babies within the previous 10 yr. The semistructured, open-ended interview protocol addressed wide-ranging pregnancy-related topics. NVivo was used to sort the texts for content analysis. RESULTS. Night care, bathing, and carrying the baby were identified as the biggest challenges. Typical adaptations (with and without occupational therapy consultation) included use of a wrap for carrying the infant, furniture adaptations for mothers using wheelchairs, and assistance from caregivers. CONCLUSION. Women with physical disability can be fully capable of caring for an infant and can find ways to adapt their environment. Further research may determine the role of occupation therapy. PMID:27767945

Library Design-Facilitated High-Throughput Sequencing of Synthetic Peptide Libraries.

PubMed

Vinogradov, Alexander A; Gates, Zachary P; Zhang, Chi; Quartararo, Anthony J; Halloran, Kathryn H; Pentelute, Bradley L

2017-11-13

A methodology to achieve high-throughput de novo sequencing of synthetic peptide mixtures is reported. The approach leverages shotgun nanoliquid chromatography coupled with tandem mass spectrometry-based de novo sequencing of library mixtures (up to 2000 peptides) as well as automated data analysis protocols to filter away incorrect assignments, noise, and synthetic side-products. For increasing the confidence in the sequencing results, mass spectrometry-friendly library designs were developed that enabled unambiguous decoding of up to 600 peptide sequences per hour while maintaining greater than 85% sequence identification rates in most cases. The reliability of the reported decoding strategy was additionally confirmed by matching fragmentation spectra for select authentic peptides identified from library sequencing samples. The methods reported here are directly applicable to screening techniques that yield mixtures of active compounds, including particle sorting of one-bead one-compound libraries and affinity enrichment of synthetic library mixtures performed in solution.

Relativistic quantum cryptography

NASA Astrophysics Data System (ADS)

Molotkov, S. N.; Nazin, S. S.

2003-07-01

The problem of unconditional security of quantum cryptography (i.e. the security which is guaranteed by the fundamental laws of nature rather than by technical limitations) is one of the central points in quantum information theory. We propose a relativistic quantum cryptosystem and prove its unconditional security against any eavesdropping attempts. Relativistitic causality arguments allow to demonstrate the security of the system in a simple way. Since the proposed protocol does not empoly collective measurements and quantum codes, the cryptosystem can be experimentally realized with the present state-of-art in fiber optics technologies. The proposed cryptosystem employs only the individual measurements and classical codes and, in addition, the key distribution problem allows to postpone the choice of the state encoding scheme until after the states are already received instead of choosing it before sending the states into the communication channel (i.e. to employ a sort of "antedate" coding).

Detection of ASC Speck Formation by Flow Cytometry and Chemical Cross-linking.

PubMed

Hoss, Florian; Rolfes, Verena; Davanso, Mariana R; Braga, Tarcio T; Franklin, Bernardo S

2018-01-01

Assembly of a relatively large protein aggregate or "speck" formed by the adaptor protein ASC is a common downstream step in the activation of most inflammasomes. This unique feature of ASC allows its visualization by several imaging techniques and constitutes a reliable and feasible readout for inflammasome activation in cells and tissues. We have previously described step-by-step protocols to generate immortalized cell lines stably expressing ASC fused to a fluorescent protein for measuring inflammasome activation by confocal microscopy, and immunofluorescence of endogenous ASC in primary cells. Here, we present two more methods to detect ASC speck formation: (1) Assessment of ASC speck formation by flow cytometry; and (2) Chemical cross-linking of ASC followed by immunoblotting. These methods allow for the discrimination of inflammasome-activated versus non-activated cells, the identification of lineage-specific inflammasome activation in complex cell mixtures, and sorting of inflammasome-activated cells for further analysis.

