bluuebunny/crossref_metadata_2025_split huggingface dataset:
BioCIDER: a Contextualisation InDEx for biological Resources discovery
Authors: Horro Carlos , Cook Martin , Attwood Teresa K , Brazas Michelle D , Hancock John M , Palagi Patricia , Corpas Manuel , Jimenez Rafael 
Published: April 2017

Abstract

Summary
The vast, uncoordinated proliferation of bioinformatics resources (databases, software tools, training materials etc.) makes it difficult for users to find them. To facilitate their discovery, various services are being developed to collect such resources into registries. We have developed BioCIDER, which, rather like online shopping ‘recommendations’, provides a contextualization index to help identify biological resources relevant to the content of the sites in which it is embedded.

Availability and Implementation
BioCIDER (www.biocider.org) is an open-source platform. Documentation is available online (https://goo.gl/Klc51G), and source code is freely available via GitHub (https://github.com/BioCIDER). The BioJS widget that enables websites to embed contextualization is available from the BioJS registry (http://biojs.io/). All code is released under an MIT licence.
Simultaneous Bilateral Hip Arthroscopy in Adolescent Athletes With Symptomatic Femoroacetabular Impingement
Authors: McConkey Mark O. , Chadayammuri Vivek , Garabekyan Tigran , Mayer Stephanie W. , Kraeutler Matthew J. , Mei-Dan Omer 
Published: April 2017

Background:
Femoroacetabular impingement represents a common cause of hip pain in adolescents. The purpose of the present study was to evaluate the safety and efficacy of simultaneous bilateral hip arthroscopy for bilateral symptomatic femoroacetabular impingement in adolescent athletes.

Methods:
Clinical data were collected in a prospective database on patients who underwent unilateral or simultaneous bilateral hip arthroscopy and included complications, reoperation rate, and return to play time. Differences in International Hip Outcome Tool (iHOT)-12 scores according to hip side and postoperative follow-up time (preoperative, 1.5, 3, 6, 12, and 24 mo) were evaluated using a 2×6 repeated-measures analysis of variance with post hoc repeated-measures 1-way analysis of variance and Bonferroni-corrected paired t tests.

Results:
In total, 24 patients (36 hips) were studied, of whom 12 underwent simultaneous bilateral hip arthroscopy (24 hips) and a case-matched control group of 12 patients underwent unilateral hip arthroscopy. There were 5 males in each group (41.7%). Average age was 15.7 and 16.5 years in the bilateral and unilateral groups, respectively. No patients were lost to follow-up. In the bilateral group, a significant increase in mean iHOT-12 score was observed between 1.5- and 3-month follow-up (61.8 vs. 82.8, respectively; P=0.003), and 6-, 12-, and 24-month follow-up (91.4, 95.1, and 96.6, respectively, P=0.004). At all follow-up times, there were no significant differences in mean iHOT-12 scores or other outcome measures between bilateral and unilateral cohorts. Time to return to preinjury level of activity was similar between the bilateral and unilateral groups (4.7 vs. 4.9 mo, respectively; P=0.40). One transient lateral femoral cutaneous nerve palsy occurred in each group, though no other complications were documented. No patients required revision surgery by latest follow-up.

Conclusions:
Bilateral simultaneous hip arthroscopy is safe and reproducible in adolescent athletes, achieving equivalent outcomes, and similar rehabilitation time when compared with unilateral surgery.

Level of Evidence:
Level II—therapeutic study.
Simultaneous Keratolimbal Autograft and Penetrating Autokeratoplasty: A Single-Stage Procedure to Restore Monocular Vision of a Blind Patient With Limbal Stem Cell Deficiency
Authors: Jarade Elias , Amro Mazen , Haydar Ali A. , Hemade Adib 
Published: April 2017

Purpose:
To describe the technique of simultaneous keratolimbal autograft and penetrating autokeratoplasty to restore monocular vision of a blind patient with limbal stem cell deficiency (LSCD).

Methods:
A patient with acquired monocular vision due to loss of the left eye owing to LSCD postblast injury presented with acute loss of vision in the right eye due to central retinal artery occlusion. Simultaneous keratolimbal autograft and penetrating autokeratoplasty were performed in attempt to restore his vision in the left eye.

