bluuebunny/crossref_metadata_2025_split huggingface dataset:
Understanding the Role and Impact of Effective Country and Community Leadership in Progress Toward the Global Plan
Authors: Lyons Charles , Pillay Yogan 
Published: April 2017

Abstract:
Individual leadership and leaders have played pivotal roles in the history of efforts to end the AIDS epidemic. The goal of this article is to reflect on and understand how leadership and leaders have impacted and enabled the success of the Global Plan Towards the Elimination of New HIV Infections among Children by 2015 and Keeping their Mothers Alive (Global Plan). To accomplish this goal, multiple interviews were conducted with individuals in positions of leadership who had been identified as people whose actions drove progress. Interviewees were selected from all levels of traditional hierarchies and sectors to provide a more complete account and representation of leadership, with a particular emphasis on the community, district, and country levels. The leaders interviewed provide insight into their work, motivations, and approaches to effective leadership. Through their experiences, they shed light on the strategies they used to drive changes in policy, programs, practice, and communities that allowed for progress toward the goals of the Global Plan. Leaders also identify future challenges and areas of improvement in the effort to end the AIDS epidemic that they feel require leadership and urgent action. In conclusion, this article identifies common characteristics of effective leadership and reflects on the experiences of individuals who are leaders in the effort to end the AIDS epidemic, and how their lessons learned can be applied to help realize future global public health goals.
Radiologist and Sonographer Interpretation Discrepancies for Biliary Sonographic Findings
Authors: Dawkins Adrian , George Nanditha , Ganesh Halemane , Ayoob Andres , Lee James , Nair Rashmi , Kiper Cassie , Duncan Kevin , Stevens Scott 
Published: April 2017

Purpose
The aim was to determine the discrepancy rate between the preliminary interpretation by sonographers and the final radiology interpretation for biliary sonographic findings.

Materials and Methods
Institutional review board approval was obtained. Four hundred consecutive right upper quadrant sonographer performed ultrasounds were reviewed retrospectively. Sonographers' worksheets were compared with the final radiology report. For the purposes of this project, only the biliary findings were compared and reviewed. Discrepant findings were reviewed by 5 ultrasound experts, and a majority vote sought to determine truth, sonographer worksheet findings, or radiologist report. The clinical impact of the discrepant findings was also evaluated.

Results
Of the 400 scans, there were 338 agreements and 62 discrepancies. The overall discrepancy rate was 15.5%. The most frequently contested discrepancy was the presence or absence of pericholecystic fluid n = 21. Sonographers (S) were deemed correct 8 times and radiologists (R) 13 times, denoted 8/13 (S/R). The overall split was 30/32 (S/R) with radiologists deemed correct 52% of the time and sonographers 48% of the time. Using a 1-sample proportion χ2 test with Yates' continuity correction, there were no statistically significant discrepancies between the 2 groups.

Conclusions
We observed an interpretation discrepancy rate of 15.5% with radiologists deemed correct slightly more frequently, although this did not meet statistical significance. Clinically impactful discrepant findings (6.5% of all discrepancies) were all correctly called by the radiologists. Both groups bring tremendous value to the ultrasound arena, and continued collaboration should be encouraged.

Purpose
The aim of this study was to determine the discrepancy rate that exists between the preliminary interpretation by sonographers and the subsequent final radiology interpretation for biliary sonographic findings.
The contribution of biological, mathematical, clinical, engineering and social sciences to combatting the West African Ebola epidemic
Authors: Whitty Christopher J. M. 
Published: April 2017