Reporter-Based Isolation of Developmental Myogenic Progenitors

PubMed Central

Kheir, Eyemen; Cusella, Gabriella; Messina, Graziella; Cossu, Giulio; Biressi, Stefano

2018-01-01

The formation and activity of mammalian tissues entail finely regulated processes, involving the concerted organization and interaction of multiple cell types. In recent years the prospective isolation of distinct progenitor and stem cell populations has become a powerful tool in the hands of developmental biologists and has rendered the investigation of their intrinsic properties possible. In this protocol, we describe how to purify progenitors with different lineage history and degree of differentiation from embryonic and fetal skeletal muscle by fluorescence-activated cell sorting (FACS). The approach takes advantage of a panel of murine strains expressing fluorescent reporter genes specifically in the myogenic progenitors. We provide a detailed description of the dissection procedures and of the enzymatic dissociation required to maximize the yield of mononucleated cells for subsequent FACS-based purification. The procedure takes ~6–7 h to complete and allows for the isolation and the subsequent molecular and phenotypic characterization of developmental myogenic progenitors. PMID:29674978

[Professor Xu Fu-song's traditional Chinese medicine protocols for male diseases: A descriptive analysis].

PubMed

Liu, Cheng-yong; Xu, Fu-song

2015-04-01

To analyze the efficacy and medication principles of Professor Xu Fu-songs traditional Chinese medicine (TCM) protocols for male diseases. We reviewed and descriptively analyzed the unpublished complete medical records of 100 male cases treated by Professor Xu Fu-song with his TCM protocols from 1978 to 1992. The 100 cases involved 32 male diseases, most of which were difficult and complicated cases. The drug compliance was 95%. Each prescription was made up of 14 traditional Chinese drugs on average. The cure rate was 32% , and the effective rate was 85%. Professor Xu Fu-song advanced and proved some new theories and therapeutic methods. Professor Xu Fu-song's TCM protocols can be applied to a wide range of male diseases, mostly complicated, and are characterized by accurate differentiation of symptoms and signs, high drug compliance, and excellent therapeutic efficacy.

Traffic placement policies for a multi-band network

NASA Technical Reports Server (NTRS)

Maly, Kurt J.; Foudriat, E. C.; Game, David; Mukkamala, R.; Overstreet, C. Michael

1990-01-01

Recently protocols were introduced that enable the integration of synchronous traffic (voice or video) and asynchronous traffic (data) and extend the size of local area networks without loss in speed or capacity. One of these is DRAMA, a multiband protocol based on broadband technology. It provides dynamic allocation of bandwidth among clusters of nodes in the total network. A number of traffic placement policies for such networks are proposed and evaluated. Metrics used for performance evaluation include average network access delay, degree of fairness of access among the nodes, and network throughput. The feasibility of the DRAMA protocol is established through simulation studies. DRAMA provides effective integration of synchronous and asychronous traffic due to its ability to separate traffic types. Under the suggested traffic placement policies, the DRAMA protocol is shown to handle diverse loads, mixes of traffic types, and numbers of nodes, as well as modifications to the network structure and momentary traffic overloads.

Evaluation of dose from kV cone-beam computed tomography during radiotherapy: a comparison of methodologies

NASA Astrophysics Data System (ADS)

Buckley, J.; Wilkinson, D.; Malaroda, A.; Metcalfe, P.

2017-01-01

Three alternative methodologies to the Computed-Tomography Dose Index for the evaluation of Cone-Beam Computed Tomography dose are compared, the Cone-Beam Dose Index, IAEA Human Health Report No. 5 recommended methodology and the AAPM Task Group 111 recommended methodology. The protocols were evaluated for Pelvis and Thorax scan modes on Varian® On-Board Imager and Truebeam kV XI imaging systems. The weighted planar average dose was highest for the AAPM methodology across all scans, with the CBDI being the second highest overall. A 17.96% and 1.14% decrease from the TG-111 protocol to the IAEA and CBDI protocols for the Pelvis mode and 18.15% and 13.10% decrease for the Thorax mode were observed for the XI system. For the OBI system, the variation was 16.46% and 7.14% for Pelvis mode and 15.93% to the CBDI protocol in Thorax mode respectively.

Impact of respiratory-correlated CT sorting algorithms on the choice of margin definition for free-breathing lung radiotherapy treatments.