Results:
Postoperatively, the anterior chamber was well formed along with mild graft edema on day 1. Topo-guided suture removal was started at 4 months. The graft maintained clear transparency at 1-year follow-up, and the best-corrected visual acuity improved from hand movement to 20/50.

Conclusions:
Keratolimbal autograft and penetrating autokeratoplasty, as a one-stage procedure, proved to be effective in restoring monocular vision in a patient with LSCD.
Influence of genetic variations in the SOD1 gene on the development of ascites and spontaneous bacterial peritonitis in decompensated liver cirrhosis
Authors: Schwab Sebastian , Lehmann Jennifer , Lutz Philipp , Jansen Christian , Appenrodt Beate , Lammert Frank , Strassburg Christian P. , Spengler Ulrich , Nischalke Hans-Dieter , Trebicka Jonel 
Published: April 2017

Background
The balance between generation and elimination of reactive oxygen species by superoxide dismutase (SOD) is crucially involved in the pathophysiology of liver cirrhosis. Reactive oxygen species damage cells and induce inflammation/fibrosis, but also play a critical role in immune defense from pathogens. As both processes are involved in the development of liver cirrhosis and its complications, genetic variation of the SOD1 gene was investigated.

Patients and methods
Two SOD1 single nucleotide polymorphisms (rs1041740 and rs3844942) were analyzed in 49 cirrhotic patients undergoing liver transplantation. In addition, 344 cirrhotic patients with ascites were analyzed in a cohort of 521 individuals in terms of the relationship of these polymorphisms with spontaneous bacterial peritonitis (SBP).

Results
Although rs3844942 showed no associations with complications of cirrhosis, we observed a significant association between rs1041740 and the presence of ascites and SBP in the discovery cohort of patients with cirrhosis. Importantly, the association with SBP was not confirmed in the validation cohort of patients with ascites. By contrast, a trend toward lower SBP rates was observed in carriers of rs1041740. In this cohort, rs1041740 was not associated with survival.

Conclusion
These data suggest a complex role of SOD1 in different processes leading to complications of liver cirrhosis. rs1041740 might be associated with the development of ascites and possibly plays a role in SBP once ascites has developed.
Increased Epicardial Fat Thickness in Sudden Death From Stable Coronary Artery Atherosclerosis
Authors: Fuller Belinda , Garland Jack , Anne Sravan , Beh Raymond , McNevin Dennis , Tse Rexson 
Published: April 2017

Background
Sudden death from stable coronary artery atherosclerosis (SCAA) is well recognized. However, individuals can have ischemic heart disease or coronary artery atherosclerosis but die of noncardiac causes. Recently, it has been recognized that increased epicardial fat is detrimental to normal heart function. We hypothesize that individuals who die of SCAA have increased epicardial fat.

Aim
The aim of this study was to investigate whether there is an increase in epicardial fat in individuals who suddenly died of SCAA.

Methods
This was a 1-year retrospective study comparing the average epicardial fat thickness using postmortem computed tomography scan between individuals who suddenly died of SCAA (SCAA group) with individuals who primarily died of natural noncardiac causes but had established ischemic heart disease or significant coronary artery atherosclerosis (NCC group).

Results
Average epicardial fat thickness was significantly higher in the SCAA group (8 ± 2 mm) than in the NCC group (6 ± 2 mm, P = 0.008).

Conclusions
Individuals who die of SCAA appear to have higher epicardial fat thickness. The increase in epicardial fat may have an additional detrimental effect to the heart predisposing sudden death in individuals with coronary artery atherosclerosis.
The Ebola outbreak, 2013–2016: old lessons for new epidemics
Authors: Coltart Cordelia E. M. , Lindsey Benjamin , Ghinai Isaac , Johnson Anne M. , Heymann David L. 
Published: April 2017

