bluuebunny/crossref_metadata_2025_split huggingface dataset:
Offshore Transport of Dense Water from the East Greenland Shelf
Authors: Harden B. E. , Pickart R. S. , Renfrew I. A. 
Published: September 2013

Abstract
Data from a mooring deployed at the edge of the East Greenland shelf south of Denmark Strait from September 2007 to October 2008 are analyzed to investigate the processes by which dense water is transferred off the shelf. It is found that water denser than 27.7 kg m−3—as dense as water previously attributed to the adjacent East Greenland Spill Jet—resides near the bottom of the shelf for most of the year with no discernible seasonality. The mean velocity in the central part of the water column is directed along the isobaths, while the deep flow is bottom intensified and veers offshore. Two mechanisms for driving dense spilling events are investigated, one due to offshore forcing and the other associated with wind forcing. Denmark Strait cyclones propagating southward along the continental slope are shown to drive off-shelf flow at their leading edges and are responsible for much of the triggering of individual spilling events. Northerly barrier winds also force spilling. Local winds generate an Ekman downwelling cell. Nonlocal winds also excite spilling, which is hypothesized to be the result of southward-propagating coastally trapped waves, although definitive confirmation is still required. The combined effect of the eddies and barrier winds results in the strongest spilling events, while in the absence of winds a train of eddies causes enhanced spilling.
The Impact of Posture on Wrist Tendinosis Among Blue-Collar Workers
Authors: Harris-Adamson Carisa , You Doohee , Eisen Ellen A. , Goldberg Robert , Rempel David 
Published: September 2013

Objective: The objective was to evaluate the effect of wrist posture on incidence of wrist tendinosis in a prospective cohort of blue-collar workers. Background: Previous studies have identified awkward wrist posture as a risk factor for wrist tendinosis, though the magnitude of the relationship is unclear. Method: Workers ( N = 413) at four industries were followed for up to 28 months with questionnaires and physical examinations every 4 months. Individualized exposure assessments of wrist posture were based on video analysis to determine the wrist extension/flexion angle for up to four tasks. Posture measures were calculated while in “heavy pinch” (> 1 kg force), “heavy power grip” (> 4 kg force), and across “all grips.” A proportional hazards model estimated the relationship between time-weighted average posture measures and incidence of dominant-side wrist tendinosis. Results: In a model based on tertiles of exposure, adjusted for age, gender, hand force, and repetition of exertions, risk of tendinosis more than doubled in the highest category (HR = 2.69, 95% CI = 1.01–7.21) across all grips. The relative risk was highest during heavy pinch (HR = 5.03, 95% CI = 0.74–34.05), though not statistically significant. Increased median wrist extension while in heavy power grip was protective (HR = 0.24, 95% CI = 0.06–0.94). Conclusion: In this study of production workers, median wrist flexion of more than 7°, across all grips, was associated with an increased risk of tendinosis. The protective findings on median wrist extension during power grip deserve further investigation. Work tasks and tools should be designed to prevent sustained wrist flexion, especially during tasks involving forceful pinch.
Neoplastic and Nonneoplastic Lesions in Aging Mice of Unique and Common Inbred Strains Contribution to Modeling of Human Neoplastic Diseases
Authors: Szymanska H. , Lechowska-Piskorowska J. , Krysiak E. , Strzalkowska A. , Unrug-Bielawska K. , Grygalewicz B. , Skurzak H. M. , Pienkowska-Grela B. , Gajewska M. 
Published: September 2013

