bluuebunny/crossref_metadata_2025_split huggingface dataset:
GlyMDB: Glycan Microarray Database and analysis toolset
Authors: Cao Yiwei , Park Sang-Jun , Mehta Akul Y , Cummings Richard D , Im Wonpil 
Published: December 2019

Abstract

Motivation
Glycan microarrays are capable of illuminating the interactions of glycan-binding proteins (GBPs) against hundreds of defined glycan structures, and have revolutionized the investigations of protein–carbohydrate interactions underlying numerous critical biological activities. However, it is difficult to interpret microarray data and identify structural determinants promoting glycan binding to glycan-binding proteins due to the ambiguity in microarray fluorescence intensity and complexity in branched glycan structures. To facilitate analysis of glycan microarray data alongside protein structure, we have built the Glycan Microarray Database (GlyMDB), a web-based resource including a searchable database of glycan microarray samples and a toolset for data/structure analysis.

Results
The current GlyMDB provides data visualization and glycan-binding motif discovery for 5203 glycan microarray samples collected from the Consortium for Functional Glycomics. The unique feature of GlyMDB is to link microarray data to PDB structures. The GlyMDB provides different options for database query, and allows users to upload their microarray data for analysis. After search or upload is complete, users can choose the criterion for binder versus non-binder classification. They can view the signal intensity graph including the binder/non-binder threshold followed by a list of glycan-binding motifs. One can also compare the fluorescence intensity data from two different microarray samples. A protein sequence-based search is performed using BLAST to match microarray data with all available PDB structures containing glycans. The glycan ligand information is displayed, and links are provided for structural visualization and redirection to other modules in GlycanStructure.ORG for further investigation of glycan-binding sites and glycan structures.

Availability and implementation
http://www.glycanstructure.org/glymdb.

Supplementary information
Supplementary data are available at Bioinformatics online.
Challenges in molecular diagnosis of X-linked Intellectual disability
Authors: De Luca Chiara , Race Valérie , Keldermans Liesbeth , Bauters Marijke , Van Esch Hilde 
Published: December 2019

Abstract

Background
Intellectual disability (ID) affects 1–3% of the Western population and is heterogeneous in origin. Mutations in X-linked genes represent 5–10% of ID in males. Fragile X syndrome, due to the silencing of the FMR1 gene, is the most common form of ID, with a prevalence of around 1:5000 males. Females are usually non- or mildly affected carriers, and in a few rare cases, the only gender affected. Array comparative genome hybridization (aCGH) and next-generation sequencing (NGS) have dramatically changed the nature of human genome analysis leading to the identification of new X-linked intellectual disability syndromes and disease-causing genes.

Sources of data
Original papers, reviews, guidelines and experiences of the diagnostic laboratories.

Areas of agreement
Family history and clinical examination still are essential to choose the appropriate diagnostic tests, including, a disease-specific genetic test, aCGH or FMR1 molecular analysis. If negative, NGS approaches like well-defined gene panels, whole exome, or even whole genome sequencing, are increasingly being used, improving diagnostics and leading to the identification of novel disease mechanisms.

Areas of controversy
The main challenge in the era of NGS is filtering and interpretation of the data generated by the analysis of a single individual. In X-linked cases, assessing pathogenicity is particularly challenging, even more when the variant is found to be inherited from a healthy carrier mother or when a heterozygous X-linked mutation is found in an impaired female.

Growing points
At present, variant interpretation remains a challenging task, especially in X-linked disorders. We review the main difficulties and propose a comprehensive overview that might aid in variant interpretation. Establishing a genetic diagnosis facilitates counseling and allows better delineation of clinical phenotypes.