PubMed

Thengumpallil, Sheeba; Germond, Jean-François; Bourhis, Jean; Bochud, François; Moeckli, Raphaël

2016-06-01

To investigate the impact of Toshiba phase- and amplitude-sorting algorithms on the margin strategies for free-breathing lung radiotherapy treatments in the presence of breathing variations. 4D CT of a sphere inside a dynamic thorax phantom was acquired. The 4D CT was reconstructed according to the phase- and amplitude-sorting algorithms. The phantom was moved by reproducing amplitude, frequency, and a mix of amplitude and frequency variations. Artefact analysis was performed for Mid-Ventilation and ITV-based strategies on the images reconstructed by phase- and amplitude-sorting algorithms. The target volume deviation was assessed by comparing the target volume acquired during irregular motion to the volume acquired during regular motion. The amplitude-sorting algorithm shows reduced artefacts for only amplitude variations while the phase-sorting algorithm for only frequency variations. For amplitude and frequency variations, both algorithms perform similarly. Most of the artefacts are blurring and incomplete structures. We found larger artefacts and volume differences for the Mid-Ventilation with respect to the ITV strategy, resulting in a higher relative difference of the surface distortion value which ranges between maximum 14.6% and minimum 4.1%. The amplitude- is superior to the phase-sorting algorithm in the reduction of motion artefacts for amplitude variations while phase-sorting for frequency variations. A proper choice of 4D CT sorting algorithm is important in order to reduce motion artefacts, especially if Mid-Ventilation strategy is used. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Efficient sampling of parsimonious inversion histories with application to genome rearrangement in Yersinia.

PubMed

Miklós, István; Darling, Aaron E

2009-06-22

Inversions are among the most common mutations acting on the order and orientation of genes in a genome, and polynomial-time algorithms exist to obtain a minimal length series of inversions that transform one genome arrangement to another. However, the minimum length series of inversions (the optimal sorting path) is often not unique as many such optimal sorting paths exist. If we assume that all optimal sorting paths are equally likely, then statistical inference on genome arrangement history must account for all such sorting paths and not just a single estimate. No deterministic polynomial algorithm is known to count the number of optimal sorting paths nor sample from the uniform distribution of optimal sorting paths. Here, we propose a stochastic method that uniformly samples the set of all optimal sorting paths. Our method uses a novel formulation of parallel Markov chain Monte Carlo. In practice, our method can quickly estimate the total number of optimal sorting paths. We introduce a variant of our approach in which short inversions are modeled to be more likely, and we show how the method can be used to estimate the distribution of inversion lengths and breakpoint usage in pathogenic Yersinia pestis. The proposed method has been implemented in a program called "MC4Inversion." We draw comparison of MC4Inversion to the sampler implemented in BADGER and a previously described importance sampling (IS) technique. We find that on high-divergence data sets, MC4Inversion finds more optimal sorting paths per second than BADGER and the IS technique and simultaneously avoids bias inherent in the IS technique.

Rapid assessment of forest canopy and light regime using smartphone hemispherical photography.

PubMed

Bianchi, Simone; Cahalan, Christine; Hale, Sophie; Gibbons, James Michael

2017-12-01

Hemispherical photography (HP), implemented with cameras equipped with "fisheye" lenses, is a widely used method for describing forest canopies and light regimes. A promising technological advance is the availability of low-cost fisheye lenses for smartphone cameras. However, smartphone camera sensors cannot record a full hemisphere. We investigate whether smartphone HP is a cheaper and faster but still adequate operational alternative to traditional cameras for describing forest canopies and light regimes. We collected hemispherical pictures with both smartphone and traditional cameras in 223 forest sample points, across different overstory species and canopy densities. The smartphone image acquisition followed a faster and simpler protocol than that for the traditional camera. We automatically thresholded all images. We processed the traditional camera images for Canopy Openness (CO) and Site Factor estimation. For smartphone images, we took two pictures with different orientations per point and used two processing protocols: (i) we estimated and averaged total canopy gap from the two single pictures, and (ii) merging the two pictures together, we formed images closer to full hemispheres and estimated from them CO and Site Factors. We compared the same parameters obtained from different cameras and estimated generalized linear mixed models (GLMMs) between them. Total canopy gap estimated from the first processing protocol for smartphone pictures was on average significantly higher than CO estimated from traditional camera images, although with a consistent bias. Canopy Openness and Site Factors estimated from merged smartphone pictures of the second processing protocol were on average significantly higher than those from traditional cameras images, although with relatively little absolute differences and scatter. Smartphone HP is an acceptable alternative to HP using traditional cameras, providing similar results with a faster and cheaper methodology. Smartphone outputs can be directly used as they are for ecological studies, or converted with specific models for a better comparison to traditional cameras.

