bluuebunny/crossref_metadata_2025_split huggingface dataset:
Predicting multicellular function through multi-layer tissue networks
Authors: Zitnik Marinka , Leskovec Jure 
Published: April 2017

Abstract

Motivation
Understanding functions of proteins in specific human tissues is essential for insights into disease diagnostics and therapeutics, yet prediction of tissue-specific cellular function remains a critical challenge for biomedicine.

Results
Here, we present OhmNet, a hierarchy-aware unsupervised node feature learning approach for multi-layer networks. We build a multi-layer network, where each layer represents molecular interactions in a different human tissue. OhmNet then automatically learns a mapping of proteins, represented as nodes, to a neural embedding-based low-dimensional space of features. OhmNet encourages sharing of similar features among proteins with similar network neighborhoods and among proteins activated in similar tissues. The algorithm generalizes prior work, which generally ignores relationships between tissues, by modeling tissue organization with a rich multiscale tissue hierarchy. We use OhmNet to study multicellular function in a multi-layer protein interaction network of 107 human tissues. In 48 tissues with known tissue-specific cellular functions, OhmNet provides more accurate predictions of cellular function than alternative approaches, and also generates more accurate hypotheses about tissue-specific protein actions. We show that taking into account the tissue hierarchy leads to improved predictive power. Remarkably, we also demonstrate that it is possible to leverage the tissue hierarchy in order to effectively transfer cellular functions to a functionally uncharacterized tissue. Overall, OhmNet moves from flat networks to multiscale models able to predict a range of phenotypes spanning cellular subsystems.

Availability and implementation
Source code and datasets are available at http://snap.stanford.edu/ohmnet.
Retirement Sequences of Older Americans: Moderately Destandardized and Highly Stratified Across Gender, Class, and Race
Authors: Calvo Esteban , Madero-Cabib Ignacio , Staudinger Ursula M 
Published: April 2017

Abstract

Purpose of the Study
A destandardization of labor-force patterns revolving around retirement has been observed in recent literature. It is unclear, however, to which degree and of which kind. This study looked at sequences rather than individual statuses or transitions and argued that differentiating older Americans’ retirement sequences by type, order, and timing and considering gender, class, and race differences yields a less destandardized picture.

Design and Methods
Sequence analysis was employed to analyze panel data from the Health and Retirement Study (HRS) for 7,881 individuals observed 6 consecutive times between ages 60–61 and 70–71.

Results
As expected, types of retirement sequences were identified that cannot be subsumed under the conventional model of complete retirement from full-time employment around age 65. However, these retirement sequences were not entirely destandardized, as some irreversibility and age-grading persisted. Further, the degree of destandardization varied along gender, class, and race. Unconventional sequences were archetypal for middle-level educated individuals and Blacks. Also, sequences for women and individuals with lower education showed more unemployment and part-time jobs, and less age-grading.

Implications
A sequence-analytic approach that models group differences uncovers misjudgments about the degree of destandardization of retirement sequences. When a continuous process is represented as individual transitions, the overall pattern of retirement sequences gets lost and appears destandardized. These patterns get further complicated by differences in social structures by gender, class, and race in ways that seem to reproduce advantages that men, more highly educated individuals, and Whites enjoy in numerous areas over the life course.
MTurk Character Misrepresentation: Assessment and Solutions
Authors: Sharpe Wessling Kathryn , Huber Joel , Netzer Oded 
Published: April 2017

Abstract
This tutorial provides evidence that character misrepresentation in survey screeners by Amazon Mechanical Turk Workers (“Turkers”) can substantially and significantly distort research findings. Using five studies, we demonstrate that a large proportion of respondents in paid MTurk studies claim a false identity, ownership, or activity in order to qualify for a study. The extent of misrepresentation can be unacceptably high, and the responses to subsequent questions can have little correspondence to responses from appropriately identified participants. We recommend a number of remedies to deal with the problem, largely involving strategies to take away the economic motive to misrepresent and to make it difficult for Turkers to recognize that a particular response will gain them access to a study. The major short-run solution involves a two-survey process that first asks respondents to identify their characteristics when there is no motive to deceive, and then limits the second survey to those who have passed this screen. The long-run recommendation involves building an ongoing MTurk participant pool (“panel”) that (1) continuously collects information that could be used to classify respondents, and (2) eliminates from the panel those who misrepresent themselves.
Ovarian Endometrioma Superinfected With Salmonella: Case Report and Review of the Literature
Authors: Adelman Max W. , Johnson Jacob H. , Hohmann Elizabeth L. , Gandhi Rajesh T. 
Published: April 2017