Areas timely for developing research
To improve variant interpretation, there is need to refine in silico predictions with specific criteria for each gene, and to develop cost-effective functional tools, which can be easily transferred to diagnostics.
Peripartum management of hypertension: a position paper of the ESC Council on Hypertension and the European Society of Hypertension
Authors: Cífková Renata , Johnson Mark R , Kahan Thomas , Brguljan Jana , Williams Bryan , Coca Antonio , Manolis Athanasios , Thomopoulos Costas , Borghi Claudio , Tsioufis Costas , Parati Gianfranco , Sudano Isabella , McManus Richard J , van den Born Bert-Jan H , Regitz-Zagrosek Vera , de Simone Giovanni 
Published: December 2019

AbstractHypertensive disorders are the most common medical complications in the peripartum period associated with a substantial increase in morbidity and mortality. Hypertension in the peripartum period may be due to the continuation of pre-existing or gestational hypertension, de novo development of pre-eclampsia or it may be also induced by some drugs used for analgesia or suppression of postpartum haemorrhage. Women with severe hypertension and hypertensive emergencies are at high risk of life-threatening complications, therefore, despite the lack of evidence-based data, based on expert opinion, antihypertensive treatment is recommended. Labetalol intravenously and methyldopa orally are then the two most frequently used drugs. Short-acting oral nifedipine is suggested to be used only if other drugs or iv access are not available. Induction of labour is associated with improved maternal outcome and should be advised for women with gestational hypertension or mild pre-eclampsia at 37 weeks’ gestation. This position paper provides the first interdisciplinary approach to the management of hypertension in the peripartum period based on the best available evidence and expert consensus.
Arteria: An automation system for a sequencing core facility
Authors: Dahlberg Johan , Hermansson Johan , Sturlaugsson Steinar , Lysenkova Mariya , Smeds Patrik , Ladenvall Claes , Guimera Roman Valls , Reisinger Florian , Hofmann Oliver , Larsson Pontus 
Published: December 2019

Abstract

Background
In recent years, nucleotide sequencing has become increasingly instrumental in both research and clinical settings. This has led to an explosive growth in sequencing data produced worldwide. As the amount of data increases, so does the need for automated solutions for data processing and analysis. The concept of workflows has gained favour in the bioinformatics community, but there is little in the scientific literature describing end-to-end automation systems. Arteria is an automation system that aims at providing a solution to the data-related operational challenges that face sequencing core facilities.

Findings
Arteria is built on existing open source technologies, with a modular design allowing for a community-driven effort to create plug-and-play micro-services. In this article we describe the system, elaborate on the underlying conceptual framework, and present an example implementation. Arteria can be reduced to 3 conceptual levels: orchestration (using an event-based model of automation), process (the steps involved in processing sequencing data, modelled as workflows), and execution (using a series of RESTful micro-services). This creates a system that is both flexible and scalable. Arteria-based systems have been successfully deployed at 3 sequencing core facilities. The Arteria Project code, written largely in Python, is available as open source software, and more information can be found at https://arteria-project.github.io/ .

Conclusions
We describe the Arteria system and the underlying conceptual framework, demonstrating how this model can be used to automate data handling and analysis in the context of a sequencing core facility.
The effects of medicines availability and stock-outs on household’s utilization of healthcare services in Dodoma region, Tanzania
Authors: Kuwawenaruwa August , Wyss Kaspar , Wiedenmayer Karin , Metta Emmy , Tediosi Fabrizio 
Published: December 2019

Abstract
Low- and middle-income countries have been undertaking health finance reforms to address shortages of medicines. However, data are lacking on how medicine availability and stock-outs influence access to health services in Tanzania. The current study assesses the effects of medicine availability and stock-outs on healthcare utilization in Dodoma region, Tanzania. We conducted a cross-sectional study that combined information from households and healthcare facility surveys. A total of 4 hospitals and 89 public primary health facilities were surveyed. The facility surveys included observation, record review over a 3-month period prior to survey date, and interviews with key staff. In addition, 1237 households within the health facility catchment areas were interviewed. Data from the facility survey were linked with data from the household survey. Descriptive analysis and multivariate logistic regressions models were used to assess the effects of medicine availability and stock-outs on utilization patterns and to identify additional household-level factors associated with health service utilization. Eighteen medicines were selected as ‘tracers’ to assess availability more generally, and these were continuously available in ∼70% of the time in facilities across all districts over 3 months of review. The main analysis showed that household’s healthcare utilization was positively and significantly associated with continuous availability of all essential medicines for the surveyed facilities [odds ratio (OR) 3.49, 95% confidence interval (CI) 1.02–12.04; P = 0.047]. Healthcare utilization was positively associated with household membership in the community health insurance funds (OR 1.97, 95% CI 1.23–3.17; P = 0.005) and exposure to healthcare education (OR 2.75, 95% CI 1.84–4.08; P = 0.000). These results highlight the importance of medicine availability in promoting access to health services in low-income settings. Effective planning and medicine supply management from national to health facility level is an important component of quality health services.
‘Somethin’ ELSE’:1 African Discourses on ICSID and on ISDS—An Introduction
Authors: Mbengue Makane Moïse 
Published: December 2019