Ebola virus causes a severe haemorrhagic fever in humans with high case fatality and significant epidemic potential. The 2013–2016 outbreak in West Africa was unprecedented in scale, being larger than all previous outbreaks combined, with 28 646 reported cases and 11 323 reported deaths. It was also unique in its geographical distribution and multicountry spread. It is vital that the lessons learned from the world's largest Ebola outbreak are not lost. This article aims to provide a detailed description of the evolution of the outbreak. We contextualize this outbreak in relation to previous Ebola outbreaks and outline the theories regarding its origins and emergence. The outbreak is described by country, in chronological order, including epidemiological parameters and implementation of outbreak containment strategies. We then summarize the factors that led to rapid and extensive propagation, as well as highlight the key successes, failures and lessons learned from this outbreak and the response.
This article is part of the themed issue ‘The 2013–2016 West African Ebola epidemic: data, decision-making and disease control’.
Characterizing risk of Ebola transmission based on frequency and type of case–contact exposures
Authors: Skrip Laura A. , Fallah Mosoka P. , Gaffney Stephen G. , Yaari Rami , Yamin Dan , Huppert Amit , Bawo Luke , Nyenswah Tolbert , Galvani Alison P. 
Published: April 2017

During the initial months of the 2013–2016 Ebola epidemic, rapid geographical dissemination and intense transmission challenged response efforts across West Africa. Contextual behaviours associated with increased risk of exposure included travel to high-transmission settings, caring for sick and preparing the deceased for traditional funerals. Although such behaviours are widespread in West Africa, high-transmission pockets were observed. Superspreading and clustering are typical phenomena in infectious disease outbreaks, as a relatively small number of transmission chains are often responsible for the majority of events. Determining the characteristics of contacts at greatest risk of developing disease and of cases with greatest transmission potential could therefore help curb propagation of infection. Our analysis of contact tracing data from Montserrado County, Liberia, suggested that the probability of transmission was 4.5 times higher for individuals who were reported as having contact with multiple cases. The probability of individuals developing disease was not significantly associated with age or sex of their source case but was higher when they were in the same household as the infectious case. Surveillance efforts for rapidly identifying symptomatic individuals and effectively messaged campaigns encouraging household members to bring the sick to designated treatment centres without administration of home care could mitigate transmission.
This article is part of the themed issue ‘The 2013–2016 West African Ebola epidemic: data, decision-making and disease control’.
Command and control of Sierra Leone's Ebola outbreak response: evolution of the response architecture
Authors: Ross Emma 
Published: April 2017

Management, coordination and logistics were critical for responding effectively to the Ebola outbreak in Sierra Leone, and the duration of the epidemic provided a rare opportunity to study the management of an outbreak that endured long enough for the response to mature. This qualitative study examines the structures and systems used to manage the response, and how and why they changed and evolved. It also discusses the quality of relationships between key responders and their impact. Early coordination mechanisms failed and the President took operational control away from the Ministry of Health and Sanitation and established a National Ebola Response Centre, headed by the Minister of Defence, and District Ebola Response Centres. British civilian and military personnel were deeply embedded in this command and control architecture and, together with the United Nations Mission for Ebola Emergency Response lead, were the dominant coordination partners at the national level. Coordination, politics and tensions in relationships hampered the response, but as the response mechanisms matured, coordination improved and rifts healed. Simultaneously setting up new organizations, processes and plans as well as attempting to reconcile different cultures, working practices and personalities in such an emergency was bound to be challenging.
This article is part of the themed issue ‘The 2013–2016 West African Ebola epidemic: data, decision-making and disease control’.
Electrochemical measurement of acetylcholine in the dorsolateral prefrontal cortex: A technical report
Authors: Vartak Devavrat , van der Togt Chris , van Vugt Bram , Roelfsema Pieter R. 
Published: April 2017