Altering Work to Rest Ratios Differentially Influences Fatigue Indices During Repeated Sprint Ability Testing.

PubMed

La Monica, Michael B; Fukuda, David H; Beyer, Kyle S; Hoffman, Mattan W; Miramonti, Amelia A; Riffe, Josh J; Baker, Kayla M; Fragala, Maren S; Hoffman, Jay R; Stout, Jeffrey R

2016-02-01

This study examined the influence of recovery time on fatigue indices, performance (total work [TW], peak power [PP], and mean power [MP]), and oxygen consumption during repeated sprint ability (RSA) on a cycle ergometer. Eight recreationally-trained men performed 3 RSA protocols consisting of 10 × 6 s sprints with 12 s, 18 s, and 24 s rest intervals between each sprint. Fatigue indices were determined as percent decrement (%Dec) and rate of decline using either a log transform method or standard slope approach for TW, PP, and MP during respective RSA protocols. The maximal VO2 value in response to given sprint intervals and the minimal VO2 value in response to given rest periods (VO2 work and VO2 rest, respectively) were recorded. A repeated measures analysis of variance was used to analyze all variables. Average VO2 work was not different among rest interval trials. Average VO2 rest with 12 s rest was greater than 18 s and 24 s (2.16 ± 0.17 L · min(-1), 1.91 ± 0.18 L · min(-1), 1.72 ± 0.15 L · min(-1), respectively), while 18 s was greater than 24 s. Average TW and MP were greater with 24 s rest than 12 s (4,604.44 ± 915.98 J vs. 4,305.46 ± 727.17 J, respectively), with no differences between RSA protocols for PP. No differences in %Dec were observed. Both methods of calculating rates of decline per sprint for PP and TW were greater during 12 s than 18 s or 24 s. Since changes were only noted between the 12 s and 24 s protocols, a 6 s differential in rest intervals may not be enough to elicit alterations in TW, PP, MP, or %Dec in RSA performance. Rate of decline may be a more sensitive measure of fatigue than %Dec.

Identification of the Optimal Protocol for Automated Office Blood Pressure Measurement Among Patients With Treated Hypertension.

PubMed

Moore, Myles N; Schultz, Martin G; Nelson, Mark R; Black, J Andrew; Dwyer, Nathan B; Hoban, Ella; Jose, Matthew D; Kosmala, Wojciech; Przewlocka-Kosmala, Monika; Zachwyc, Jowita; Otahal, Petr; Picone, Dean S; Roberts-Thomson, Philip; Veloudi, Panagiota; Sharman, James E

2018-02-09

Automated office blood pressure (AOBP) involving repeated, unobserved blood pressure (BP) readings during one clinic visit is recommended for in-office diagnosis and assessment of hypertension. However, the optimal AOBP protocol to determine BP control in the least amount of time with the fewest BP readings is yet to be determined and was the aim of this study. One hundred and eighty-nine patients (mean age 62.8 ± 12.1 years; 50.3% female) with treated hypertension referred to specialist clinics at 2 sites underwent AOBP in a quiet room alone. Eight BP measurements were taken starting immediately after sitting and then at 2-minute intervals (15 minutes total). The optimal AOBP protocol was defined by the smallest mean difference and highest intraclass correlation coefficient (ICC) compared with daytime ambulatory BP (ABP). The same BP device (Mobil-o-graph, IEM) was used for both AOBP and daytime ABP. Average 15-minute AOBP and daytime ABP were 134 ± 22/82 ± 13 and 137 ± 17/83 ± 11 mm Hg, respectively. The optimal AOBP protocol was derived within a total duration of 6 minutes from the average of 2 measures started after 2 and 4 minutes of seated rest (systolic BP: mean difference (95% confidence interval) 0.004(-2.21, 2.21) mm Hg, P = 1.0; ICC = 0.81; diastolic BP: mean difference 0.37(-0.90, 1.63) mm Hg, P = 0.57; ICC = 0.86). AOBP measures taken after 8 minutes tended to underestimate daytime ABP (whether as a single BP or the average of more than 1 BP reading). Only 2 AOBP readings taken over 6 minutes (excluding an initial reading immediately after sitting) may be needed to be comparable with daytime ABP. © American Journal of Hypertension, Ltd 2017. All rights reserved. For Permissions, please email: journals.permissions@oup.com

