bluuebunny/crossref_metadata_2025_split huggingface dataset:
Structural feature of N-glycans of bamboo shoot glycoproteins: useful source of plant antigenic N-glycans
Authors: Tanabe Chinatsu , Furuta Kaori , Maeda Megumi , Kimura Yoshinobu 
Published: May 2017

Abstract
An effective method to prepare plant complex type (PCT) N-glycans in large amounts has been required to evaluate their immunological activity. In this study, we found that glycoproteins in bamboo shoots predominantly carry PCT N-glycans including the Lewis a epitope-containing ones, suggesting that bamboo shoot is an excellent source for the plant antigenic glycans to synthesize immunoactive neoglycopolymers.
Genetic screening revealed usher syndrome in a paediatric Chinese patient
Authors: Qu Chunyan , Liang Fenghe , Long Qin , Zhao Min , Shang Haiqiong , Fan Lynn , Wang Li , Yan Denise , Liu Xuezhong 
Published: May 2017

Introduction:
Usher syndrome (USH) is the most common cause of hereditary deaf-blindness. Three clinical subtypes have been classified. USH type I is the most severe subtype characterized by congenital severe-to-profound hearing loss, retinitis pigmentosa and vestibular dysfunction.

Methods:
One family was analyzed and the analysis included the combination of a custom capture/next-generation sequencing panel of 180 known deafness gene, Sanger sequencing and bioinformatics approaches.

Results:
Compound heterozygous mutations in the MYO7A gene: a known missense mutation c.494C > T (p.Thr165Met) and a novel missense mutation c.6113G > A (p.Gly2038Glu) were identified in a proband. This Chinese hearing-impaired child was misdiagnosed as non-syndromic hearing loss which was later changed to the diagnosis of USH type I after comprehensive audiometric, vestibular and ophthalmological examinations at 9 years old.

Conclusions:
Due to the features of genetic heterogeneity and variation in clinical manifestation, molecular diagnosis and ophthalmological examinations by skilled ophthalmologists with knowledge of USH should be suggested as a routine assessment which may improve the accuracy and reliability of etiological diagnosis for hearing loss.
CCQM-K103 key comparison melanine in milk powder
Authors: Li Xiuqin , Zhang Qinghe , Li Hongmei , Li Mengwan , Wong Siu-kay , Lee Foo-Wing , Kakoulides Elias , Naujaus Evaldas , Fernandes-Whaley Maria , Prevoo-Franzsen Des , Quinn Laura , Pookrod Preeyaporn , Konopelko Leonid 
Published: May 2017

Under the Comité Consultatif pour la Quantité de Matière (CCQM), a key comparison, CCQM-K103, was coordinated by the National Institute of Metrology (NIM) and Government Laboratory, Hong Kong, China (GLHK). The comparison was designed to demonstrate NMIs/DIs ability to analyze traces of melamine in milk and milk powder at concentration levels resulting from requirements for food safety. Seven NMIs or DIs participated in the comparison. Final reference value (KCRV) is 0.286 mg/kg, with standard uncertainty of the median as 0.011 mg/kg (3.8 %). The k-factor for the estimation of the expanded uncertainty was chosen as k = 2.57 ( t (0.05;5) ), thus the expanded uncertainty is 0.028 mg/kg (9.8%). The degrees of equivalence with melamine in milk powder KCRV for each participant were reported. The measurement results and degrees of equivalence should be indicative of the performance of a laboratory's measurement capability for IDMS in determining mass fractions in the range from 0.1 to 5.0 mg/kg of analytes with low molar mass (range 50-300 Da) with high polarity (pKow > -2.0) in milk and milk products. Extension to other analytes and matrices should be applied with care since there is a close linkage to other relevant parameters as e.g. sample preparation procedures (liquid/liquid extraction, SPE clean-up) and analytical separation techniques (e.g., GC-MS, LC-MS/MS etc).