The evaluation of spontaneous lesions in classical inbred strains of mice has become increasingly important because genetically engineered mice (GEMs) are created on these backgrounds. Novel inbred strains—genetically diverse from classic strains—are valuable both as a new background for GEM mice and to increase the genetic variation found in laboratory mice. Newly arising spontaneous genetic alterations in commonly used strains may also lead to new and valuable mouse models of disease. This report evaluates gross and histological lesions in relatively new, classic, and rarely explored mouse inbred strains. Pathological lesions of 1273 mice from 12 inbred strains (129S1/SvW, A.CA- H2f/W, AKR/W, BALB/cW, BN/aW, C57BL/6 W, C57BL/10 W, C3H/W, C3H wad/W, CBA/W, DBA/2 W, and WOM/W) are reported. BN/aW, WOM/W, and C3H wad/W are novel inbred strains produced and maintained in the Department of Genetics and Laboratory Animal Breeding at the Center of Oncology, Warsaw, Poland. Both neoplastic and nonneoplastic lesions were examined. The prevalence of lung neoplasms was significantly higher in A.CA- H2f/W (33.3%) and BALB/cW (33.8%) mice ( P < .01). The prevalence of liver neoplasms was significantly higher in the CBA/W strain ( P < .01). Mammary gland neoplasms arose at a greater frequency in C3H/W mice ( P < .01). The occurrence of uterine neoplasms was higher in DBA/W and 129S1/SvW mice. AKR/W and WOM/W mice developed T-cell lymphoblastic lymphoma with high frequency (110/121 [90.9%] and 159/175 [90.9%], respectively) before 1 year of age. The occurrence of nonneoplastic lesions in the kidneys of BN/aW mice was increased ( P < .01).
Biomechanical Comparison of Syndesmotic Injury Fixation Methods Using a Cadaveric Model
Authors: Ebramzadeh Edward , Knutsen Ashleen R. , Sangiorgio Sophia N. , Brambila Maximino , Harris Thomas G. 
Published: September 2013

Background: There is growing interest in suture-button devices for syndesmosis injury, which are intended to offer less rigid fixation than screw fixation. Methods: The fixation strength with 2 different suture-button devices, ZipTight and TightRope, were compared using 5 cadaveric leg pairs (n = 10). In an additional 5 pairs (n = 10), ZipTight was compared to 3.5 mm quadricortical screw fixation. Ankle motion was measured intact, then following simulated syndesmosis injury and fixation. Cyclic loads (peak 750 N, 7.5 Nm) were applied. Finally, external rotation to failure was measured and failure mode was documented. Results: Range of motion increased after simulated injury and fixation with all devices (max 14.5 degrees). In all groups, diastasis remained below 1.0 mm intact and below 2.0 mm during cyclic loading. Compared to intact, under load to failure, diastasis with ZipTight devices increased by 4.7 ± 1.3 mm and 7.6 ± 4.3 mm, with TightRope, 6.3 mm, and screw construct, 1.3 mm. ZipTight specimens rotated approximately 80 ± 22 degrees before failure, TightRope, 67 ± 13 degrees, screw constructs, 76 ± 27 degrees. Mean failure torque was between 22.2 ± 6.9 Nm and 28.1 ± 12.7 Nm for ZipTight, compared to 32.9 ± 8.0 Nm for TightRope ( P = .07), and 30.1 ± 9.6 Nm for screw constructs ( P = .03). The majority of suture-button constructs failed by fibular fracture (ZipTight = 6, TightRope = 4), the remaining by device pull-through (ZipTight = 3, TightRope = 1) and loosening (ZipTight = 1). Conversely, 3 of screw-fixed specimens failed by device failure, 2 from bone fracture. Conclusion: Suture-button devices provided torsional strength below that of screw fixation. However, all devices may provide failure torques well above 20 Nm, exceeding likely torques applied in casts during healing.1,2,4 Clinical Relevance: Suture-button devices appear to have provided adequate fixation strength for syndesmosis injuries.
Comparing long-term results of PASAT and SDMT scores in relation to neuropsychological testing in multiple sclerosis
Authors: Sonder Judith M , Burggraaff Jessica , Knol Dirk L , Polman Chris H , Uitdehaag Bernard MJ 
Published: September 2013

Background and objectives: The Symbol Digit Modalities Test (SDMT) shows advantages over the Paced Auditory Serial Addition Test (PASAT) as a cognitive test in patients with multiple sclerosis (MS). To determine which of these tests is most valid and reliable over time as an indicator of the cognitive state of MS patients, long-term test results of both tests were compared in relation to scores of the Brief Repeatable Battery of Neuropsychological tests (BRBN). Methods: For 485 MS patients visiting the VU University Medical Center Amsterdam for different research projects, a total number of 1078 visits with BRBN (including PASAT and SDMT) was planned. Observed and model-based correlations were used to calculate the construct validity of the SDMT and PASAT 3 seconds test (PASAT3) by comparing correlations with the BRBN-sumscore. The test-retest reliability of each test was also computed. Results: For the construct validity, higher correlations were found between SDMT and BRBN compared to PASAT3 and BRBN, especially for the model-based correlations at baseline. The reliability of the measurements was good for all instruments, with the highest coefficients for the SDMT. Conclusion: As a single assessment tool for cognition in MS, the SDMT is more valid and reliable compared to PASAT3.
Black social work students’ experiences of practice learning: Understanding differential progression rates
Authors: Fairtlough Anna , Bernard Claudia , Fletcher Joan , Ahmet Akile 
Published: September 2013

