bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effects of Vacuum-Assisted Socket Suspension on Energetic Costs of Walking, Functional Mobility, and Prosthesis-Related Quality of Life
Authors: Rosenblatt Noah J. , Ehrhardt Tess , Fergus Rachel , Bauer Angela , Caldwell Ryan 
Published: February 2017

ABSTRACT

Introduction
Proper suspension is critical to maintaining socket comfort and fit. Vacuum-assisted socket suspension (VASS) improves fit and comfort by reducing peak socket pressure and pistoning of the residual limb. The purpose of this study was to quantify the effects of VASS on metabolic costs of gait and performance-based outcomes by evaluating changes in these measures immediately after altering suspension and to compare self-reported outcome measures between groups of VASS and non-VASS users.

Materials and Methods
Eighteen current VASS users and 18 non-VASS users, all of whom were active community ambulators, participated in two related studies. For study 1, VASS users completed three tasks in the following order: 1) a quantitative gait analysis, 2) function and mobility tests (10-m walk test [10MWT] and timed up and go [TUG]); and 3) 6 minutes of walking at self-selected speed (SSS) to determine energetic costs of walking and socket comfort. Participants performed each task under three suspension conditions, in random order, before proceeding to the next task. The conditions were altering VASS by inactivating the vacuum and blocking the one-way valve. Participants completed tasks immediately after alterations in suspension; that is, we provided no specific accommodation period. All tasks in study 1 were completed during a single testing session. For study 2, both VASS and non-VASS subjects completed electronic versions of surveys to assess prosthetic use and locomotor function including sections of the Prosthetic Evaluation Questionnaire.

Results
Study 1: There was no effect of suspension on cost of transport (p = 0.47 for main effect of suspension). However, participants performed TUG in shorter time using VASS and suction (p = 0.02 VASS vs. sleeve; p = 0.049 suction vs. sleeve; p = 0.54 VASS vs. suction) and performed the 10MWT with greater speed while using VASS compared with both suction (p = 0.027) and sleeve (p = 0.011). The use of VASS resulted in a significant within-subject increase of 1.5 and 3 points in socket comfort compared to suction (p = 0.001) and sleeve (p = 0.001), respectively. Study 2: There were no significant differences in any self-reported outcomes measures between VASS and non-VASS users.

Conclusions
In absence of active vacuum, current users of VASS experience an immediate reduction in comfort, presumably reflecting worse fit, which may limit their ability to attain faster walking speeds but which does not have an immediate negative affect on the cost of transport. The self-reported measures used to quantify the effects of suspension on prosthetic use, locomotor capabilities, and domains reflecting prosthesis-related quality of life may have been ill-suited for identifying difference in the high-functioning heterogeneous population considered.
Adolescent transition clinic in inflammatory bowel disease: quantitative assessment of self-efficacy skills
Authors: Yerushalmy-Feler Anat , Ron Yulia , Barnea Efrat , Nachum Ayala , Matalon Shay , Dali-levy Margalit , Dotan Iris , Cohen Shlomi 
Published: February 2017

Objectives
There is no model for the process of transition of adolescents with inflammatory bowel diseases (IBD) to the adult care protocol. We recently established a transition clinic where 17-year-old to 18-year-old IBD patients are seen by a multidisciplinary team including pediatric and adult gastroenterologists with expertise in IBD treatments, an IBD nurse, and a psychologist. We quantitatively describe this model and its benefits, and correlate demographic and transition parameters to self-efficacy in IBD adolescent patients before and after transition.

Patients and methods
All adolescent IBD patients enrolled in our transition clinic between January 2013 and December 2015 were included. They completed a self-efficacy questionnaire (‘IBD-yourself’) before and after the transition. The scores were correlated to demographic, disease, and transition parameters.

Results
Thirty of the 36 enrolled patients (mean age: 19±1.8 years, range: 17–27) had Crohn’s disease. Twenty-seven patients completed the transition protocol, which included an average of 3–4 meetings (range: 2–8) over 6.9±3.5 months. Self-efficacy scores in all domains of the questionnaire were significantly higher after completion of the transition. The weighted average score of the questionnaire’s domains was 1.85±0.3 before and 1.41±0.21 after transition (P<0.0001). Age, sex, disease duration, duration of transition, and the number of meetings in the clinic correlated with the questionnaire’s scores in the domains of coping with IBD, knowledge of the transition process, and medication use.