Three-Dimensional Echocardiographic Assessment of Left Heart Chamber Size and Function with Fully Automated Quantification Software in Patients with Atrial Fibrillation.

PubMed

Otani, Kyoko; Nakazono, Akemi; Salgo, Ivan S; Lang, Roberto M; Takeuchi, Masaaki

2016-10-01

Echocardiographic determination of left heart chamber volumetric parameters by using manual tracings during multiple beats is tedious in atrial fibrillation (AF). The aim of this study was to determine the usefulness of fully automated left chamber quantification software with single-beat three-dimensional transthoracic echocardiographic data sets in patients with AF. Single-beat full-volume three-dimensional transthoracic echocardiographic data sets were prospectively acquired during consecutive multiple cardiac beats (≥10 beats) in 88 patients with AF. In protocol 1, left ventricular volumes, left ventricular ejection fraction, and maximal left atrial volume were validated using automated quantification against the manual tracing method in identical beats in 10 patients. In protocol 2, automated quantification-derived averaged values from multiple beats were compared with the corresponding values obtained from the indexed beat in all patients. Excellent correlations of left chamber parameters between automated quantification and the manual method were observed (r = 0.88-0.98) in protocol 1. The time required for the analysis with the automated quantification method (5 min) was significantly less compared with the manual method (27 min) (P < .0001). In protocol 2, there were excellent linear correlations between the averaged left chamber parameters and the corresponding values obtained from the indexed beat (r = 0.94-0.99), and test-retest variability of left chamber parameters was low (3.5%-4.8%). Three-dimensional transthoracic echocardiography with fully automated quantification software is a rapid and reliable way to measure averaged values of left heart chamber parameters during multiple consecutive beats. Thus, it is a potential new approach for left chamber quantification in patients with AF in daily routine practice. Copyright © 2016 American Society of Echocardiography. Published by Elsevier Inc. All rights reserved.

Evaluation of autonomous recording units for detecting 3 species of secretive marsh birds

USGS Publications Warehouse

Sidie-Slettehahl, Anna M.; Jensen, Kent C.; Johnson, Rex R.; Arnold, Todd W.; Austin, Jane; Stafford, Joshua D.

2015-01-01

Population status and habitat use of yellow rails (Coturnicops noveboracensis), Nelson's sparrows (Ammodramus nelsoni), and Le Conte's sparrows (A. leconteii) are poorly known, so standardized surveys of these species are needed to inform conservation planning and management. A protocol for monitoring secretive marsh birds exists; however, these species regularly call at night and may be missed during early morning surveys. We tested the effectiveness of autonomous recording units (hereafter, recording units) to survey these species by analyzing recorded vocalizations using bioacoustics software. We deployed 22 recording units at 54 sites in northern Minnesota and eastern North Dakota, USA, and conducted traditional broadcast surveys during May–June, 2010 and 2011. We compared detection probabilities between recording units and standard monitoring protocols using robust-design occupancy models. On average, recording units detected 0.59 (SE = 0.11) fewer Le Conte's sparrows, 0.76 (SE = 0.15) fewer Nelson's sparrows, and 1.01 (SE = 0.14) fewer yellow rails per survey than were detected using the standard protocol. Detection probabilities using the standard protocol averaged 0.95 (yellow rail; 95% CI = 0.86–0.98), 0.93 (Le Conte's sparrow; 95% CI = 0.78–0.98), and 0.89 (Nelson's sparrow; 95% CI = 0.56–0.98), but averaged 0.71 (yellow rail; 95% CI = 0.56–0.83), 0.61 (Le Conte's sparrow; 95% CI = 0.42–0.78), and 0.51 (Nelson's sparrow; 95% CI = 0.19–0.82) using recording units. Reduced detection by recording units was likely due to the ability of human listeners to identify birds calling at greater distances. Recording units may be effective for surveying nocturnal secretive marsh birds if investigators correct for differential detectability. Reduced detectability may be outweighed by the increased spatial and temporal coverage feasible with recording units.