The tragic West African Ebola epidemic claimed many lives, but would have been worse still if scientific insights from many disciplines had not been integrated to create a strong technical response. Epidemiology and modelling triggered the international response and guided where response efforts were directed; virology, engineering and clinical science helped reduce deaths and transmission in and from hospitals and treatment centres; social sciences were key to reducing deaths from funerals and in the community; diagnostic and operational research made the response more efficient; immunology and vaccine research contributed to the final stages of the epidemic and will help prevent future epidemics. These varied scientific contributions had to be integrated into a combined narrative, communicated to policymakers to inform decisions, and used by courageous local and international responders in the field in real time. Not every area of science was optimal, and in particular, clinical trials of simple interventions such as fluid management were slow to be adopted and sharing of data was initially poor. This Ebola epidemic demonstrated how science can respond to a major emergency, but also has lessons for better responses in future infectious emergencies.
This article is part of the themed issue ‘The 2013–2016 West African Ebola epidemic: data, decision-making and disease control’.
Case study: design and implementation of training for scientists deploying to Ebola diagnostic field laboratories in Sierra Leone: October 2014 to February 2016
Authors: Logue Christopher H. , Lewis Suzanna M. , Lansley Amber , Fraser Sara , Shieber Clare , Shah Sonal , Semper Amanda , Bailey Daniel , Busuttil Jason , Evans Liz , Carroll Miles W. , Silman Nigel J. , Brooks Tim , Shallcross Jane A. 
Published: April 2017

As part of the UK response to the 2013–2016 Ebola virus disease (EVD) epidemic in West Africa, Public Health England (PHE) were tasked with establishing three field Ebola virus (EBOV) diagnostic laboratories in Sierra Leone by the UK Department for International Development (DFID). These provided diagnostic support to the Ebola Treatment Centre (ETC) facilities located in Kerry Town, Makeni and Port Loko. The Novel and Dangerous Pathogens (NADP) Training group at PHE, Porton Down, designed and implemented a pre-deployment Ebola diagnostic laboratory training programme for UK volunteer scientists being deployed to the PHE EVD laboratories. Here, we describe the training, workflow and capabilities of these field laboratories for use in response to disease epidemics and in epidemiological surveillance. We discuss the training outcomes, the laboratory outputs, lessons learned and the legacy value of the support provided. We hope this information will assist in the recruitment and training of staff for future responses and in the design and implementation of rapid deployment diagnostic field laboratories for future outbreaks of high consequence pathogens.
This article is part of the themed issue ‘The 2013–2016 West African Ebola epidemic: data, decision-making and disease control’.
Heterogeneities in the case fatality ratio in the West African Ebola outbreak 2013–2016
Authors: Garske Tini , Cori Anne , Ariyarajah Archchun , Blake Isobel M. , Dorigatti Ilaria , Eckmanns Tim , Fraser Christophe , Hinsley Wes , Jombart Thibaut , Mills Harriet L. , Nedjati-Gilani Gemma , Newton Emily , Nouvellet Pierre , Perkins Devin , Riley Steven , Schumacher Dirk , Shah Anita , Van Kerkhove Maria D. , Dye Christopher , Ferguson Neil M. , Donnelly Christl A. 
Published: April 2017

The 2013–2016 Ebola outbreak in West Africa is the largest on record with 28 616 confirmed, probable and suspected cases and 11 310 deaths officially recorded by 10 June 2016, the true burden probably considerably higher. The case fatality ratio (CFR: proportion of cases that are fatal) is a key indicator of disease severity useful for gauging the appropriate public health response and for evaluating treatment benefits, if estimated accurately. We analysed individual-level clinical outcome data from Guinea, Liberia and Sierra Leone officially reported to the World Health Organization. The overall mean CFR was 62.9% (95% CI: 61.9% to 64.0%) among confirmed cases with recorded clinical outcomes. Age was the most important modifier of survival probabilities, but country, stage of the epidemic and whether patients were hospitalized also played roles. We developed a statistical analysis to detect outliers in CFR between districts of residence and treatment centres (TCs), adjusting for known factors influencing survival and identified eight districts and three TCs with a CFR significantly different from the average. From the current dataset, we cannot determine whether the observed variation in CFR seen by district or treatment centre reflects real differences in survival, related to the quality of care or other factors or was caused by differences in reporting practices or case ascertainment.
This article is part of the themed issue ‘The 2013–2016 West African Ebola epidemic: data, decision-making and disease control’.
Key data for outbreak evaluation: building on the Ebola experience
Authors: Cori Anne , Donnelly Christl A. , Dorigatti Ilaria , Ferguson Neil M. , Fraser Christophe , Garske Tini , Jombart Thibaut , Nedjati-Gilani Gemma , Nouvellet Pierre , Riley Steven , Van Kerkhove Maria D. , Mills Harriet L. , Blake Isobel M. 
Published: April 2017

