bluuebunny/crossref_metadata_2025_split huggingface dataset:
Analysis in case–control sequencing association studies with different sequencing depths
Authors: Chen Sixing , Lin Xihong 
Published: October 2018

SummaryWith the advent of next-generation sequencing, investigators have access to higher quality sequencing data. However, to sequence all samples in a study using next generation sequencing can still be prohibitively expensive. One potential remedy could be to combine next generation sequencing data from cases with publicly available sequencing data for controls, but there could be a systematic difference in quality of sequenced data, such as sequencing depths, between sequenced study cases and publicly available controls. We propose a regression calibration (RC)-based method and a maximum-likelihood method for conducting an association study with such a combined sample by accounting for differential sequencing errors between cases and controls. The methods allow for adjusting for covariates, such as population stratification as confounders. Both methods control type I error and have comparable power to analysis conducted using the true genotype with sufficiently high but different sequencing depths. We show that the RC method allows for analysis using naive variance estimate (closely approximates true variance in practice) and standard software under certain circumstances. We evaluate the performance of the proposed methods using simulation studies and apply our methods to a combined data set of exome sequenced acute lung injury cases and healthy controls from the 1000 Genomes project.
Sensitive Period for Cognitive Repurposing of Human Visual Cortex
Authors: Kanjlia Shipra , Pant Rashi , Bedny Marina 
Published: October 2018

Abstract
Studies of sensory loss are a model for understanding the functional flexibility of human cortex. In congenital blindness, subsets of visual cortex are recruited during higher-cognitive tasks, such as language and math tasks. Is such dramatic functional repurposing possible throughout the lifespan or restricted to sensitive periods in development? We compared visual cortex function in individuals who lost their vision as adults (after age 17) to congenitally blind and sighted blindfolded adults. Participants took part in resting-state and task-based fMRI scans during which they solved math equations of varying difficulty and judged the meanings of sentences. Blindness at any age caused “visual” cortices to synchronize with specific frontoparietal networks at rest. However, in task-based data, visual cortices showed regional specialization for math and language and load-dependent activity only in congenital blindness. Thus, despite the presence of long-range functional connectivity, cognitive repurposing of human cortex is limited by sensitive periods.
Silent Synapse Unsilencing in Hippocampal CA1 Neurons for Associative Fear Memory Storage
Authors: Wang Yao , Liu Yu-zhang , Wang Lidan , Tang Wei , Wang Zhiru 
Published: October 2018

Abstract
Clarifying learning-induced synaptic plasticity in hippocampal circuits is critical for understanding hippocampal mechanisms of memory acquisition and storage. Many in vitro studies have demonstrated learning-associated plasticity at hippocampal synapses. However, as a neural basis of memory encoding, the nature of synaptic plasticity underlying hippocampal neuronal responses to memorized stimulation remains elusive. Using in vivo whole-cell recording in anaesthetized adult rats and mice, we investigated synaptic activity of hippocampal CA1 pyramidal cells (PCs) in response to a flash of visual stimulation as the conditioned stimulus (CS) in associative fear conditioning. We found that shortly (<3 days) after conditioning, excitatory synaptic responses and spiking responses to the flash CS emerged in a large number (~70%) of CA1 PCs, a neuronal population previously unresponsive to the flash before conditioning. The learning-induced CA1 excitatory responsiveness was further indicated to result from postsynaptic unsilencing at flash-associated silent synapses, with NMDA receptor-gated responses we recently reported in naive animals. Our findings suggest that associative fear learning can induce excitatory responsiveness to the memorized CS in a large population of CA1 neurons, via a process of postsynaptic unsilencing at CA1 silent synapses, which may be critical for hippocampal acquisition and storage of associative memory.
Age validation of juvenile cod in the Western Baltic Sea
Authors: McQueen Kate , Hrabowski Josef , Krumme Uwe 
Published: October 2018