AbstractWe present the case of a 28-year-old woman with Salmonella serovar Schwarzengrund gastroenteritis acquired during foreign travel. Her case was complicated by superinfection of a pre-existing ovarian endometrioma with a quinolone-resistant organism; the resultant ovarian abscess ultimately required surgical removal for resolution. We review the key features of this case and the previous literature on Salmonella ovarian abscess. This report highlights (1) the potential for metastatic spread of Salmonella to the ovary in women with pre-existing cysts or endometriomas and (2) the increasing worldwide burden of quinolone-resistant Salmonella.
Cross-sectional Area of the Median Nerve Before Revision Carpal Tunnel Release—A Cross-sectional Study
Authors: Duetzmann Stephan , Tas Suleyman , Seifert Volker , Marquardt Gerhard , Dombert Thomas , Staub Frank 
Published: April 2017

Abstract

BACKGROUND
High-resolution ultrasound can be used for diagnosis of carpal tunnel syndrome with an equal accuracy to electrodiagnostic studies. Up to date there has been no investigation published that examined the median nerve in a large patient cohort with recurrent or persistent symptoms. Reference and cutoff values are lacking.

OBJECTIVE
To provide reference values for detection of ongoing or recurrent compression in patients with recurring or persisting symptoms in carpal tunnel syndrome.

METHODS
One hundred and sixteen patients undergoing revision decompression of the median nerve at the carpal tunnel between January 2010 and October 2015 were studied retrospectively to determine the cross-sectional area of the median nerve at the wrist by the technique of neurosonography.

RESULTS
In cases of insufficient primary release, the mean cross-sectional area was 20.0 mm2 preop. In cases of scar or synovitis, the mean cross-sectional area was 17.0 mm2 (significantly less than in cases of insufficient primary release, P = .008). Compared to successfully operated patients with de novo carpal tunnel syndrome (n = 74), a cutoff value of 14.5 mm2 yielded a sensitivity of 78% and a specificity of 97% to diagnose ongoing or recurrent compression in case of a typical clinical presentation of ongoing or recurrent symptoms (tested via comparison of patients who are symptom free vs patients with symptoms).

CONCLUSION
For the first time, we provide reference values in patients with recurring or persisting symptoms in carpal tunnel syndrome based on a large patient population. Ultrasound can aid in the evaluation of patients with entrapment neuropathy of the median nerve and recurring or persisting symptoms.
Investigation of protein synthesis in Drosophila larvae using puromycin labelling
Authors: Deliu Lisa , Ghosh Abhishek , Grewal Savraj S. 
Published: April 2017

ABSTRACTTranslational control of gene expression is an important regulator of growth, homeostasis and aging in Drosophila. The ability to measure changes in protein synthesis in response to genetic and environmental cues is therefore important in studying these processes. Here we describe a simple and cost effective approach to assay protein synthesis in Drosophila larval cells and tissues. The method is based on the incorporation of puromycin into nascent peptide chains. Using an ex vivo approach, we label newly synthesized peptides in larvae with puromycin and then measure levels of new protein synthesis using an anti-puromycin antibody. We show that this method can detect changes in protein synthesis in specific cells and tissues in the larvae, either by immunostaining or western blotting. We find that the assay reliably detects changes in protein synthesis induced by two known stimulators of mRNA translation - the nutrient/TORC1 kinase pathway and the transcription factor dMyc. We also use the assay to describe how protein synthesis changes through larval development and in response to two environmental stressors – hypoxia and heat-shock. We propose that this puromycin-labelling assay is a simple but robust method to detect protein synthesis changes at the levels of cells, tissues or whole body in Drosophila.
Involvement of herpes simplex virus type 1 UL13 protein kinase in induction of SOCS genes, the negative regulators of cytokine signaling
Authors: Sato Yuka , Koshizuka Tetsuo , Ishibashi Kei , Hashimoto Koichi , Ishioka Ken , Ikuta Kazufumi , Yokota Shin‐ichi , Fujii Nobuhiro , Suzutani Tatsuo 
Published: April 2017