Summary As a group, Black and ethnic minority students progress more slowly on their social work programmes in England than their white counterparts. The article reports on a qualitative study with social work students and key informants in a purposive sample of eight social work programmes. Findings Factors relating to the characteristics of individual students, the social work programme, the HEI and practice learning environments appeared to be affecting student experience and progression. The article focuses on practice learning. Many student participants reported experiences of disadvantaged educational backgrounds, economic pressures and caring responsibilities. Key informants in some sites described particular challenges faced by these students. Students reported experiences of racism in placements where the majority of staff or service users were white. Application Concepts drawn from work by Pierre Bourdieu such as ‘habitus’, ‘field’ and ‘social and cultural capital’ are used to make sense of these findings. Some practical ways in which social work programmes might seek to counter educational disparities and racism faced by black and ethnic minority students are suggested: these include monitoring systems, training for practice educators and tutors, support for black and ethnic minority students and agreements between HEIs and placement providers.
Exposure to UV radiation and risk of Hodgkin lymphoma: a pooled analysis
Authors: Monnereau Alain , Glaser Sally L. , Schupp Clayton W. , Ekström Smedby Karin , de Sanjosé Silvia , Kane Eleanor , Melbye Mads , Forétova Lenka , Maynadié Marc , Staines Anthony , Becker Nikolaus , Nieters Alexandra , Brennan Paul , Boffetta Paolo , Cocco Pierluigi , Glimelius Ingrid , Clavel Jacqueline , Hjalgrim Henrik , Chang Ellen T. 
Published: September 2013

Key PointsOur pooled analysis found an inverse association between several measures of UVR exposure and Hodgkin lymphoma. Significant UVR-related inverse associations of EBV-positive HL with a dose-response relationship support etiologic heterogeneity in HL.
On the improvement of Mocanu’s conditions
Authors: Nunokawa M , Owa S , Cho NE , Sokół J , Yavuz Duman E 
Published: September 2013

Abstract
We estimate

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under several assumptions. By using Nunokawa’s lemma, we improve a few of Mocanu’s results obtained by differential subordinations. Some applications for strongly starlikeness and convexity are formulated.

MSC:30C45, 30C80.
Human adipose-derived stem cells cultured in keratinocyte serum free medium: Donor’s age does not affect the proliferation and differentiation capacities
Authors: Ding Dah-Ching , Chou Hsiang-Lan , Hung Wei-Ting , Liu Hwan-Wun , Chu Tang-Yuan 
Published: September 2013

Abstract

Background
Although donor age-related effects of characteristics of mesenchymal stem cells (MSC), such as a decrease in the proliferation and differentiation capacity and an increase of senescence and apoptosis, are evident, such effects are generally less prominent in adipose-derived stem cells (ASC). Using a hormone and growth factor rich medium (KFSM), this study cultured ASC from abdominal subcutaneous fat of 27 adult females in three age groups: 30-39 y, 40-49 y and 50-60 y, and investigated the growth and differentiation characteristics.

Results
The derived ASC had an immunophenotype similar to that of bone marrow derived MSC (BMSC). They could be stably expanded with an average population doubling time of 21.5 ± 2.3 h. Other than a higher pre-adipogenic commitment and a lower adipogenic differentiation capability in ASC derived from the old age group, other characteristics including proliferation rate, doubling time, telomere length, as well as the osteogenic and chondrogenic differentiation capacity were the same regardless of the donor’s age.

Conclusions
The study demonstrates a promising proliferation and differentiation capabilities of ASC regardless of the donor’s age. The compromised adipogenic potential in the older donors could be a benefit for their application in regeneration therapy.
Dengue virus infection induces autophagy: an in vivo study
Authors: Lee Ying-Ray , Hu Hsuan-Yun , Kuo Szu-Han , Lei Huan-Yao , Lin Yee-Shin , Yeh Trai-Ming , Liu Ching-Chuan , Liu Hsiao-Sheng 
Published: September 2013

Abstract

Background
We and others have reported that autophagy is induced by dengue viruses (DVs) in various cell lines, and that it plays a supportive role in DV replication. This study intended to clarify whether DV infection could induce autophagy in vivo. Furthermore, the effect of DV induced autophagy on viral replication and DV-related pathogenesis was investigated.