Abstract
This Special Issue of the ICSID Review offers for the first time in the history of the Review a comprehensive and complete overview of Africa's contribution to investor-State dispute settlement (ISDS), in general, and to the ICSID system, in particular. The present Introduction explores the various facets of Africa's contribution: Africa as a ‘catalyzer’ of the ICSID system; Africa as ‘crystallizer’ of investment jurisprudence; and, Africa as a ‘customizer’ of ISDS.
Determinants of Urogenital Schistosomiasis Among Pregnant Women and its Association With Pregnancy Outcomes, Neonatal Deaths, and Child Growth
Authors: Murenjekwa Wellington , Makasi Rachel , Ntozini Robert , Chasekwa Bernard , Mutasa Kuda , Moulton Lawrence H , Tielsch James M , Humphrey Jean H , Smith Laura E , Prendergast Andrew J , Bourke Claire D 
Published: December 2019

AbstractBackgroundSchistosoma haematobium is a parasitic helminth that causes urogenital pathology. The impact of urogenital schistosomiasis during pregnancy on birth outcomes and child growth is poorly understood.MethodsRisk factors for urogenital schistosomiasis were characterized among 4437 pregnant women enrolled in a cluster-randomized community-based trial in rural Zimbabwe. Infection was defined via urine microscopy (≥1 S. haematobium egg) and urinalysis (hematuria). Associations between infection and pregnancy outcomes were assessed in case-control analyses using conditional logistic regression. The association of maternal infection with birthweight and length-for-age Z scores (LAZ) at 1 and 18 months of age were assessed using generalized estimating equations.ResultsUrogenital schistosomiasis (egg positive and/or hematuria positive) was detected in 26.8% of pregnant women. Risk factors significantly associated with infection were maternal age, education, marital status, and religion; household drinking water source and latrine; study region; and season. Urogenital schistosomiasis was not significantly associated with adverse pregnancy outcomes (miscarriage, stillbirth, preterm, and small-for-gestational age), birthweight, neonatal death, or LAZ.ConclusionsIncluding pregnant women in antihelminthic treatment programs would benefit a large number of women in rural Zimbabwe. However, clearance of the low-intensity infections that predominate in this context is unlikely to have additive benefits for pregnancy outcomes or child growth.Clinical Trials RegistrationNCT01824940.
Assessing the performance of indicators during their life cycle: the mixed QUID method
Authors: Michel Philippe , Fraticelli Laurie , Parneix Pierre , Daucourt Valentin , Farges Olivier , Gasquet Isabelle , Occelli Pauline , Ray-Coquard Isabelle , Duclos Antoine ,   For the QUID Workgroup, Bertillot Hugo , Ceretti Alain-Michel , Daucourt Valentin , Delonca Julien , Duclos Antoine , El Khoury Carlos , Farges Olivier , Gasquet Isabelle , Lajonchere Jean-Patrick , Luigi Emmanuel , Michel Philippe , Millat Bertrand , Parneix Pierre , Ray-Coquard Isabelle , Woimant France , Aragona Estelle , Baron-Gutty Audrey , Fraticelli Laurie 
Published: December 2019

Abstract

Background
Quality indicators (QI) are mandatory in French hospitals. After a decade of use, the Ministry of Health set up an expert workgroup to enhance informed decision-making regarding currently used national QI, i.e. to propose a decision of withdrawing, revising or continuing their use. We report the development of an integrated method for a comprehensive appraisal of quality/safety indicators (QI) during their life cycle, for three purposes, quality improvement, public disclosure and regulation purposes. The method was tested on 10 national QI on use for up to 10 years to identify operational issues.