ABSTRACTThe suppressor of cytokine signaling (SOCS) family has eight members and suppresses various cytokine signaling pathways, including IFN signaling. Therefore, some viruses have evolved molecular mechanisms for inducing SOCS proteins and thus escaping host immunity. Herpes simplex virus type 1 (HSV‐1) has a mechanism for escaping from type I IFN by induction of both SOCS1 and SOCS3. In this study, expression of the eight members of the SOCS family stimulated by HSV‐1 infection was comparatively analyzed by qRT‐PCR. It was found that SOCS1 and SOCS3 are induced by HSV‐1‐infection at 4 hr post infection. However, such induction was not observed in UL13 deficient virus‐infected cells, suggesting that UL13 protein kinase participates in induction of both genes. The transcription factor Sp1‐binding sites of SOCS3 promoter/enhancer region were identified as the regulatory elements for induction of SOCS3 in HSV‐1 infected cells. Accumulation of activated Sp1 was detectable in the nuclei of HSV‐1‐infected cells before induction of SOCS3. Taken together, these results suggest that HSV‐1 has a potent mechanism for escaping from the IFN system.
An Arctic predator–prey system in flux: climate change impacts on coastal space use by polar bears and ringed seals
Authors: Hamilton Charmain D. , Kovacs Kit M. , Ims Rolf A. , Aars Jon , Lydersen Christian 
Published: April 2017

Summary

Climate change is impacting different species at different rates, leading to alterations in biological interactions with ramifications for wider ecosystem functioning. Understanding these alterations can help improve predictive capacity and inform management efforts designed to mitigate against negative impacts.

We investigated how the movement and space use patterns of polar bears (Ursus maritimus) in coastal areas in Svalbard, Norway, have been altered by a sudden decline in sea ice that occurred in 2006. We also investigated whether the spatial overlap between polar bears and their traditionally most important prey, ringed seals (Pusa hispida), has been affected by the sea‐ice decline, as polar bears are dependent on a sea‐ice platform for hunting seals.

We attached biotelemetry devices to ringed seals (n = 60, both sexes) and polar bears (n = 67, all females) before (2002–2004) and after (2010–2013) a sudden decline in sea ice in Svalbard. We used linear mixed‐effects models to evaluate the association of these species to environmental features and an approach based on Time Spent in Area to investigate changes in spatial overlap between the two species.

Following the sea‐ice reduction, polar bears spent the same amount of time close to tidal glacier fronts in the spring but less time in these areas during the summer and autumn. However, ringed seals did not alter their association with glacier fronts during summer, leading to a major decrease in spatial overlap values between these species in Svalbard's coastal areas. Polar bears now move greater distances daily and spend more time close to ground‐nesting bird colonies, where bear predation can have substantial local effects.

Our results indicate that sea‐ice declines have impacted the degree of spatial overlap and hence the strength of the predator–prey relationship between polar bears and ringed seals, with consequences for the wider Arctic marine and terrestrial ecosystems. Shifts in ecological interactions are likely to become more widespread in many ecosystems as both predators and prey respond to changing environmental conditions induced by global warming, highlighting the importance of multi‐species studies.
The “rectosigmoid brake”: Review of an emerging neuromodulation target for colorectal functional disorders
Authors: Lin Anthony Y , Dinning Phil G , Milne Tony , Bissett Ian P , O'Grady Gregory 
Published: April 2017