Abstract
The methods routinely used to estimate fish age are often un-validated and susceptible to errors and uncertainties. Despite numerous attempts, age determination of western Baltic cod (WBC, Gadus morhua) using otoliths is still unreliable, predominantly due to inconsistent interpretation of the first translucent zone (TZ). Length-frequencies of undersized (&lt;38 cm) cod collected during 2013–2016 from pound nets near Fehmarn Island were analysed to understand TZ formation patterns. A clear minimum separated two cohorts within the length-frequency samples every year. The length-frequency information was combined with otolith edge analysis to observe the development of TZs in age-0 and age-1 cod otoliths, and to validate the timing of TZ formation, which was consistently completed between September and December. Mean TZ diameters of 4 917 juvenile cod otoliths varied between cohorts (mean diameters of the first TZ: 2.0 ± 0.5 mm; second TZ: 3.9 mm ± 0.5) and TZ diameter variation was found to be related to individual growth rate. The timing of formation of the first TZ was positively related to water temperature, and was confirmed as a “summer ring” rather than a “winter ring”. TZ formation and shallow-water occupancy suggest an influence of peak summer water temperatures on WBC ecology. An age reading guide for juvenile WBC otoliths is provided.
Noma—knowledge and practice competence among primary healthcare workers: a cross-sectional study in Burkina Faso
Authors: Brattström-Stolt Louise , Funk Tjede , Sié Ali , Ndiaye Charlotte , Alfvén Tobias 
Published: October 2018

Abstract

Background
Noma is a quickly progressing, neglected opportunistic infection. It starts in the mouth as an oral lesion but can relatively quickly develop into extensive facial destruction and lead to death if not treated in time. This study aims to shed light on primary healthcare workers’ practice competences in working with and knowledge of noma.

Methods
A structured questionnaire using questions and case scenarios was filled out by 76 healthcare workers in Burkina Faso. Half of the nurses included in this study participated in a 2-day noma training. Data were analysed descriptively and Fisher’s exact test was used to study differences between occupational groups using Stata.

Results
Most healthcare workers reported having examined the mouth of children with diseases predisposing to noma. The total practice competence was poor, with almost 70% having suboptimal or very low competences. However, competences varied between different stages of noma disease. Knowledge scores varied between occupational groups. The majority of nurses and odontostomatology specialist nurses had optimal or good knowledge of noma. Significant differences in knowledge and practice competence were found between nurses who attended a 2-day training course on noma and those who did not.

Conclusions
Health care workers in this study had quite poor practice competences in managing noma. The knowledge scores of these health workers were moderate. It is important for healthcare workers to be able to identify noma patients at an early stage, as at this point the disease can still be completely reversed.
Neonatal Conjunctivitis Caused by Neisseria cinerea: A Case of Mistaken Identity
Authors: Fiorito Theresa M , Noor Asif , Silletti Rodger , Krilov Leonard R 
Published: October 2018

AbstractWe report a case of a 3-day-old boy with Neisseria cinerea conjunctivitis, originally misidentified as Neisseria gonorrhoeae conjunctivitis. Neonates are at increased risk for disseminated gonococcal infection, and physicians should be cognizant of N cinerea and its potential to be mistaken for N gonorrhoeae.
Machine learning, template matching, and the International Tracing Service digital archive: Automating the retrieval of death certificate reference cards from 40 million document scans
Authors: Lee Benjamin Charles Germain 
Published: October 2018

AbstractScattered throughout the International Tracing Service (ITS) digital archive, one of the largest and most heterogeneous collections of Holocaust-related material, are hundreds of thousands of reference cards to official death certificates recording a fraction of individuals who perished within concentration camps. These cards represent the most comprehensive collection of digital material pertaining to these death certificates issued by Sonderstandesamt Arolsen, a German civil registry office. However, the reference cards can only be found dispersed throughout the Central Name Index (CNI), ITS’s 46+ million-card finding aid that is indexed only by name. Consequently, aggregating the death certificate reference cards for research requires an intractable manual search. I adopt template matching and machine learning to automate the retrieval of these cards from the ITS digital archive. I demonstrate the efficacy of my method on a test set of 22,117 hand-classified cards, reporting 100% precision and 100% recall. Running this algorithm on 39,967,358 scans of cards from the CNI, I identify 312,183 death certificate reference cards in 13.75 days of elapsed real runtime on a personal computer with only a single, $600 Intel processor. Finally, I demonstrate that this approach can be generalized to many different card types within the CNI, showing great promise for application to other archives.
An introduction to the functioning process of embedded paratext of digital literature: Technoeikon of digital poetry
Authors: Shanmugapriya T , Menon Nirmala , Campbell Andy 
Published: October 2018