A pilot-scale steam autoclave system for treating municipal solid waste for recovery of renewable organic content: Operational results and energy usage.

PubMed

Holtman, Kevin M; Bozzi, David V; Franqui-Villanueva, Diana; Offeman, Richard D; Orts, William J

2016-05-01

A pilot-scale (1800 kg per batch capacity) autoclave used in this study reduces municipal solid waste to a debris contaminated pulp product that is efficiently separated into its renewable organic content and non-renewable organic content fractions using a rotary trommel screen. The renewable organic content can be recovered at nearly 90% efficiency and the trommel rejects are also much easier to sort for recovery. This study provides the evaluation of autoclave operation, including mass and energy balances for the purpose of integration into organic diversion systems. Several methods of cooking municipal solid waste were explored from indirect oil heating only, a combination of oil and direct steam during the same cooking cycle, and steam only. Gross energy requirements averaged 1290 kJ kg(-1) material in vessel, including the weight of free water and steam added during heating. On average, steam recovery can recoup 43% of the water added and 30% of the energy, supplying on average 40% of steam requirements for the next cook. Steam recycle from one vessel to the next can reduce gross energy requirements to an average of 790 kJ kg(-1). © The Author(s) 2016.

Evaluation of a single-scan protocol for radiochromic film dosimetry.

PubMed

Shimohigashi, Yoshinobu; Araki, Fujio; Maruyama, Masato; Nakaguchi, Yuji; Kuwahara, Satoshi; Nagasue, Nozomu; Kai, Yudai

2015-03-08

The purpose of this study was to evaluate a single-scan protocol using Gafchromic EBT3 film (EBT3) by comparing it with the commonly used 24-hr measurement protocol for radiochromic film dosimetry. Radiochromic film is generally scanned 24 hr after film exposure (24-hr protocol). The single-scan protocol enables measurement results within a short time using only the verification film, one calibration film, and unirradiated film. The single-scan protocol was scanned 30 min after film irradiation. The EBT3 calibration curves were obtained with the multichannel film dosimetry method. The dose verifications for each protocol were performed with the step pattern, pyramid pattern, and clinical treatment plans for intensity-modulated radiation therapy (IMRT). The absolute dose distributions for each protocol were compared with those calculated by the treatment planning system (TPS) using gamma evaluation at 3% and 3 mm. The dose distribution for the single-scan protocol was within 2% of the 24-hr protocol dose distribution. For the step pattern, the absolute dose discrepancies between the TPS for the single-scan and 24-hr protocols were 2.0 ± 1.8 cGy and 1.4 ± 1.2 cGy at the dose plateau, respectively. The pass rates were 96.0% for the single-scan protocol and 95.9% for the 24-hr protocol. Similarly, the dose discrepancies for the pyramid pattern were 3.6 ± 3.5cGy and 2.9 ± 3.3 cGy, respectively, while the pass rates for the pyramid pattern were 95.3% and 96.4%, respectively. The average pass rates for the four IMRT plans were 96.7% ± 1.8% for the single-scan protocol and 97.3% ± 1.4% for the 24-hr protocol. Thus, the single-scan protocol measurement is useful for dose verification of IMRT, based on its accuracy and efficiency.