Methods
A modified Delphi technique to select relevant criteria and a development of a mixed evaluation method by the workgroup. A ‘real-life’ test on 10 national QI.

Results
Twelve criteria were selected for the appraisal of QI used for regulation goals, 11 were selected for hospital improvement and seven for public disclosure. The perceived feasibility and relevance were studied including hospital workers, patients and health authorities professionals; the scientific soundness of the indicator development phase was reviewed by analyzing reference documents; the metrological performance (limited to the discriminatory power and dynamics of change during the life cycle dimensions) was analyzed on the national datasets.
Applied to the 10 QI, the workgroup proposed to withdraw four of them and to modify or suspend the six others.

Conclusions
The value of the method was supported by the clear-cut conclusions and endorsement of the proposed decisions by the health authorities.
CamCutter: Impromptu Vision-Based Cross-Device Application Sharing
Authors: Hagiwara Takuma , Takashima Kazuki , Fjeld Morten , Kitamura Yoshifumi 
Published: December 2019

AbstractAs the range of handheld, mobile and desktop devices expands and worldwide demand for collaborative application tools increases, there is a growing need for higher speed impromptu cross-device application sharing to keep up with workplace requirements for on-site or remote collaborations. To address this, we have developed CamCutter, a cross-device interaction technique enabling a user to quickly select and share an application running on another screen using the camera of a handheld device. This technique can accurately identify the targeted application on a display using our adapted computer vision algorithm, system architecture and software implementation, allowing impromptu real-time and synchronized application sharing between devices. For desktop and meeting room set-ups, we performed a technical evaluation, measuring accuracy and speed of migration. For a single-user reading task and a collaborative composition task, we carried out a user study comparing our technique with commercial screen sharing applications. The results of this study showed both higher performance and preference for our system. Finally, we discuss CamCutter’s limitations and present insights for future vision-based cross-device application sharing.
An Insight into Gabapentin and Pregabalin in Scottish Prisoners
Authors: Deeb Shaza , Wylie Fiona M , Torrance Hazel J , Scott Karen S 
Published: December 2019

Abstract
The aim of this study was to evaluate the prevalence and abuse potential of antiepileptic drugs (AEDs) among prison populations in Scotland, UK. Participants consisted of all admitted and released prisoners over a 1 month period who consented to provide samples. Urine samples were collected and analyzed by liquid chromatography coupled with triple quadrupole tandem mass spectrometry using a method validated for the simultaneous quantification of 21 AEDs in urine. A total of 904 samples were collected. The samples were also screened for drugs of abuse by using point-of-care testing kits. A total of 18% of the samples were positive for AEDs. Gabapentin (GBP) was identified in 118 samples (13%) and pregabalin (PRG) in 32 samples (3.5%). Interestingly, 12 samples contained both drugs (1.3%). The concentrations ranged from 0.5 to 1,100 mg/L (median, 15 mg/L) for GBP and from 0.5 to 440 mg/L (median, 7.3 mg/L) for PRG. Four samples were found to have concentrations &gt;400 mg/L, two samples for GBP and two samples for PRG. These concentrations are at least 20 times above the median concentrations. Other AEDs detected were levetiracetam (four samples), vigabatrin (four samples), lamotrigine (three samples), valproic acid (three samples), carbamazepine (two samples) and topiramate (one sample). Illicit or non-prescribed drugs were detected in 81% of urine samples of which 80% were from admitted prisoners and 20% from released prisoners. Benzodiazepines, opiates and cannabis were the most frequently detected drugs. Other drugs found in positive AED samples were methadone (26%), cocaine (18%), buprenorphine (17%), amphetamines (4%), methamphetamines (4%) and barbiturates (4%). This study shows a high prevalence of AEDs within the Scottish prison system, primarily due to GBP and PRG; however, due to the anonymity of the sample collection, it is unknown if these are prescribed or illicit drug ingestions.
The Persistent Effect of Temporary Input Cost Advantages in Shipbuilding, 1850 to 1911
Authors: Hanlon W Walker 
Published: December 2019