SummaryThe regulation of gastrointestinal motility encompasses several overlapping mechanisms including highly regulated and coordinated neurohormonal circuits. Various feedback mechanisms or “brakes” have been proposed. While duodenal, jejunal, and ileal brakes are well described, a putative distal colonic brake is less well defined. Despite the high prevalence of colonic motility disorders, there is little knowledge of colonic motility owing to difficulties with organ access and technical difficulties in recording detailed motor patterns along its entire length. The motility of the colon is not under voluntary control. A wide range of motor patterns is seen, with long intervals of intestinal quiescence between them. In addition, the use of traditional manometric catheters to record contractile activity of the colon has been limited by the low number of widely spaced sensors, which has resulted in the misinterpretation of colonic motor patterns. The recent advent of high‐resolution (HR) manometry is revolutionising the understanding of gastrointestinal motor patterns. It has now been observed that the most common motor patterns in the colon are repetitive two to six cycles per minute (cpm) propagating events in the distal colon. These motor patterns are prominent soon after a meal, originate most frequently in the rectosigmoid region, and travel in the retrograde direction. The distal prominence and the origin of these motor patterns raise the possibility of them serving as a braking mechanism, or the “rectosigmoid brake,” to limit rectal filling. This review aims to describe what is known about the “rectosigmoid brake,” including its physiological and clinical significance and potential therapeutic applications.
Temporal changes in cutaneous bacterial communities of terrestrial‐ and aquatic‐phase newts (Amphibia)
Authors: Sabino‐Pinto Joana , Galán Pedro , Rodríguez Silvia , Bletz Molly C. , Bhuju Sabin , Geffers Robert , Jarek Michael , Vences Miguel 
Published: April 2017

SummaryAnimal‐associated bacterial communities play essential roles for their host's ecology, physiology and health. Temporal dynamics of these communities are poorly understood, but might be of high relevance for amphibians with a well‐expressed biphasic biology of adults where the structure of their skin changes drastically between the aquatic and terrestrial phases. Here, we investigated the temporal dynamics of cutaneous bacterial communities of Lissotriton boscai and Triturus marmoratus by monthly sampling populations from a pond and surrounding terrestrial habitats near A Coruña, Spain. These communities were characterized by 16S rRNA gene amplicons from DNA isolated from skin swabs. Newt bacterial communities displayed variation at three levels: between larvae and aquatic adults, between adult life phases (terrestrial versus aquatic), and temporally within life phases. The skin bacterial communities tended to differ to a lesser extent temporally and between larvae and adults, and more strongly between life phases. Larvae had a higher proportion of reads associated with antifungal taxa compared with adults, while no differences were found among adult life phases. Terrestrial specimens exhibited the highest community diversity. The regular transitions of adult newts between aquatic and terrestrial environments might contribute to the diversity of their skin microbiota and could increase disease resistance.
The Effect of Medicaid Physician Fee Increases on Health Care Access, Utilization, and Expenditures
Authors: Callison Kevin , Nguyen Binh T. 
Published: April 2017

ObjectiveTo evaluate the effect of Medicaid fee changes on health care access, utilization, and spending for Medicaid beneficiaries.Data SourceWe use the 2008 and 2012 waves of the Medical Expenditure Panel Survey linked to state‐level Medicaid‐to‐Medicare primary care reimbursement ratios obtained through surveys conducted by the Urban Institute. We also incorporate data from the Current Population Survey and the Area Resource Files.Study DesignUsing a control group made up of the low‐income privately insured, we conduct a difference‐in‐differences analysis to assess the relationship between Medicaid fee changes and access to care, utilization of health care services, and out‐of‐pocket medical expenditures for Medicaid enrollees.Principal FindingsWe find that an increase in the Medicaid‐to‐Medicare payment ratio for primary care services results in an increase in outpatient physician visits, emergency department utilization, and prescription fills, but only minor improvements in access to care. In addition, we report an increase in total annual out‐of‐pocket expenditures and spending on prescription medications.ConclusionsCompared to the low‐income privately insured, increased primary care reimbursement for Medicaid beneficiaries leads to higher utilization and out‐of‐pocket spending for Medicaid enrollees.
High occurrence of Bathyarchaeota (MCG) in the deep‐sea sediments of South China Sea quantified using newly designed PCR primers
Authors: Yu Tiantian , Liang Qianyong , Niu Mingyang , Wang Fengping 
Published: April 2017