Evaluation of a single‐scan protocol for radiochromic film dosimetry

PubMed Central

Araki, Fujio; Maruyama, Masato; Nakaguchi, Yuji; Kuwahara, Satoshi; Nagasue, Nozomu; Kai, Yudai

2015-01-01

The purpose of this study was to evaluate a single‐scan protocol using Gafchromic EBT3 film (EBT3) by comparing it with the commonly used 24‐hr measurement protocol for radiochromic film dosimetry. Radiochromic film is generally scanned 24 hr after film exposure (24‐hr protocol). The single‐scan protocol enables measurement results within a short time using only the verification film, one calibration film, and unirradiated film. The single‐scan protocol was scanned 30 min after film irradiation. The EBT3 calibration curves were obtained with the multichannel film dosimetry method. The dose verifications for each protocol were performed with the step pattern, pyramid pattern, and clinical treatment plans for intensity‐modulated radiation therapy (IMRT). The absolute dose distributions for each protocol were compared with those calculated by the treatment planning system (TPS) using gamma evaluation at 3% and 3 mm. The dose distribution for the single‐scan protocol was within 2% of the 24‐hr protocol dose distribution. For the step pattern, the absolute dose discrepancies between the TPS for the single‐scan and 24‐hr protocols were 2.0±1.8 cGy and 1.4±1.2 cGy at the dose plateau, respectively. The pass rates were 96.0% for the single‐scan protocol and 95.9% for the 24‐hr protocol. Similarly, the dose discrepancies for the pyramid pattern were 3.6±3.5 cGy and 2.9±3.3 cGy, respectively, while the pass rates for the pyramid pattern were 95.3% and 96.4%, respectively. The average pass rates for the four IMRT plans were 96.7%±1.8% for the single‐scan protocol and 97.3%±1.4% for the 24‐hr protocol. Thus, the single‐scan protocol measurement is useful for dose verification of IMRT, based on its accuracy and efficiency. PACS number: 87.55.Qr PMID:26103194

Quality and Variability of Online Physical Therapy Protocols for Isolated Meniscal Repairs.

PubMed

Trofa, David P; Parisien, Robert L; Noticewala, Manish S; Noback, Peter C; Ahmad, Christopher S; Moutzouros, Vasilios; Makhni, Eric C

2018-05-31

The ideal meniscal repair postoperative rehabilitation protocol has yet to be determined. Further, patients are attempting to access health care content online at a precipitously increasing rate given the efficiency of modern search engines. The purpose of this investigation was to assess the quality and variability of meniscal repair rehabilitation protocols published online with the hypothesis that there would be a high degree of variability found across available protocols. To this end, Web-based meniscal repair physical therapy protocols from U.S. academic orthopaedic programs as well as the first 10 protocols identified by the Google search engine for the term "meniscal repair physical therapy protocol" were reviewed and assessed via a custom scoring rubric. Twenty protocols were identified from 155 U.S. academic orthopaedic programs for a total of 30 protocols. Twenty-six protocols (86.6%) recommended immediate postoperative bracing. Twelve (40.0%) protocols permitted immediate weight-bearing as tolerated (WBAT) postoperatively, while the remaining protocols permitted WBAT at an average of 4.0 (range, 1-7) weeks. There was considerable variation in range of motion (ROM) goals, with most protocols (73.3%) initiating immediate passive ROM to 90°. The types and timing of strength, proprioception, agility, and pivoting exercises advised were extremely diverse. Only five protocols (16.7%) employed functional testing as a marker for return to athletics. The results of this study indicate that only a minority of academic orthopaedic programs publish meniscal repair physical therapy protocols online and that within the most readily available online protocols there are significant disparities in regards to brace use, ROM, weight-bearing, and strengthening and proprioception exercises. These discrepancies reflect the fact that the best rehabilitation practices after a meniscal repair have yet to be elucidated. This represents a significant area for improved patient care through standardization. Thieme Medical Publishers 333 Seventh Avenue, New York, NY 10001, USA.

Frequency and Type of Prosthetic Complications Associated with Interim, Immediately Loaded Full-Arch Prostheses: A 2-Year Retrospective Chart Review.