AbstractThe recent digital-born electronic literature has heterogeneous components such as kinetic texts, kinetic images, graphical designs, sounds, and videos. These digital components are embedded with the main text as the paratext of print and digital works such as preface, author’s name, illustrations, and title. However, the comparative study between paratext and embedded paratext of electronic literature shows the different strategic patterns and functions of these entities. We discuss the conceptual framework of illuminant devices of paratexts and propose a new term technoeikon to recognize the functions of embedded literary artifact in digital literary works. We examine the critical construction of new term technoeikon which has a unique characteristic that makes electronic literary works different from print literature. This essay reviews the cyclical process of technoeikon from the historical perspective of pre-print culture and print culture and acknowledges technoeikon as inherited from our tradition. Due to digital contrivances, technoeikon takes a new expression as performing in digital ecology which is different from our traditional analog. This article presents a case study on Andy Campbell's (2007b) Dim O'Gauble. Also, Campbell responds to the interpretation of new term technoeikon in the fourth section of the essay.
Automatic profiling of L2-simplified texts: Identifying discriminate features of linguistic proficiency
Authors: Zarco-Tejada Maria Angeles 
Published: October 2018

AbstractWe describe the first wide results of the linguistic profiling of the Common European Framework of Reference (CEFR)-levelled English Corpus (CLEC), a corpus built up for Natural Language Processing purposes. The CLEC is a proficiency-levelled English corpus that covers A1, A2, B1, B2, and C1 CEFR levels and that has been built up to train statistic models for automatic proficiency assessment. We describe not only the main aspects of the corpus development but also display the linguistic features and the statistic results for levels A2, B1, and B2 written examples, carried out automatically. We show how raw text, lexical, morphosyntactic, or syntactic statistic outcomes can help to identify levels of proficiency, to test teaching materials accurate proficiency classification, to provide computable support to new text proficiency validation, and to specify level boundaries. In fact, upper levels strengthen proficiency by showing higher outcomes of lexical and syntactic complexity. This analysis validates the use of automatic tools for proficiency level identification based on lexical and syntactic data, whereas morphosyntactic features strengthen competence-level distinctions. Finally, we suggest that these results are a first step onto the CEFR-levelled automatic assessment of new texts.
Abominable KK Failures
Authors: Dorst Kevin 
Published: October 2018