Conclusion
A well-planned adolescent IBD transition clinic contributes significantly toward improved self-efficacy in IBD. We recommend its implementation in IBD centers to enable a personalized transition program tailored to the needs of adolescents with IBD in specific domains.
Spherical Soft Contact Lens Designs and Peripheral Defocus in Myopic Eyes
Authors: Moore Kelly E. , Benoit Julia S. , Berntsen David A. 
Published: February 2017

ABSTRACT

Purpose
Peripheral retinal defocus has been implicated in myopia progression. The effect of commercially available spherical soft contact lenses (SCLs) on peripheral defocus of adult myopic eyes was investigated.

Methods
Twenty-five young adults with spherical equivalent (SE) refractions between −0.50D and −6.00D were enrolled. Cycloplegic autorefraction (right eye) was measured centrally and ±20°, ±30°, and ±40° from the line of sight along the horizontal meridian using an autorefractor. Four commercially available spherical SCLs (Biofinity, Acuvue2, PureVision2, and Air Optix Night & Day Aqua) were evaluated. SE defocus (M) was used to calculate relative peripheral defocus (RPD) while wearing each SCL and relative peripheral refraction of the uncorrected eye. Spherical aberration (SA) changes caused by each SCL were measured along the line of sight by aberrometry. Peripheral defocus was analyzed using repeated-measures analyses of variance (RM-ANOVA). The association between changes in axial SA and the change in peripheral defocus was evaluated using linear mixed models.

Results
The mean age (±SD) and central SE refractive error were 24.0 ± 1.3 years and −3.45 ± 1.42D, respectively. PureVision2 did not change RPD (P = .33). Significant myopic shifts on the temporal retina were found with three lenses: Acuvue 2 (−0.29D at 30°; −0.80D at 40°; both P ≤ .01), Biofinity (−1.21 D at 40°; P = .02), and Air Optix Night & Day Aqua (−0.23D at 20°, −0.48D at 30°, and −1.50D at 40°; all P < .004). All SCLs caused a negative change in SA. SCLs inducing less negative (more positive) SA changes were associated with a less hyperopic change in RPD.

Conclusions
Spherical SCL design can influence the peripheral defocus profile experienced by a myopic eye. Several, but not all, SCLs reduced peripheral hyperopia. Differences in how SCL types influence peripheral defocus may have implications for myopia progression.
The Continuum of HIV Care in Rural Communities in the United States and Canada: What Is Known and Future Research Directions
Authors: Schafer Katherine R. , Albrecht Helmut , Dillingham Rebecca , Hogg Robert S. , Jaworsky Denise , Kasper Ken , Loutfy Mona , MacKenzie Lauren J. , McManus Kathleen A. , Oursler Kris Ann K. , Rhodes Scott D. , Samji Hasina , Skinner Stuart , Sun Christina J. , Weissman Sharon , Ohl Michael E. ,   on behalf of the North American Rural HIV Working Group
Published: February 2017

Abstract:
The nature of the HIV epidemic in the United States and Canada has changed with a shift toward rural areas. Socioeconomic factors, geography, cultural context, and evolving epidemics of injection drug use are coalescing to move the epidemic into locations where populations are dispersed and health care resources are limited. Rural–urban differences along the care continuum demonstrate the implications of this sociogeographic shift. Greater attention is needed to build a more comprehensive understanding of the rural HIV epidemic in the United States and Canada, including research efforts, innovative approaches to care delivery, and greater community engagement in prevention and care.
Two Cases of Oral Somatic Delusions Ameliorated With Brain Perfusion Asymmetry: A Case Report
Authors: Umezaki Yojiro , Uezato Akihito , Toriihara Akira , Nishikawa Toru , Toyofuku Akira 
Published: February 2017

Background
Oral cenesthopathy is the complaint of abnormal oral sensation where no underlying organic cause can be identified. It is also called oral dysesthesia or oral somatic delusion and classified as delusional disorder, somatic type. The patients with oral cenesthopathy show right > left asymmetric regional cerebral blood flow (rCBF) in the broad brain region. However, the studies scrutinizing the rCBF change before and after the successful treatment are still a few so far.