PubMed

Drago, Carl

2016-08-01

The purpose of this report was to retrospectively evaluate implant and immediate full-arch prosthesis survival rates over a 24-month period; patients were consecutively treated with immediate occlusal loading. Dental arch, gender, and implant orientation (vertical vs. tilted) were also noted. All Brånemark System implants (Nobel Active) and interim, all-acrylic resin prostheses placed in patients following an All-on-Four™ protocol, in a single private practice were assessed by retrospective patient chart review. The amount of space provided surgically for implant restorative components and prostheses was determined from measurements of the vertical heights of the interim prostheses in the right/left anterior and posterior segments. These measurements were made in the laboratory. Interim prosthetic repairs (type, frequency, length of time from insertion) were analyzed by type, arch, gender, and implant orientation. Implant survival and insertion torque values were also measured. Inclusion criteria consisted of all Brånemark System implants placed with the All-on-Four protocol from September 1, 2011, until August 31, 2013. Specific dietary instructions were given for the first 7 days immediately postoperatively and for the weeks prior to insertion of the definitive prostheses. One hundred twenty-nine patients, comprising 191 arches (766 implants) from September 1, 2011, until August 31, 2013, were included in the study. One patient experienced implant failure yielding an overall implant survival rate (SR) of 99.5% (762 of 766). Four hundred twenty-six of 430 maxillary implants and 336 of 336 mandibular implants survived for SRs of 99.1% and 100%, respectively. Regarding implant orientation, 415 of 417 tilted implants (SR 99.5%) and 343 of 345 (CSR 95.6%) vertical implants were noted to be clinically stable. Interim, all-acrylic resin prostheses were in place for a mean of 199.2 days; mandibular prostheses were in place for an average of 195.4 days; maxillary prostheses were in place for an average of 202.0 days. Thirty four of the 191 interim prostheses (17.8%) warranted at least one repair during the treatment period. The average overall implant insertion torque value was 60.74 Ncm; mandibular torque values averaged 63.08 Ncm; maxillary torque values averaged 59.00 Ncm. The results from this study suggest that dental arch, gender, and implant orientation for implants placed and immediately restored with interim, all-acrylic resin, full-arch prostheses per the All-on-Four protocol did not have significant statistical or clinical effects on prosthetic complications of the interim prostheses or implant survival. Only one of the 129 patients experienced implant failures, indicating that the All-on-Four treatment protocol used in this study is a viable alternative to other protocols for rehabilitating edentulous patients. © 2015 by the American College of Prosthodontists.

Global warming potential of material fractions occurring in source-separated organic household waste treated by anaerobic digestion or incineration under different framework conditions.

PubMed

Naroznova, Irina; Møller, Jacob; Scheutz, Charlotte

2016-12-01

This study compared the environmental profiles of anaerobic digestion (AD) and incineration, in relation to global warming potential (GWP), for treating individual material fractions that may occur in source-separated organic household waste (SSOHW). Different framework conditions representative for the European Union member countries were considered. For AD, biogas utilisation with a biogas engine was considered and two potential situations investigated - biogas combustion with (1) combined heat and power production (CHP) and (2) electricity production only. For incineration, four technology options currently available in Europe were covered: (1) an average incinerator with CHP production, (2) an average incinerator with mainly electricity production, (3) an average incinerator with mainly heat production and (4) a state-of-the art incinerator with CHP working at high energy recovery efficiencies. The study was performed using a life cycle assessment in its consequential approach. Furthermore, the role of waste-sorting guidelines (defined by the material fractions allowed for SSOHW) in relation to GWP of treating overall SSOHW with AD was investigated. A case-study of treating 1tonne of SSOHW under framework conditions in Denmark was conducted. Under the given assumptions, vegetable food waste was the only material fraction which was always better for AD compared to incineration. For animal food waste, kitchen tissue, vegetation waste and dirty paper, AD utilisation was better unless it was compared to a highly efficient incinerator. Material fractions such as moulded fibres and dirty cardboard were attractive for AD, albeit only when AD with CHP and incineration with mainly heat production were compared. Animal straw, in contrast, was always better to incinerate. Considering the total amounts of individual material fractions in waste generated within households in Denmark, food waste (both animal and vegetable derived) and kitchen tissue are the main material fractions allowing GWP mitigation with AD when it is compared to incineration. The inclusion of other material fractions in SSOHW sorting guidelines may be considered of less importance. Copyright © 2016 Elsevier Ltd. All rights reserved.