Results and conclusions
The physiopathological parameters were evaluated after DV2 was intracranially injected into 6-day-old ICR suckling mice. Autophagy-related markers were monitored by immunohistochemical/immunofluorescent staining and Western blotting. Double-membrane autophagic vesicles were investigated by transmission-electron-microscopy. DV non-structural-protein-1 (NS1) expression (indicating DV infection) was detected in the cerebrum, medulla and midbrain of the infected mice. In these infected tissues, increased LC3 puncta formation, LC3-II expression, double-membrane autophagosome-like vesicles (autophagosome), amphisome, and decreased p62 accumulation were observed, indicating that DV2 induces the autophagic progression in vivo. Amphisome formation was demonstrated by colocalization of DV2-NS1 protein or LC3 puncta and mannose-6-phosphate receptor (MPR, endosome marker) in DV2-infected brain tissues. We further manipulated DV-induced autophagy by the inducer rapamycin and the inhibitor 3-methyladenine (3MA), which accordingly promoted or suppressed the disease symptoms and virus load in the brain of the infected mice.
We demonstrated that DV2 infection of the suckling mice induces autophagy, which plays a promoting role in DV replication and pathogenesis.
Maximum-parsimony haplotype frequencies inference based on a joint constrained sparse representation of pooled DNA
Authors: Jajamovich Guido H , Iliadis Alexandros , Anastassiou Dimitris , Wang Xiaodong 
Published: September 2013

Abstract

Background
DNA pooling constitutes a cost effective alternative in genome wide association studies. In DNA pooling, equimolar amounts of DNA from different individuals are mixed into one sample and the frequency of each allele in each position is observed in a single genotype experiment. The identification of haplotype frequencies from pooled data in addition to single locus analysis is of separate interest within these studies as haplotypes could increase statistical power and provide additional insight.

Results
We developed a method for maximum-parsimony haplotype frequency estimation from pooled DNA data based on the sparse representation of the DNA pools in a dictionary of haplotypes. Extensions to scenarios where data is noisy or even missing are also presented. The resulting method is first applied to simulated data based on the haplotypes and their associated frequencies of the AGT gene. We further evaluate our methodology on datasets consisting of SNPs from the first 7Mb of the HapMap CEU population. Noise and missing data were further introduced in the datasets in order to test the extensions of the proposed method. Both HIPPO and HAPLOPOOL were also applied to these datasets to compare performances.

Conclusions
We evaluate our methodology on scenarios where pooling is more efficient relative to individual genotyping; that is, in datasets that contain pools with a small number of individuals. We show that in such scenarios our methodology outperforms state-of-the-art methods such as HIPPO and HAPLOPOOL.
L_RNA_scaffolder: scaffolding genomes with transcripts
Authors: Xue Wei , Li Jiong-Tang , Zhu Ya-Ping , Hou Guang-Yuan , Kong Xiang-Fei , Kuang You-Yi , Sun Xiao-Wen 
Published: September 2013

Abstract

Background
Generation of large mate-pair libraries is necessary for de novo genome assembly but the procedure is complex and time-consuming. Furthermore, in some complex genomes, it is hard to increase the N50 length even with large mate-pair libraries, which leads to low transcript coverage. Thus, it is necessary to develop other simple scaffolding approaches, to at least solve the elongation of transcribed fragments.

Results
We describe L_RNA_scaffolder, a novel genome scaffolding method that uses long transcriptome reads to order, orient and combine genomic fragments into larger sequences. To demonstrate the accuracy of the method, the zebrafish genome was scaffolded. With expanded human transcriptome data, the N50 of human genome was doubled and L_RNA_scaffolder out-performed most scaffolding results by existing scaffolders which employ mate-pair libraries. In these two examples, the transcript coverage was almost complete, especially for long transcripts. We applied L_RNA_scaffolder to the highly polymorphic pearl oyster draft genome and the gene model length significantly increased.