Case
We present 2 cases of oral cenesthopathy, who responded well to aripiprazole. The asymmetric rCBF patterns were attenuated after successful treatment in both cases.

Conclusions
We found a marked improvement of oral cenesthopathy with aripiprazole. It is suggested that right > left rCBF asymmetry in the frontal and temporal lobes and thalamus, and the dopaminergic and serotonergic dysfunctions are involved in the pathology of oral cenesthopathy.
François Jacob. 17 June 1920 — 19 April 2013
Authors: Morange Michel 
Published: February 2017

Biological research was a late vocation for François Jacob, who entered the laboratory of André Lwoff at the Institut Pasteur in Paris at the age of 30. Ten years before, in 1940, he had abruptly left France, after the German troops entered Paris, and joined the Free French Forces organized by de Gaulle in London. He served as a medic in battles against the German troops in Africa, and was severely wounded in Normandy in August 1944. He could no longer be a surgeon as he had expected, and his return to a civilian life was difficult.
Fifteen years after he entered the Institut Pasteur, in 1965, he received the Nobel Prize in Physiology or Medicine, together with André Lwoff and Jacques Monod, for the discovery of the mechanisms controlling gene expression in bacteria, the operon model. The impact of this discovery was immense and triggered the conversion of molecular biologists to the study of higher organisms and their development. Jacob decided to work on mice, and his characterization of embryonal carcinoma cells and of their differentiation foreshadowed recent studies on embryonic stem cells. His comparison between evolution and the work of a tinkerer was also highly influential.
Jacob wrote many books on the history and philosophy of the biological sciences. He was convinced that reflection on these issues was necessary for researchers to defend the value of scientific knowledge. He also continuously fought for an ethical use of scientific knowledge.
Single-cell epigenomics maps the continuous regulatory landscape of human hematopoietic differentiation
Authors: Buenrostro Jason D , Corces M Ryan , Wu Beijing , Schep Alicia N , Lareau Caleb A , Majeti Ravindra , Chang Howard Y. , Greenleaf William J. 
Published: February 2017

AbstractNormal human hematopoiesis involves cellular differentiation of multipotent cells into progressively more lineage-restricted states. While epigenomic landscapes of this process have been explored in immunophenotypically-defined populations, the single-cell regulatory variation that defines hematopoietic differentiation has been hidden by ensemble averaging. We generated single-cell chromatin accessibility landscapes across 8 populations of immunophenotypically-defined human hematopoietic cell types. Using bulk chromatin accessibility profiles to scaffold our single-cell data analysis, we constructed an epigenomic landscape of human hematopoiesis and characterized epigenomic heterogeneity within phenotypically sorted populations to find epigenomic lineage-bias toward different developmental branches in multipotent stem cell states. We identify and isolate sub-populations within classically-defined granulocyte-macrophage progenitors (GMPs) and use ATAC-seq and RNA-seq to confirm that GMPs are epigenomically and transcriptomically heterogeneous. Furthermore, we identified transcription factors andcis-regulatory elements linked to changes in chromatin accessibility within cellular populations and across a continuous myeloid developmental trajectory, and observe relatively simple TF motif dynamics give rise to a broad diversity of accessibility dynamics at cis-regulatory elements. Overall, this work provides a template for exploration of complex regulatory dynamics in primary human tissues at the ultimate level of granular specificity – the single cell.One Sentence SummarySingle cell chromatin accessibility reveals a high-resolution, continuous landscape of regulatory variation in human hematopoiesis.
Learning multiple variable-speed sequences in striatum via cortical tutoring
Authors: Murray James M. , Sean Escola G. 
Published: February 2017