SummaryThe archaeal phylum Bathyarchaeota, which is composed of a large number of diverse lineages, is widespread and abundant in marine sediments. Environmental factors that control the distribution, abundance and evolution of this largely diversified archaeal phylum are currently unclear. In this study, a new pair of specific primers that target the major marine subgroups of bathyarchaeotal 16S rRNA genes was designed and evaluated to investigate the distribution and abundance of Bathyarchaeota in marine sediments. The abundance of Bathyarchaeota along two sediment cores from the deep‐sea sediments of South China Sea (SCS, each from the Dongsha and Shenhu area) was determined. A strong correlation was found between the bathyarchaeotal abundance and the content of total organic carbon (TOC), suggesting an important role of Bathyarchaeota in organic matter remineralisation in the sediments of SCS. Furthermore, diversity analysis revealed that subgroups Bathy‐2, Bathy‐8 and Bathy‐10 were dominant bathyarchaeotal members of the deep‐sea sediments in the SCS. Bathy‐8 was found predominantly within the reducing and deeper sediment layers, while Bathy‐10 occurred preferentially in the oxidizing and shallower sediment layers. Our study lays a foundation for the further understanding of the ecological functions and niche differentiation of the important but not well‐understood sedimentary archaeal group.
Anti‐Müllerian hormone exhibits a great variation in infertile women with different ovarian reserve patterns
Authors: Gorkem Umit , Kucukler Ferit Kerim , Togrul Cihan , Gungor Tayfun 
Published: April 2017

BackgroundSeveral conflicting studies with results on the biological variability of serum anti‐Müllerian hormone (AMH) levels have been reported. Most of the studies have not focused on whether the level of AMH fluctuations shows variability by a baseline ovarian follicular reserve.AimTo reveal whether intracyclic variation in AMH levels occurs among women with adequate, high and diminished ovarian reserve patterns.Study designIn this prospective cross‐sectional study, 171 infertile women between the ages of 18 and 42 years were recruited. All participants were divided into three types of ovarian reserve patterns (adequate, high and diminished). Serum samples were tested for levels of follicular AMH (F‐AMH), luteal AMH (L‐AMH), estradiol (E2), and follicle stimulating hormone (FSH) and progesterone.ResultsThe median age of the 171 participating women was 28 (18–42) years. The three ovarian reserve groups had similar body mass index (BMI) and E2 (P = 0.797 and P = 0.135, respectively). The serum AMH levels of all women and the three ovarian reserve groups in the follicular phase were higher compared to those in the luteal phase (P < 0.001). There were strong positive correlations between follicular and luteal AMH levels in adequate, high and diminished reserve groups (Spearman r = 0.864, P < 0.001 vs r = 0.899, P < 0.001 vs r = 0.863, P < 0.001, respectively).ConclusionSerum AMH levels were higher during the follicular phase than the luteal phase in women with adequate, high and diminished ovarian patterns. Since the highest AMH levels are demonstrated during the follicular phase, the optimal time to measure AMH concentration might be during the follicular phase.
Receiving early information and trusting Swedish child health centre nurses increased parents’ willingness to vaccinate against rotavirus infections
Authors: Schollin Ask Lina , Hjern Anders , Lindstrand Ann , Olen Ola , Sjögren Eva , Blennow Margareta , Örtqvist Åke 
Published: April 2017

AbstractAimRotavirus vaccines are effective against severe infections, but have a modest impact on mortality in high‐income countries. Parental knowledge and attitudes towards vaccines are crucial for high vaccination coverage. This study aimed to identify why parents refused to let their infant have the vaccination or were unsure.MethodsThis cross‐sectional study was based on 1,063 questionnaires completed by the parents of newborn children in 2014. Stepwise logistic regression was used to identify the main predictors.ResultsMost (81%) parents intended to vaccinate their child against the rotavirus, while 19% were unwilling or uncertain. Parents with less education and children up to five weeks of age were more likely to be unwilling or uncertain about vaccinating their child. Factors associated with a refusal or uncertainty about vaccinating were not having enough information about the vaccine, no intention of accepting other vaccines, paying little heed to the child health nurses’ recommendations, thinking that the rotavirus was not a serious illness and not believing that the vaccine provided protection against serious forms of gastroenteritis.ConclusionEarly information, extra information for parents with less education and close positive relationships between parents and child health nurses were important factors in high rotavirus vaccination rates.