Main text

To reach the main text of this paper, click on Final Report. Note that this text is that which appears in Appendix B of the BIPM key comparison database kcdb.bipm.org/.
The final report has been peer-reviewed and approved for publication by the CCQM, according to the provisions of the CIPM Mutual Recognition Arrangement (CIPM MRA).
Coriolanus
Authors: Wells Stanley 
Published: May 2017

Abstract
For what is believed to be his last tragedy, Shakespeare turned once again to Ancient Rome. He chose to write a political and personal drama about a great Roman warrior of the 5th century bc whose personal fate is bound up with that of his nation. Shakespeare depicts a unique, psychologically complex individual caught up in a web of difficult personal relationships that reflect basic human situations. ‘Coriolanus’ describes the play as knotty, harsh, austere, intellectually rigorous, and resolutely unlyrical, where the dialogue is leavened with humour, sometimes conscious on the part of the speakers, but no less frequently oblique and ironical.
MarDRe: efficient MapReduce-based removal of duplicate DNA reads in the cloud
Authors: Expósito Roberto R , Veiga Jorge , González-Domínguez Jorge , Touriño Juan 
Published: May 2017

Abstract

Summary
This article presents MarDRe, a de novo cloud-ready duplicate and near-duplicate removal tool that can process single- and paired-end reads from FASTQ/FASTA datasets. MarDRe takes advantage of the widely adopted MapReduce programming model to fully exploit Big Data technologies on cloud-based infrastructures. Written in Java to maximize cross-platform compatibility, MarDRe is built upon the open-source Apache Hadoop project, the most popular distributed computing framework for scalable Big Data processing. On a 16-node cluster deployed on the Amazon EC2 cloud platform, MarDRe is up to 8.52 times faster than a representative state-of-the-art tool.

Availability and implementation
Source code in Java and Hadoop as well as a user’s guide are freely available under the GNU GPLv3 license at http://mardre.des.udc.es.
Sixteen lessons from a 40-year quest to understand the mysterious life of the grey triggerfish
Authors: Gerlotto François 
Published: May 2017

Abstract
Fish stock assessments based solely on energy flow through the ecosystem are not good predictors of population dynamics. To accurately forecast the response of populations within one or more ecological regimes, consideration must be given to non-trophic mechanisms allowing interactions inside the system, and fish behaviour in response to changes in their habitats. The example of the grey triggerfish (Balistes capriscus) in West Africa shows that fisheries biology is unable to model satisfactorily the life of a fish population. The Ecosystem Approach to Fisheries improves the models but does not overcome this fundamental limitation. Data from direct observations of fish biology and behaviour must be added to the catch and environmental data to help to design energetic-cybernetic models in order to anticipate non-linear and chaotic dynamics. This requires adding data collected by fishers (e.g. underwater acoustics) to scientific data bases, conceiving environmental indicators (e.g. habitat), and using scenarios to anticipate the reactions of populations to regime shifts. It also requires a good understanding of the population structures and strategies. We developed the concept of “pelagic metapopulation” which, through comparative analysis with the jack mackerel (Trachurus murphyi), allowed us to propose a hypothesis explaining the history of the grey triggerfish population.
Antimicrobial Stewardship Lessons From Mupirocin Use and Resistance in Methicillin-Resitant Staphylococcus Aureus
Authors: Peterson Lance R. , Samia Noelle I. , Skinner Andrew M , Chopra Amit , Smith Becky 
Published: May 2017

AbstractBackgroundThe quantitative relationship between antimicrobial agent consumption and rise or fall of antibiotic resistance has rarely been studied. We began all admission surveillance testing for methicillin-resistant Staphylococcus aureus (MRSA) in August 2005 with subsequent contact isolation and decolonization using nasally applied mupirocin ointment for those colonized. In October 2012, we discontinued decolonization of medical (nonsurgical service) patients.MethodsWe conducted a retrospective study from 2007 through 2014 of 445680 patients; 35235 were assessed because of mupirocin therapy and positive test results for MRSA. We collected data on those patients receiving 2% mupirocin ointment for decolonization to determine the defined daily doses (DDDs). A nonparametric regression technique was used to quantitate the effect of mupirocin consumption on drug resistance in MRSA.ResultsUsing regressive modeling, we found that, when consumption was consistently &gt;25 DDD/1000 patient-days, there was a statistically significant increase in mupirocin resistance with a correlating positive rate of change. When consumption was ≤25 DDD/1000 patient-days, there was a statistically significant decrease in mupirocin resistance with a correlating negative rate of change. The scatter plot of fitted versus observed mupirocin resistance values showed an R2 value of 0.89—a high correlation between mupirocin use and resistance.ConclusionsUse of the antimicrobial agent mupirocin for decolonization had a threshold of approximately 25 DDD/1000 patient-days that separated a rise and fall of resistance within the acute-care setting. This has implications for how widely mupirocin can be used for decolonization, as well as for setting consumption thresholds when prescribing antimicrobials as part of stewardship programs.
Reference-Dependent Job Search: Evidence from Hungary*
Authors: DellaVigna Stefano , Lindner Attila , Reizer Balázs , Schmieder Johannes F. 
Published: May 2017