Following the detection of an infectious disease outbreak, rapid epidemiological assessment is critical for guiding an effective public health response. To understand the transmission dynamics and potential impact of an outbreak, several types of data are necessary. Here we build on experience gained in the West African Ebola epidemic and prior emerging infectious disease outbreaks to set out a checklist of data needed to: (1) quantify severity and transmissibility; (2) characterize heterogeneities in transmission and their determinants; and (3) assess the effectiveness of different interventions. We differentiate data needs into individual-level data (e.g. a detailed list of reported cases), exposure data (e.g. identifying where/how cases may have been infected) and population-level data (e.g. size/demographics of the population(s) affected and when/where interventions were implemented). A remarkable amount of individual-level and exposure data was collected during the West African Ebola epidemic, which allowed the assessment of (1) and (2). However, gaps in population-level data (particularly around which interventions were applied when and where) posed challenges to the assessment of (3). Here we highlight recurrent data issues, give practical suggestions for addressing these issues and discuss priorities for improvements in data collection in future outbreaks.This article is part of the themed issue ‘The 2013–2016 West African Ebola epidemic: data, decision-making and disease control’.
Diagnostic prediction tools for bacteraemia caused by 3rd generation cephalosporin-resistant Enterobacteriaceae in suspected bacterial infections: a nested case-control study
Authors: Rottier Wouter C. , van Werkhoven Cornelis H. , Bamberg Yara R.P. , Dorigo-Zetsma J. Wendelien , van de Garde Ewoudt M. , van Hees Babette C. , Kluytmans Jan A.J.W. , Kuck Emile M. , van der Linden Paul D. , Prins Jan M. , Thijsen Steven F.T. , Verbon Annelies , Vlaminckx Bart J.M. , Ammerlaan Heidi S.M. , Bonten Marc J.M. 
Published: April 2017

AbstractObjectivesCurrent guidelines for empirical antibiotic treatment poorly predict the presence of 3rd generation cephalosporin resistant Enterobacteriaceae (3GC-R EB) as a cause of infection, thereby increasing unnecessary carbapenem use. We aimed to develop diagnostic scoring systems to better predict the presence of 3GC-R EB as a cause of bacteraemia.MethodsA retrospective nested case-control study was performed that included patients ≥18 years in whom blood cultures were obtained and intravenous antibiotics were initiated. Each patient with 3GC-R EB bacteraemia was matched to four control infection episodes within the same hospital, based on blood culture date and onset location (community or hospital). Starting from 32 described clinical risk factors at infection onset, selection strategies were used to derive scoring systems for the probability of community- and hospital-onset 3GC-R EB bacteraemia.Results3GC-R EB bacteraemia occurred in 90 of 22,506 (0.4%) community-onset and in 82 of 8,110 (1.0%) hospital-onset infections, and these cases were matched to 360 community-onset and 328 hospital-onset control episodes, respectively. The derived community-onset and hospital-onset scoring system consisted of 6 and 9 predictors, respectively, with c-statistics of 0.807 (95% confidence interval 0.756-0.855) and 0.842 (0.794-0.887). With selected score cutoffs, the models identified 3GC-R EB bacteraemia with equal sensitivity as existing guidelines, but reduced the proportion of patients classified as at risk for 3GC-R EB bacteraemia (i.e. eligible for empiric carbapenem therapy) with 40% in patients with community-onset and 49% in patients with hospital-onset infection.ConclusionsThese prediction rules for 3GC-R EB bacteraemia may reduce unnecessary empiric carbapenem use.
The Developing Human Connectome Project: a Minimal Processing Pipeline for Neonatal Cortical Surface Reconstruction
Authors: Makropoulos Antonios , Robinson Emma C. , Schuh Andreas , Wright Robert , Fitzgibbon Sean , Bozek Jelena , Counsell Serena J. , Steinweg Johannes , Vecchiato Katy , Passerat-Palmbach Jonathan , Lenz Gregor , Mortari Filippo , Tenev Tencho , Duff Eugene P. , Bastiani Matteo , Cordero-Grande Lucilio , Hughes Emer , Tusor Nora , Tournier Jacques-Donald , Hutter Jana , Price Anthony N. , Teixeira Rui Pedro A. G. , Murgasova Maria , Victor Suresh , Kelly Christopher , Rutherford Mary A. , Smith Stephen M. , Edwards A. David , Hajnal Joseph V. , Jenkinson Mark , Rueckert Daniel 
Published: April 2017