Abstract
KK is the thesis that if you can know p, you can know that you can know p. Though it’s unpopular, a flurry of considerations has recently emerged in its favour. Here we add fuel to the fire: standard resources allow us to show that any failure of KK will lead to the knowability and assertability of abominable indicative conditionals of the form ‘If I don’t know it, p’. Such conditionals are manifestly not assertable—a fact that KK defenders can easily explain. I survey a variety of KK-denying responses and find them wanting. Those who object to the knowability of such conditionals must either (i) deny the possibility of harmony between knowledge and belief, or (ii) deny well-supported connections between conditional and unconditional attitudes. Meanwhile, those who grant knowability owe us an explanation of such conditionals’ unassertability—yet no successful explanations are on offer. Upshot: we have new evidence for KK.
The temporal relationship between cancer and adult onset anti-transcriptional intermediary factor 1 antibody–positive dermatomyositis
Authors: Oldroyd Alexander , Sergeant Jamie C , New Paul , McHugh Neil J , Betteridge Zoe , Lamb Janine A , Ollier William E , Cooper Robert G , Chinoy Hector ,   UKMyoNet, Ahmed Yasmeen , Armstrong Raymond , Bernstein Robert , Black Carol , Bowman Simon , Bruce Ian , Butler Robin , Carty John , Chattopadhyay Chandra , Chelliah Easwaradhas , Clarke Fiona , Dawes Peter , Devlin Joseph , Edwards Christopher , Emery Paul , Fordham John , Fraser Alexander , Gaston Hill , Gordon Patrick , Griffiths Bridget , Gunawardena Harsha , Hall Frances , Harrison Beverley , Hay Elaine , Horden Lesley , Isaacs John , Jones Adrian , Kamath Sanjeet , Kennedy Thomas , Kitas George , Klimiuk Peter , Knights Sally , Lambert John , Lanyon Peter , Laxminarayan Ramasharan , Lecky Bryan , Luqmani Raashid , Marks Jeffrey , Martin Michael , McGonagle Dennis , McHugh Neil , McKenna Francis , McLaren John , McMahon Michael , McRorie Euan , Merry Peter , Miles Sarah , Miller James , Nicholls Anne , Nixon Jennifer , Ong Voon , Packham John , Pipitone Nicolo , Plant Michael , Pountain Gillian , Pullar Thomas , Roberts Mark , Sanders Paul , Scott David , Scott David , Shadforth Michael , Sheeran Thomas , Srinivasan Arul , Swinson David , Teh Lee-Suan , Webley Michael , Williams Brian , Winer Jonathan 
Published: October 2018

Abstract

Objectives
To characterize the 10 year relationship between anti-transcriptional intermediary factor 1 antibody (anti-TIF1-Ab) positivity and cancer onset in a large UK-based adult DM cohort.

Methods
Data from anti-TIF1-Ab-positive/-negative adults with verified diagnoses of DM from the UK Myositis Network register were analysed. Each patient was followed up until they developed cancer. Kaplan–Meier methods and Cox proportional hazard modelling were employed to estimate the cumulative cancer incidence.

Results
Data from 263 DM cases were analysed, with a total of 3252 person-years and a median 11 years of follow-up; 55 (21%) DM cases were anti-TIF1-Ab positive. After 10 years of follow-up, a higher proportion of anti-TIF1-Ab-positive cases developed cancer compared with anti-TIF1-Ab-negative cases: 38% vs 15% [hazard ratio 3.4 (95% CI 2.2, 5.4)]. All the detected malignancy cases in the anti-TIF1-Ab-positive cohort occurred between 3 years prior to and 2.5 years after DM onset. No cancer cases were detected within the following 7.5 years in this group, whereas cancers were detected during this period in the anti-TIF1-Ab-negative cases. Ovarian cancer was more common in the anti-TIF1-Ab-positive vs -negative cohort: 19% vs 2%, respectively (P < 0.05). No anti-TIF1-Ab-positive case <39 years of age developed cancer, compared with 21 (53%) of those ≥39 years of age.

Conclusion
Anti-TIF1-Ab-positive-associated malignancy occurs exclusively within the 3 year period on either side of DM onset, the risk being highest in those ≥39 years of age. Cancer types differ according to anti-TIF1-Ab status, and this may warrant specific cancer screening approaches.
Acute Kidney Injury Secondary to Severe Hand, Foot and Mouth Disease Caused by Enterovirus-A71: Hypertension Is a Common
Authors: Xu Yao , Wu Yang Fang , Luo Huang Huang , Zhang Dong Dong , Wu Yue , Hu Peng 
Published: October 2018

AbstractHand, foot and mouth disease (HFMD) is a common infectious disease among children, caused primarily by human enterovirus-A71 (EV-A71) and coxsackievirus-A16 (CV-A16). To date, only two case reports mention that renal involvement can be secondary to or coexisting with CV-A16-associated HFMD. In the present report, we describe a 10-year-old girl who was infected with EV-A71 and subsequently developed a definite acute kidney injury (AKI), mainly based on the characteristic rash, virus isolation, eyelid edema, hypertension, decreased urine output, mild proteinuria and impaired renal function. She was treated with intravenous ribavirin, immunoglobulin, oral administration of nifedipine and ramipril. After 7 days of intensive observations, she recovered fully. Hypertension is a common feature in both HFMD and AKI. On one hand, hypertension serves as a risk factor for severe HFMD; on the other hand, hypertension induces AKI onset and is also deteriorated by AKI.
Evidence-Based Improvisation: Facing the Challenges of Cervical Cancer Care in Uganda
Authors: Swanson Megan , Ueda Stefanie , Chen Lee-May , Huchko Megan J. , Nakisige Carol , Namugga Jane 
Published: October 2018