AbstractEver since the discovery of acetylcholine in 1913, its role as neuromodulator has been extensively studied in a variety of model systems. These previous studies revealed that acetylcholine is of critical importance for several cognitive functions including attention, learning and memory. In spite of these previous findings, it has proven difficult to determine the amount of acetylcholine that is released during cognitive tasks with sub-second temporal resolution. One method that might be used to measure acetylcholine release is the use of an enzyme-coupled amperometric sensor, which has been suggested to measure acetylcholine with high sensitivity, selectivity and relatively high temporal resolution (< 1 second). In the present study, we have tried to adapt the technique developed in the rodent model system by Parikh and colleagues1,2for use in non-human primates. We aimed to measure in-vivo levels of acetylcholine in the macaque dorsolateral prefrontal cortex while the monkey performed an attention demanding curve-tracing task3,4. We report that our attempts to measure acetylcholine using amperometry in an awake behaving macaque monkey proved difficult and tedious and that our results are inconsistent and prone to noise. In the discussion, we will outline the challenges that will need to be addressed to use this technique in non-human primates and hope that our observations inspire solutions to help future research on the role of this important neurotransmitter.
Looking into Pandora’s Box: The Content ofSci-Huband its Usage
Authors: Greshake Bastian 
Published: April 2017

AbstractDespite the growth of Open Access, illegally circumventing paywalls to access scholarly publications is becoming a more mainstream phenomenon. The web serviceSci-Hubis amongst the biggest facilitators of this, offering free access to around 62 million publications. So far it is not well studied how and why its users are accessing publications throughSci-Hub. By utilizing the recently released corpus ofSci-Huband comparing it to the data of ˜28 million downloads done through the service, this study tries to address some of these questions. The comparative analysis shows that both the usage and complete corpus is largely made up of recently published articles, with users disproportionately favoring newer articles and 35% of downloaded articles being published after 2013. These results hint that embargo periods before publications become Open Access are frequently circumnavigated using Guerilla Open Access approaches likeSci-Hub. On a journal level, the downloads show a bias towards some scholarly disciplines, especially Chemistry, suggesting increased barriers to access for these. Comparing the use and corpus on a publisher level, it becomes clear that only 11% of publishers are highly requested in comparison to the baseline frequency, while 45% of all publishers are significantly less accessed than expected. Despite this, the oligopoly of publishers is even more remarkable on the level of content consumption, with 80% of all downloads being published through only 9 publishers. All of this suggests thatSci-Hubis used by different populations and for a number of different reasons, and that there is still a lack of access to the published scientific record. A further analysis of these openly available data resources will undoubtedly be valuable for the investigation of academic publishing.
Abnormal social behaviors and dysfunction of autism-related genes associated with daily agonistic interactions in mice
Authors: Kudryavtseva Natalia N. , Kovalenko Irina L. , Smagin Dmitry A. , Galyamina Anna G. , Babenko Vladimir N. 
Published: April 2017

AbstractBackgroundThe ability of people to communicate with each other is a necessary component of social behavior and the normal development of individuals who live in a community. An apparent decline in sociability may be the result of a negative social environment or the development of affective and neurological disorders, including autistic spectrum disorders. The behavior of these humans may be characterized by the deterioration of socialization, low communication, and repetitive and restricted behaviors. This study aimed to analyze changes in the social behaviors of male mice induced by daily agonistic interactions and investigate the involvement of genes, related with autistic spectrum disorders in the process of the impairment of social behaviors.MethodsAbnormal social behavior is induced by repeated experiences of aggression accompanied by wins (winners) or chronic social defeats (losers) in daily agonistic interactions in male mice. The collected brain regions (the midbrain raphe nuclei, ventral tegmental area, striatum, hippocampus, and hypothalamus) were sequenced at JSC Genoanalytica (http://genoanalytica.ru/, Moscow, Russia). The Cufflinks program was used to estimate the gene expression levels. Bioinformatic methods were used for the analysis of differentially expressed genes in male mice.ResultsThe losers exhibited an avoidance of social contacts toward unfamiliar conspecific, immobility and low communication on neutral territory. The winners demonstrated aggression and hyperactivity in this condition. The exploratory activity (rearing) and approaching behavior time towards the partner were decreased, and the number of episodes of repetitive self-grooming behavior was increased in both social groups. These symptoms were similar to the symptoms observed in animal models of autistic spectrum disorders. In an analysis of the RNA-Seq database of the whole transcriptome in the brain regions of the winners and losers, we identified changes in the expression of the following genes, which are associated with autism in humans:Tph2, Maoa, Slc6a4, Htr7,Gabrb3, Nrxn1, Nrxn2, Nlgn1, Nlgn2, Nlgn3, Shank2, Shank3, Fmr1, Ube3a, Pten, Cntn3, Foxp2, Oxtr, Reln, Cadps2, Pcdh10, Ctnnd2, En2, Arx, Auts2, Mecp2, andPtchd1.Common and specific changes in the expression of these genes in different brain regions were identified in the winners and losers.ConclusionsThis research demonstrates for the first time that abnormalities in social behaviors that develop under a negative social environment in adults may be associated with alterations in expression of genes, related with autism in the brain.
Hardwired synthetic lethality within the cohesin complex in human cancer cells
Authors: Lelij Petra van der , Lieb Simone , Jude Julian , Wutz Gordana , Santos Catarina P. , Falkenberg Katrina , Schlattl Andreas , Ban Jozef , Schwentner Raphaela , Kovar Heinrich , Real Francisco X. , Waldman Todd , Pearson Mark A. , Kraut Norbert , Peters Jan-Michael , Zuber Johannes , Petronczki Mark 
Published: April 2017