AbstractSparse, sequential patterns of neural activity have been observed in numerous brain areas during time-keeping and motor sequence tasks. Inspired by such observations, we construct a model of the striatum, an all-inhibitory circuit where sequential activity patterns are prominent, addressing the following key challenges: (i) obtaining control over temporal rescaling of the sequence speed, with the ability to generalize to new speeds; (ii) facilitating flexible expression of distinct sequences via selective activation, concatenation, and recycling of specific subsequences; and (iii) enabling the biologically plausible learning of sequences, consistent with the decoupling of learning and execution suggested by lesion studies showing that cortical circuits are necessary for learning, but that subcortical circuits are sufficient to drive learned behaviors. The same mechanisms that we describe can also be applied to circuits with both excitatory and inhibitory populations, and hence may underlie general features of sequential neural activity pattern generation in the brain.
Spatial and seasonal dynamics of cholera (Vibrio cholerae) in an estuary in southern coastal Ecuador
Authors: Ryan Sadie J. , Stewart Ibarra Anna M. , Ordóñez Eunice , Chu Winnie , Finkelstein Julia L. , King Christine A. , Escobar Luis E. , Lupone Christina , Heras Froilan , Tauzer Erica , Waggoner Egan , James Tyler G. , Cárdenas Washington B. , Polhemus Mark 
Published: February 2017

AbstractCholera emergence is strongly linked to local environmental and ecological context. The 1991-2004 pandemic emerged in Perú and spread north into Ecuador’s El Oro province, making this a key site for potential re-emergence. Machala, El Oro, is a port city of 250,000, near the Peruvian border. Many livelihoods depend on the estuarine system, from fishing for subsistence and trade, to domestic water use. In 2014, we conducted biweekly sampling for 10 months in five estuarine locations, across a gradient of human use, and ranging from inland to ocean. We measured water characteristics implicated inV. choleraegrowth and persistence: pH, temperature, salinity, and algal concentration, and evaluated samples in five months for pathogenic and non-pathogenicVibrio cholerae, by polymerase chain reaction (PCR). We found environmental persistence of strains O1 and O139, but no evidence for toxigene presence.V. choleraepresence was coupled to algal and salinity concentration, and sites exhibited considerable seasonal and spatial heterogeneity. This study indicates that environmental conditions in Machala are optimal for human cholera re-emergence, with risk peaking during September, and higher risk near urban periphery low-income communities. This highlights a need for surveillance of this coupled cholera– estuarine system to anticipate potential future outbreaks.
Histone H3 Lysine 4 methyltransferases MLL3 and MLL4 Modulate Long-range Chromatin Interactions at Enhancers
Authors: Yan Jian , Chen Shi-An A , Local Andrea , Liu Tristin , Qiu Yunjiang , Lee Ah Young , Jung Inkyung , Preißl Sebastian , Rivera Chloe M , Wang Chaochen , Ishii Haruhiko , Fang Rongxin , Ye Zhen , Ge Kai , Hu Ming , Ren Bing 
Published: February 2017

SUMMARYRegulation of gene expression in mammalian cells depends on long-range chromatin interactions between enhancers and promoters. Currently, the exact mechanisms that connect distal enhancers to their specific target promoters remain to be fully elucidated. Here we show that the histone H3 Lysine 4 monomethylation (H3K4me1) writer proteins MLL3 and MLL4 (MLL3/4) play an active role in this process. We demonstrate that in differentiating mouse embryonic stem cells, MLL3/4-dependent deposition of H3K4me1 at enhancers correlates with increased levels of chromatin interactions, whereas loss of MLL3/4 leads to greatly reduced frequencies of chromatin interactions and failure of lineage-specific gene expression programs. We further show that H3K4me1 facilitates recruitment of the Cohesin complex to chromatinin vitroandin vivo, providing a potential mechanism for MLL3/4 to promote chromatin looping. Taken together, our results support an active role for MLL3/4 in modulating chromatin organization at enhancers in mammalian cells.
SAVE: A secure cloud-based pipeline for CRISPR pooled screen deconvolution
Authors: Jeong Hyun-Hwan , Kim Seon Young , Rosseaux Maxime WC , Zoghbi Huda Y , Liu Zhandong 
Published: February 2017