(Abstracted from Gynecol Oncol Rep 2018;24:30–35)
In 2012, cervical cancer accounted for more than a half million new cases and 250,000 deaths worldwide. This cancer is the most common malignancy in Uganda and is responsible for the greatest cancer-related mortality among women in that country.
Developing the Agile Implementation Playbook for Integrating Evidence-Based Health Care Services Into Clinical Practice
Authors: Boustani Malaz A. , van der Marck Marjolein A. , Adams Nadia , Azar Jose M. , Holden Richard J. , Vollmar Horst C. , Wang Sophia , Williams Christopher , Alder Catherine , Suarez Shelley , Khan Babar , Zarzaur Ben , Fowler Nicole R. , Overley Ashley , Solid Craig A. , Gatmaitan Alfonso 
Published: October 2018

Problem
Despite the more than $32 billion the National Institutes of Health has invested annually, evidence-based health care services are not reliably implemented, sustained, or distributed in health care delivery organizations, resulting in suboptimal care and patient harm. New organizational approaches and frameworks that reflect the complex nature of health care systems are needed to achieve this goal.

Approach
To guide the implementation of evidence-based health care services at their institution, the authors used a number of behavioral theories and frameworks to develop the Agile Implementation (AI) Playbook, which was finalized in 2015. The AI Playbook leverages these theories in an integrated approach to selecting an evidence-based health care service to meet a specific opportunity, rapidly implementing the service, evaluating its fidelity and impact, and sustaining and scaling up the service across health care delivery organizations. The AI Playbook includes an interconnected eight-step cycle: (1) identify opportunities; (2) identify evidence-based health care services; (3) develop evaluation and termination plans; (4) assemble a team to develop a minimally viable service; (5) perform implementation sprints; (6) monitor implementation performance; (7) monitor whole system performance; and (8) develop a minimally standardized operating procedure.

Outcomes
The AI Playbook has helped to improve care and clinical outcomes for intensive care unit survivors and is being used to train clinicians and scientists in AI to be quality improvement advisors.

Next Steps
The authors plan to continue disseminating the details of the AI Playbook and illustrating how health care delivery organizations can successfully leverage it.
Developing a Culture of Mentorship to Strengthen Academic Medical Centers
Authors: Choi Augustine M.K. , Moon Jennifer E. , Steinecke Ann , Prescott John E. 
Published: October 2018

Mentorship is central to academic medicine and its missions, and it has long played a critical role in the training and career development of physicians and scientists. A growing body of literature has documented the positive impact of mentorship on various outcomes, including research productivity, academic promotion, faculty retention, and career satisfaction. These benefits span academic medical centers’ missions and have the potential to enhance biomedical research, patient care, education, and faculty diversity and leadership.
In this Invited Commentary, the authors argue that a dynamic culture of mentorship is essential to the success of academic medical centers and should be elevated to the level of a major strategic priority. This culture of mentorship would capitalize on an institution’s intellectual resources and seek to develop leaders in biomedical discovery, patient care, and education. The bidirectional transmission of knowledge between mentors and mentees, through both formal programs and informal relationships, can foster the growth of faculty members needed to meet the complex challenges currently confronting medical schools and teaching hospitals.
Developing a culture of mentorship requires a strong commitment by leaders at all levels to nurture the next generation of physicians and scientists as well as grassroots efforts by trainees and faculty to seek out and create mentorship opportunities. The authors conclude by outlining possible mechanisms and incentives for elevating mentorship to the level of a strategic priority to strengthen academic medical centers across their missions.