AbstractCan temporary input cost advantages have a long-run impact on production patterns? I study this question in the context of shipbuilding from 1850 to 1911. Although North America was the dominant wood shipbuilding region in the mid-19th century, the introduction of metal shipbuilding shifted the industry to Britain, where metal inputs were less expensive. After 1890, Britain’s input price advantages largely disappeared but its dominant position in the industry persisted. I show that American shipbuilders exposed to British competition struggled to transition to metal shipbuilding and present evidence that the mechanism behind Britain’s persistent lead was the development of pools of skilled workers.
Antimicrobial resistance in sexually transmitted infections
Authors: Tien Vivian , Punjabi Chitra , Holubar Marisa K 
Published: December 2019

AbstractRationale for reviewInternational travel facilitates the spread of drug-resistant infections, including sexually transmitted infections (STIs). In 2016, the World Health Organization highlighted the global burden of ‘curable’ STIs, estimating 376 million new infections of gonorrhoea, chlamydia, syphilis and trichomoniasis annually, with considerable geographic variation in both the burden of disease and prevalence of resistance. Travelers’ risk of contracting and transmitting drug-resistant STIs depends in part on their geographic exposure. In this review, we describe the epidemiology of antimicrobial resistance (AMR) and the management of these four common STIs and Mycoplasma genitalium, an increasingly recognized cause of non-gonococcal urethritis.Key findingsMulti-drug and extensively drug resistant gonorrhoea strains have been associated with international spread, particularly in travelers returning from Southeast Asia. Chlamydia is the most common bacterial STI worldwide. Although in vitro resistance has been reported, surveillance data suggest that clinically significant resistance to macrolides and tetracyclines is rare. Macrolide resistance in syphilis is now endemic in much of the world but there is no documented penicillin resistance, which remains first-line therapy. Trichomoniasis is the most common non-viral STI worldwide. Although clinical failure after treatment occurs, resistance to metronidazole is thought to be uncommon. Mycoplasma genitalium exhibits intrinsic resistance to many antibiotics, and the prevalence of resistance to both first- and second-line regimens (macrolides and fluoroquinolones) is increasing worldwide, with limited alternative therapeutic options.RecommendationsInternational travelers are at risk for acquiring resistant STIs with limited therapeutic options. Improved diagnostics are urgently needed to improve AMR surveillance and the management of infected patients. As no vaccinations are currently available for these STIs, and pre-exposure prophylaxis is an area of active study with limited data, condom use is critical for prevention. Travel medicine providers should incorporate STI risk reduction counselling, with an emphasis on condom use, into the routine pre-travel consultation.
John Brown's Description of the Lake at Keswick: New Clues and Clarifications
Authors: Donaldson Christopher 
Published: December 2019

Abstract
This article reports on the discovery of hitherto undocumented printings of John Brown’s Description of the Lake at Keswick. Brown’s Description has long been recognised as a foundational document in the development of interest in the English Lake District during the eighteenth century. The history of the Description, however, has not been fully documented, and this lack of documentation has led to a number of mistaken assumptions. The present article, therefore, not only updates the bibliographical record, but also clarifies a few inaccuracies in previous discussions of Brown’s account. In the process, the article explains how the early versions of the Description add a new dimension to the reception history of the text and shift our understanding of the way the private circulation of unpublished print informed eighteenth-century appreciations of the Lakes region. The article includes an appendix, which presents a copy of the early printings of Brown’s text.
Prices of English Books at Auction c. 1680
Authors: Orr Leah 
Published: December 2019

Abstract
Scholars have noted the significance and spread of the second-hand book trade in seventeenth-century England, but so far little information about the books and their prices has been available. This essay examines the evidence from annotations to an early book auction catalogue relating to ten auctions that took place in London between 1676 and 1682, providing the prices for thousands of books. A comparison between the prices for which books sold at auction, and the prices of the same books new in the Term Catalogues in the decade prior to these auctions reveals that most of the relatively new books sold at auction for a considerable discount off their retail price. For older books, the prices primarily depended on condition and demand rather than the expense of producing the book or its age. This shows a turn towards a customer-driven pricing structure which has significant implications for how we understand the connection between book prices and readers in the late seventeenth century.