AbstractWe present a user-friendly, cloud-based, data analysis pipeline for the deconvolution of pooled screening data. This tool, termed SAVE for Screening Analysis Visual Explorer, serves a dual purpose of extracting, clustering and analyzing raw next generation sequencing files derived from pooled screening experiments while at the same time presenting them in a user-friendly way on a secure web-based platform. Moreover, SAVE serves as a useful web-based analysis pipeline for reanalysis of pooled CRISPR screening datasets. Taken together, the framework described in this study is expected to accelerate development of web-based bioinformatics tool for handling all studies which include next generation sequencing data. SAVE is available athttp://save.nrihub.org.
Atomic resolution structure of serine protease proteinase K at ambient temperature
Authors: Masuda Tetsuya , Suzuki Mamoru , Inoue Shigeyuki , Song Changyong , Nakane Takanori , Nango Eriko , Tanaka Rie , Tono Kensuke , Joti Yasumasa , Kameshima Takashi , Hatsui Takaki , Yabashi Makina , Mikami Bunzo , Nureki Osamu , Numata Keiji , Iwata So , Sugahara Michihiro 
Published: February 2017

AbstractAtomic resolution structures (beyond 1.20 Å) at ambient temperature, which is usually hampered by the radiation damage in synchrotron X-ray crystallography (SRX), will add to our understanding of the structure-function relationships of enzymes. Serial femtosecond crystallography (SFX) has attracted surging interest by providing a route to bypass such challenges. Yet the progress on atomic resolution analysis with SFX has been rather slow. In this report, we describe the 1.20 Å resolution structure of proteinase K using 13 keV photon energy. Hydrogen atoms, water molecules, and a number of alternative side-chain conformations have been resolved. The increase in the value ofB-factor in SFX suggests that the residues and water molecules adjacent to active sites were flexible and exhibited dynamic motions at specific substrate-recognition sites.
GRIDSS: sensitive and specific genomic rearrangement detection using positional de Bruijn graph assembly
Authors: Cameron Daniel L , Schroeder Jan , Penington Jocelyn Sietsma , Do Hongdo , Molania Ramyar , Dobrovic Alexander , Speed Terence P , Papenfuss Anthony T 
Published: February 2017

ABSTRACTThe identification of genomic rearrangements, particularly in cancers, with high sensitivity and specificity using massively parallel sequencing remains a major challenge. Here, we describe the Genome Rearrangement IDentification Software Suite (GRIDSS), a high-speed structural variant (SV) caller that performs efficient genome-wide break-end assembly prior to variant calling using a novel positional de Bruijn graph assembler. By combining assembly, split read and read pair evidence using a probabilistic scoring, GRIDSS achieves high sensitivity and specificity on simulated, cell line and patient tumour data, recently winning SV sub-challenge #5 of the ICGC-TCGA DREAM Somatic Mutation Calling Challenge. On human cell line data, GRIDSS halves the false discovery rate compared to other recent methods. GRIDSS identifies non-template sequence insertions, micro-homologies and large imperfect homologies, and supports multi-sample analysis. GRIDSS is freely available athttps://github.com/PapenfussLab/gridss.
Replication and characterization ofCADM2andMSRAgenes on human behavior
Authors: Boutwell Brian , Hinds David ,   the 23andMe Research Team, Tielbeek Jorim , Ong Ken K. , Day Felix R. , Perry John R.B. 
Published: February 2017

AbstractProgress identifying the genetic determinants of personality has historically been slow, with candidate gene studies and small-scale genome-wide association studies yielding few reproducible results. In the UK Biobank study, genetic variants inCADM2andMSRAwere recently shown to influence risk taking behavior and irritability respectively, representing some of the first genomic loci to be associated with aspects of personality. We extend this observation by performing a personality “phenome-scan” across 16 traits in up to 140,487 participants from 23andMe for these two genes. Heritability estimates for these traits ranged from 5-19%, with bothCADM2andMSRAdemonstrating significant effects on multiple personality types. These associations covered all aspects of the big five personality domains, including specific facet traits such as compliance, altruism, anxiety and activity / energy. This study both confirms and extends the original observations, highlighting the role of genetics in aspects of mental health and behavior.