AbstractWe propose a model of job search with reference-dependent preferences, with loss aversion relative to recent income (the reference point). In this model, newly unemployed individuals search hard since consumption is below their reference point. Over time, though, they get used to lower income and thus reduce their search effort. In anticipation of a benefit cut, their search effort rises again, then declines once they get accustomed to the lower postcut benefit level. The model fits the typical pattern of exit from unemployment, even with no unobserved heterogeneity. To distinguish between this and other models, we use a unique reform in the unemployment insurance (UI) benefit path. In 2005, Hungary switched from a single-step UI system to a two-step system, with overall generosity unchanged. The system generated increased hazard rates in anticipation of, and especially following, benefit cuts in ways the standard model has a hard time explaining. We estimate a model with optimal consumption, endogenous search effort, and unobserved heterogeneity. The reference-dependent model fits the hazard rates substantially better than plausible versions of the standard model, including habit formation. Our estimates indicate a slow-adjusting reference point and substantial impatience, likely reflecting present-bias.
Mycoplasma Pneumoniae: A Cross-sectional Population-based Comparison of Disease Severity in Preschool and School-age Children
Authors: Inchley Christopher Stephen , Berg Are Stuwitz , Vahdani Benam Afsaneh , Kvissel Anne Katrine , Leegaard Truls Michael , Nakstad Britt 
Published: May 2017

Background:

Mycoplasma pneumoniae causes epidemics of upper respiratory disease and pneumonia. It is thought that M. pneumoniae usually causes milder upper respiratory disease in preschool children, with a greater chance of pneumonia in school-age children. In this population-based cross-sectional study, we present evidence that severe M. pneumoniae infection is more common in preschool children than previously thought.

Methods:
During an M. pneumoniae epidemic in our area, widespread health service and public awareness lead to extensive testing for M. pneumoniae. Medical records of hospital-referred M. pneumoniae–positive children were assessed retrospectively for respiratory disease and chest radiographic results. Severe disease was defined as supplementary oxygen or fluid requirement, mechanical ventilatory support or neurologic disease. Age-specific population figures were used to calculate incidence during the study period. Those who were 0–5-year-olds were considered preschool, whereas 6–17-year-olds were considered school-aged.

Results:
Thirty-seven preschool and 55 school-age children were referred to the hospital and tested positive for M. pneumoniae. Twenty-two (60%) preschool and 23 (42%) school-age children had severe disease [incidence 56 vs. 29 per 100,000; relative risk: 1.9; 95% confidence interval (CI): 1.06–3.4; P = 0.03]. Twenty (54%) preschool and 19 (35%) school-age children had severe pneumonia (incidence 51 vs. 24 per 100,000; relative risk: 2.1; 95% CI: 1.1–3.9; P = 0.03).

Conclusions:
During an M. pneumoniae epidemic in Akershus and North Oslo in 2011–2012, preschool children infected with M. pneumoniae had significantly higher risk of severe disease, particularly severe pneumonia, when compared with school-age children. M. pneumoniae should be considered a potential pathogen in younger children with respiratory distress, particularly during an epidemic period.
T-cell Responses to HSV-1 in Persons Who Have Survived Childhood Herpes Simplex Encephalitis
Authors: Ott Mariliis , Jing Lichen , Lorenzo Lazaro , Casanova Jean-Laurent , Zhang Shen-Ying , Koelle David M. 
Published: May 2017

Background:
Herpes simplex encephalitis (HSE) after primary herpes simplex virus (HSV)-1 infection can occur in children due to inborn errors of cell-intrinsic immunity in the central nervous system. Paradoxically, symptomatic mucocutaneous HSV-1 recurrences are rare survivors of childhood HSE. T-cell–acquired immunity is thought to be involved in control of recurrent mucocutaneous HSV infection. We thus tested HSV-1–specific immunity in HSE survivors.