AbstractThe Developing Human Connectome Project (dHCP) seeks to create the first 4-dimensional connectome of early life. Understanding this connectome in detail may provide insights into normal as well as abnormal patterns of brain development. Following established best practices adopted by the WU-MINN Human Connectome Project (HCP), and pioneered by FreeSurfer, the project utilises cortical surface-based processing pipelines. In this paper, we propose a fully automated processing pipeline for the structural Magnetic Resonance Imaging (MRI) of the developing neonatal brain. This proposed pipeline consists of a refined framework for cortical and sub-cortical volume segmentation, cortical surface extraction, and cortical surface inflation, which has been specifically designed to address considerable differences between adult and neonatal brains, as imaged using MRI. Using the proposed pipeline our results demonstrate that images collected from 465 subjects ranging from 28 to 45 weeks post-menstrual age (PMA) can be processed fully automatically; generating cortical surface models that are topologically correct, and correspond well with manual evaluations of tissue boundaries in 85% of cases. Results improve on state-of-the-art neonatal tissue segmentation models and significant errors were found in only 2% of cases, where these corresponded to subjects with high motion. Downstream, these surfaces will enhance comparisons of functional and diffusion MRI datasets, supporting the modelling of emerging patterns of brain connectivity.
“A different gut microbiome linked to inflammation found in cirrhotic patients with and without hepatocellular carcinoma”
Authors: Piñero Federico , Vazquez Martín , Baré Patricia , Rohr Cristian , Mendizabal Manuel , Sciara Mariela , Alonso Cristina , Fay Fabián , Silva Marcelo 
Published: April 2017

SUMMARYBackgroundNo specific microbiome in patients with hepatocellular carcinoma (HCC) has been reported to date.AimTo compare the gut microbiome found in cirrhotic patients with and without HCC.MethodsFrom 407 patients with Child Pugh A/B cirrhosis prospectively followed, 25 with HCC (cases) were matched with 25 without HCC (wo-HCC) in a 1:1 ratio according to age, gender, etiology, Child Pugh and severity of portal hypertension. In addition results were also compared with 25 healthy subjects. Faecal stool samples were collected noninvasively, aliquoted for DNA extraction and sequenced for the V3-V4 region of the microbial 16S rRNA (Illumina MiSeq Platform).ResultsThere were no significant clinical differences among cases and controls. We found a differential abundance in family members of Firmicutes with a 3-fold increased of Erysipelotrichaceae and a 5-fold decrease in family Leuconostocaceae in HCC when compared to wo-HCC controls. Genus Fusobacterium was found 5-fold decreased in HCC versus wo-HCC. The ratio bacteriodes/prevotella was increased in HCC due to the significant decrease in the genus prevotella. Genus Odoribacter and Butyricimonas were more differentialy abundant in HCC. This pattern has been previously associated with an inflammatory milieu with a putative increased activation of NOD-like receptor signalling pathways. A Random Forest model trained with differential abundant taxa correctly classifyed HCC individuals with an error of 22%.ConclusionsA pattern of microbiome linked to inflammation was observed in cirrhotic patients with HCC. These findings open the discussion whether or not microbiota has a physiopathologic role in HCC development in cirrhosis.
Efficient Information Contents Flow Down from Memory to Predict the Identity of Faces
Authors: Zhan Jiayu , Garrod Oliver G. B. , van Rijsbergen Nicola , Schyns Philippe G. 
Published: April 2017