AbstractRecent genome analyses have identified recurrent mutations in the cohesin complex in a wide range of human cancers. Here we demonstrate that the most frequently mutated subunit of the cohesin complex,STAG2, displays a strong synthetic lethal interaction with its paralogSTAG1. Mechanistically, STAG1 loss abrogates sister chromatid cohesion inSTAG2mutated but not in wild-type cells leading to mitotic catastrophe, defective cell division and apoptosis. STAG1 inactivation inhibits the proliferation of STAG2 mutated but not wild-type bladder cancer and Ewing sarcoma cell lines. Restoration of STAG2 expression in a mutated bladder cancer model alleviates the dependency on STAG1. Thus, STAG1 and STAG2 act redundantly to support sister chromatid cohesion and cell survival. STAG1 represents a hardwired, context independent vulnerability of cancer cells carrying mutations in the major emerging tumor suppressorSTAG2. Exploiting synthetic lethal interactions to target recurrent cohesin mutations in cancer, e.g. by inhibiting STAG1, holds the promise for the development of selective therapeutics.
A protein phosphatase network controls the temporal and spatial dynamics of differentiation commitment in human epidermis
Authors: Mishra Ajay , Pisco Angela Oliveira , Oules Benedicte , Ly Tony , Liakath-Ali Kifayathullah , Walko Gernot , Viswanathan Priyalakshmi , Nijjher Jagdeesh , Dunn Sara-Jane , Lamond Angus I. , Watt Fiona M. 
Published: April 2017

AbstractEpidermal homeostasis depends on a balance between stem cell renewal and terminal differentiation. The transition between the two cell states, termed commitment, is poorly understood. Here we characterise commitment by integrating transcriptomic and proteomic data from disaggregated primary human keratinocytes held in suspension for up to 12h to induce differentiation. We find that cell detachment induces a network of protein phosphatases. The pro-commitment phosphatases – including DUSP6, PPTC7, PTPN1, PTPN13 and PPP3CA – promote differentiation by negatively regulating ERK MAPK and positively regulating AP1 transcription factors. Their activity is antagonised by concomitant upregulation of DUSP10. Boolean network modelling of phosphatase interactions identifies commitment as an inherently unstable biological switch between the stem and differentiated cell states. Furthermore, phosphatase expression is spatially regulated both in vivo and in vitro. We conclude that an auto-regulatory phosphatase network maintains epidermal homeostasis by controlling the onset and duration of commitment.
Comparative genomic evidence for self-domestication inHomo sapiens
Authors: Theofanopoulou Constantina , Gastaldon Simone , O’Rourke Thomas , Samuels Bridget D. , Messner Angela , Martins Pedro Tiago , Delogu Francesco , Alamri Saleh , Cedric Boeckx 
Published: April 2017

ABSTRACTThis study identifies and analyzes statistically significant overlaps between selective sweep screens in anatomically modern humans and several domesticated species. The results obtained suggest that (paleo-) genomic data can be exploited to complement the fossil record and support the idea of self-domestication inHomo sapiens,a process that likely intensified as our species populated its niche. Our analysis lends support to attempts to capture the “domestication syndrome” in terms of alterations to certain signaling pathways and cell lineages, such as the neural crest.