Methods:
We obtained serum and peripheral blood mononuclear cells (PBMCs) from participants a median of 13.5 years after HSE. HSV-1 and HSV-2 IgG was detected by type-specific immunoblot. PBMCs from subjects passing quality control criteria were tested using enzyme-linked immunospot assay for CD4 interferon-γ responses with an HSV-1 lysate and for CD8 responses using pooled synthetic HSV-1 peptide CD8 T-cell epitopes. Healthy adult PBMCs were used to standardize assays and as comparators.

Results:
All participants were HSV-1 seropositive. Most (23/24) HSE survivors had human leukocyte antigen class I types matching the human leukocyte antigen restriction of the pooled peptides. We detected HSV-specific CD8 T-cell responses in 14 of 24 (58%) HSE survivors and in 9 of 9 healthy HSV-1 seropositive adults. HSV-specific CD4 T-cell responses were present in all 5 HSE subjects tested and in 8 of 9 healthy adults. Response magnitudes were overlapping between subject groups.

Conclusions:
The defects in cell-intrinsic immunity leading to failure to control primary central nervous system HSV-1 infection do not preclude the acquisition of specific immunity or the control of recurrent mucocutaneous HSV infections. The rarity and lack of severe or recurrent mucocutaneous HSV infection in survivors of childhood HSE corresponds with intact adaptive T-cell immunity.
Magnesium Supplementation in Vitamin D Deficiency
Authors: Reddy Pramod , Edwards Linda R. 
Published: May 2017

Background:
Vitamin D and magnesium (Mg) are some of the most studied topics in medicine with enormous implications for human health and disease. Majority of the adults are deficient in both vitamin D and magnesium but continue to go unrecognized by many health care professionals.

Areas of Uncertainty:
Mg and vitamin D are used by all the organs in the body, and their deficiency states may lead to several chronic medical conditions. Studies described in the literature regarding these disease associations are contradictory, and reversal of any of these conditions may not occur for several years after adequate replacement. One should consider the supplementation therapy to be preventative rather than curative at this time.

Data Sources:
PubMed search of several reported associations between vitamin D and Mg with diseases.

Results:
Vitamin D and Mg replacement therapy in elderly patients is known to reduce the nonvertebral fractures, overall mortality, and the incidence of Alzheimer dementia.

Conclusions:
Vitamin D screening assay is readily available, but the reported lower limit of the normal range is totally inadequate for disease prevention. Based on the epidemiologic studies, ∼75% of all adults worldwide have serum 25(OH)D levels of <30 ng/mL. Because of the recent increase in global awareness, vitamin D supplementation has become a common practice, but Mg deficiency still remains unaddressed. Screening for chronic magnesium deficiency is difficult because a normal serum level may still be associated with moderate to severe deficiency. To date, there is no simple and accurate laboratory test to determine the total body magnesium status in humans. Mg is essential in the metabolism of vitamin D, and taking large doses of vitamin D can induce severe depletion of Mg. Adequate magnesium supplementation should be considered as an important aspect of vitamin D therapy.
Are global hotspots of endemic richness shaped by plate tectonics?
Authors: Loïc Pellissier , Heine Christian , Albouy Camille 
Published: May 2017

AbstractSingular regions of the globe harbour a disproportionally large fraction of extant biodiversity. Spatial biodiversity gradients are frequently associated to extant ecological conditions using statistical models, but more rarely to paleo-environmental conditions, especially beyond the Quaternary. On one hand the role of plate tectonics in shaping the extant diversity of lineages is supported by numerous phylogenetic and fossil evidences, and on the other hand the spatial variation of biodiversity across the globe is rarely associated to geodynamic variables. In this study, we propose that plate tectonics explain the current location of hotspots of endemic richness across the globe. As an illustration, we used paleogeographies in a model, which quantifies through time and for each cell the potential dispersal across disconnected habitat patches. Rare events of dispersal across dynamic straits of unsuitable habitats allows species colonisation and that a subsequent absence of gene flow could lead to in-situ speciation. We evaluated whether this process could pinpoint the locations of hotspots of endemic richness computed from the ranges of 181,603 species across 14 taxonomic groups. The significant congruence between the regions highlighted by the model and the endemic richness provides evidences of the contribution of plate tectonics in shaping global biodiversity gradients. Places with high tectonic complexity, predominantly located at the confluence of major lithospheric plates such as the Mediterranean basin, Central America, Madagascar and South East Asia likely provided favourable circumstances for allopatric speciation and the emergence of new species across straits. While our illustration supports the role of plate tectonics, accounting for deep time geological events in spatial models of extant biodiversity is not straightforward. Future research should develop quantitative spatial models of biodiversity including the dynamic of ancient habitats.
Spatial distribution of extensively drug-resistant tuberculosis (XDR-TB) patients in KwaZulu-Natal, South Africa
Authors: Kapwata Thandi , Morris Natashia , Gandhi Neel R. , Campbell Angela , Mthiyane Thuli , Mpangase Primrose , Nelson Kristin N. , Allana Salim , Brust James C.M. , Moodley Pravi , Mlisana Koleka , Sarita Shah N. 
Published: May 2017