AbstractIn the sciences of cognition, an influential idea is that the brain makes predictions about incoming sensory information to reduce inherent ambiguity. In the visual hierarchy, this implies that information content originating in memory–the identity of a face–propagates down to disambiguate incoming stimulus information. However, understanding this powerful prediction-for-recognition mechanism will remain elusive until we uncover the content of the information propagating down from memory. Here, we address this foundational limitation with a task ubiquitous to humans–familiar face identification. We developed a unique computer graphics platform that combines a generative model of random face identity information with the subjectivity of perception. In 14 individual participants, we reverse engineered the predicted information contents propagating down from memory to identify 4 familiar faces. In a follow-up validation, we used the predicted face information to synthesize the identity of new faces and confirmed the causal role of the predictions in face identification. We show these predictions comprise both local 3D surface patches, such as a particularly thin and pointy nose combined with a square chin and a prominent brow, or more global surface characteristics, such as a longer or broader face. Further analyses reveal that the predicted contents are efficient because they represent objective features that maximally distinguish each identity from a model norm. Our results reveal the contents that propagate down the visual hierarchy from memory, showing this coding scheme is efficient and compatible with norm-based coding, with implications for mechanistic accounts of brain and machine intelligence.
A versatile compressed sensing scheme for faster and less phototoxic 3D fluorescence microscopy
Authors: Woringer Maxime , Darzacq Xavier , Zimmer Christophe , Mir Mustafa 
Published: April 2017

AbstractThree-dimensional fluorescence microscopy based on Nyquist sampling of focal planes faces harsh trade-offs between acquisition time, light exposure, and signal-to-noise. We propose a 3D compressed sensing approach that uses temporal modulation of the excitation intensity during axial stage sweeping and can be adapted to fluorescence microscopes without hardware modification. We describe implementations on a lattice light sheet microscope and an epifluorescence microscope, and show that images of beads and biological samples can be reconstructed with a 5-10 fold reduction of light exposure and acquisition time. Our scheme opens a new door towards faster and less damaging 3D fluorescence microscopy.OCIS codes:(110.1758) Computational imaging; (170.2520) Fluorescence microscopy; (170.6900) Three-dimensional microscopy.
Cataloguing over-expressed genes in Epstein Barr Virus immortalized lymphoblastoid cell lines through consensus analysis of PacBio transcriptomes corroborates hypomethylation of chromosome 1
Authors: Chakraborty Sandeep 
Published: April 2017

AbstractThe ability of Epstein Barr Virus (EBV) to transform resting cell B-cells into immortalized lymphoblastoid cell lines (LCL) provides a continuous source of peripheral blood lymphocytes that are used to model conditions in which these lymphocytes play a key role. Here, the PacBio generated transcriptome of three LCLs from a parent-daughter trio (SRAid:SRP036136) provided by a previous study [1] were analyzed using a kmer-based version of YeATS (KEATS). The set of over-expressed genes in these cell lines were determined based on a comparison with the PacBio transcriptome of twenty tissues provided by another study (hOPTRS) [2]. MIR155 long non-coding RNA (MIR155HG), Fc fragment of IgE receptor II (FCER2), T-cell leukemia/lymphoma 1A (TCL1A), and germinal center associated signaling and motility (GCSAM) were genes having the highest expression counts in the three LCLs with no expression in hOPTRS. Other over-expressed genes, having low expression in hOPTRS, were membrane spanning 4-domains A1 (MS4A1) and ribosomal protein S2 pseudogene 55 (RPS2P55). While some of these genes are known to be over-expressed in LCLs, this study provides a comprehensive cataloguing of such genes. A recent work involving a patient with EBV-positive large B-cell lymphoma was ‘unusually lacking various B-cell markers’, but over-expressing CD30 [3] - a gene ranked 79 among uniquely expressed genes here. Hypomethylation of chromosome 1 observed in EBV immortalized LCLs [4, 5] is also corroborated here by mapping the genes to chromosomes. Extending previous work identifying un-annotated genes [6], 80 genes were identified which are expressed in the three LCLs, not in hOPTRS, and missing in the GENCODE, RefSeq and RefSeqGene databases. KEATS introduces a method of determining expression counts based on a partitioning of the known annotated genes, has runtimes of a few hours on a personal workstation and provides detailed reports enabling proper debugging.