Conclusions
The simplicity and high-throughput of RNA-seq data makes this approach suitable for genome scaffolding. L_RNA_scaffolder is available at http://www.fishbrowser.org/software/L_RNA_scaffolder.
Predicting whole genome protein interaction networks from primary sequence data in model and non-model organisms using ENTS
Authors: Rodgers-Melnick Eli , Culp Mark , DiFazio Stephen P 
Published: September 2013

Abstract

Background
The large-scale identification of physical protein-protein interactions (PPIs) is an important step toward understanding how biological networks evolve and generate emergent phenotypes. However, experimental identification of PPIs is a laborious and error-prone process, and current methods of PPI prediction tend to be highly conservative or require large amounts of functional data that may not be available for newly-sequenced organisms.

Results
In this study we demonstrate a random-forest based technique, ENTS, for the computational prediction of protein-protein interactions based only on primary sequence data. Our approach is able to efficiently predict interactions on a whole-genome scale for any eukaryotic organism, using pairwise combinations of conserved domains and predicted subcellular localization of proteins as input features. We present the first predicted interactome for the forest tree Populus trichocarpa in addition to the predicted interactomes for Saccharomyces cerevisiae, Homo sapiens, Mus musculus, and Arabidopsis thaliana. Comparing our approach to other PPI predictors, we find that ENTS performs comparably to or better than a number of existing approaches, including several that utilize a variety of functional information for their predictions. We also find that the predicted interactions are biologically meaningful, as indicated by similarity in functional annotations and enrichment of co-expressed genes in public microarray datasets. Furthermore, we demonstrate some of the biological insights that can be gained from these predicted interaction networks. We show that the predicted interactions yield informative groupings of P. trichocarpa metabolic pathways, literature-supported associations among human disease states, and theory-supported insight into the evolutionary dynamics of duplicated genes in paleopolyploid plants.

Conclusion
We conclude that the ENTS classifier will be a valuable tool for the de novo annotation of genome sequences, providing initial clues about regulatory and metabolic network topology, and revealing relationships that are not immediately obvious from traditional homology-based annotations.
The St. Louis African American health-heart study: methodology for the study of cardiovascular disease and depression in young-old African Americans
Authors: Bruchas Robin R , de las Fuentes Lisa , Carney Robert M , Reagan Joann L , Bernal-Mizrachi Carlos , Riek Amy E , Gu Chi Charles , Bierhals Andrew , Schootman Mario , Malmstrom Theodore K , Burroughs Thomas E , Stein Phyllis K , Miller Douglas K , Dávila-Román Victor G 
Published: September 2013

Abstract

Background
Coronary artery disease (CAD) is a major cause of death and disability worldwide. Depression has complex bidirectional adverse associations with CAD, although the mechanisms mediating these relationships remain unclear. Compared to European Americans, African Americans (AAs) have higher rates of morbidity and mortality from CAD. Although depression is common in AAs, its role in the development and features of CAD in this group has not been well examined. This project hypothesizes that the relationships between depression and CAD can be explained by common physiological pathways and gene-environment interactions. Thus, the primary aims of this ongoing project are to: a) determine the prevalence of CAD and depression phenotypes in a population-based sample of community-dwelling older AAs; b) examine the relationships between CAD and depression phenotypes in this population; and c) evaluate genetic variants from serotoninP and inflammatory pathways to discover potential gene-depression interactions that contribute significantly to the presence of CAD in AAs.

Methods/design
The St. Louis African American Health (AAH) cohort is a population-based panel study of community-dwelling AAs born in 1936–1950 (inclusive) who have been followed from 2000/2001 through 2010. The AAH-Heart study group is a subset of AAH participants recruited in 2009–11 to examine the inter-relationships between depression and CAD in this population. State-of-the-art CAD phenotyping is based on cardiovascular characterizations (coronary artery calcium, carotid intima-media thickness, cardiac structure and function, and autonomic function). Depression phenotyping is based on standardized questionnaires and detailed interviews. Single nucleotide polymorphisms of selected genes in inflammatory and serotonin-signaling pathways are being examined to provide information for investigating potential gene-depression interactions as modifiers of CAD traits. Information from the parent AAH study is being used to provide population-based prevalence estimates. Inflammatory and other biomarkers provide information about potential pathways.

Discussion
This population-based investigation will provide valuable information on the prevalence of both depression and CAD phenotypes in this population. The study will examine interactions between depression and genetic variants as modulators of CAD, with the intent of detecting mechanistic pathways linking these diseases to identify potential therapeutic targets. Analytic results will be reported as they become available.