ABSTRACTBackgroundKwaZulu-Natal province, South Africa, has among the highest burden of XDR-TB worldwide with the majority of cases occurring due to transmission. Poor access to health facilities can be a barrier to timely diagnosis and treatment of TB, which can contribute to ongoing transmission. We sought to determine the geographic distribution of XDR-TB patients and proximity to health facilities in KwaZulu-Natal.MethodsWe recruited adults and children with XDR-TB diagnosed in KwaZulu-Natal. We calculated distance and time from participants’ home to the closest hospital or clinic, as well as to the actual facility that diagnosed XDR-TB, using tools within ArcGIS Network analyst. Speed of travel was assigned to road classes based on Department of Transport regulations. Results were compared to guidelines for the provision of social facilities in South Africa: 5km to a clinic and 30km to a hospital.ResultsDuring 2011–2014, 1027 new XDR-TB cases were diagnosed throughout all 11 districts of KwaZulu-Natal, of whom 404 (39%) were enrolled and had geospatial data collected. Participants would have had to travel a mean distance of 2.9 km (CI 95%: 1.8-4.1) to the nearest clinic and 17.6 km (CI 95%: 11.4-23.8) to the nearest hospital. Actual distances that participants travelled to the health facility that diagnosed XDR-TB ranged from <10 km (n=143, 36%) to >50 km (n=109, 27%). The majority (77%) of participants travelled farther than the recommended distance to a clinic (5 km) and 39% travelled farther than the recommended distance to a hospital (30 km). Nearly half (46%) of participants were diagnosed at a health facility in eThekwini district, of whom, 36% resided outside the Durban metropolitan area.ConclusionsXDR-TB cases are widely distributed throughout KwaZulu-Natal province with a denser focus in eThekwini district. Patients travelled long distances to the health facility where they were diagnosed with XDR-TB, suggesting a potential role for migration or transportation in the XDR-TB epidemic.
An efficient platform for astrocyte differentiation from human induced pluripotent stem cells
Authors: Julia TCW , Wang Minghui , Pimenova Anna A. , Bowles Kathryn R. , Hartley Brigham J. , Lacin Emre , Machlovi Saima , Abdelaal Rawan , Karch Celeste M. , Phetnani Hemali , Slesinger Paul A. , Zhang Bin , Goate Alison M. , Brennand Kristen J. 
Published: May 2017

SUMMARYGrowing evidence implicates the importance of glia, particularly astrocytes, in neurological and psychiatric diseases. Here, we describe a rapid and robust method for the differentiation of highly pure populations of replicative astrocytes from human induced pluripotent stem cells (hiPSCs), via a neural progenitor cell (NPC) intermediate. Using this method, we generated hiPSC-derived astrocyte populations (hiPSC-astrocytes) from 42 NPC lines (derived from 30 individuals) with an average of ∼90% S100β-positive cells. Transcriptomic analysis demonstrated that the hiPSC-astrocytes are highly similar to primary human fetal astrocytes and characteristic of a non-reactive state. hiPSC-astrocytes respond to inflammatory stimulants, display phagocytic capacity and enhance microglial phagocytosis. hiPSC-astrocytes also possess spontaneous calcium transient activity. Our novel protocol is a reproducible, straightforward (single media) and rapid (<30 days) method to generate homogenous populations of hiPSC-astrocytes that can be used for neuron-astrocyte and microglia-astrocyte co-cultures for the study of neuropsychiatric disorders.ABBREVIATIONShiPSChuman induced pluripotent stem cellNPCneural progenitor cell