bluuebunny/crossref_metadata_2025_split huggingface dataset:
Profiling of aminoxyTMT-labeled bovine milk oligosaccharides reveals substantial variation in oligosaccharide abundance between dairy cattle breeds
Authors: Robinson Randall C. , Poulsen Nina A. , Colet Emeline , Duchene Chloe , Larsen Lotte Bach , Barile Daniela 
Published: April 2019

AbstractFree milk oligosaccharides are bioactive molecules that function as prebiotics and prevent infections that commonly afflict developing infants. To date, few publications have examined the factors affecting bovine milk oligosaccharide production among cattle in the dairy industry. Here we have applied a high-throughput isobaric labeling technique to measure oligosaccharide abundances in milk collected from Danish Holstein-Friesian and Jersey dairy cattle by liquid chromatography-mass spectrometry. With a total of 634 milk samples, this collection represents the largest sample set used for milk oligosaccharide profiling in the current literature. This study is also the first to use isobaric labeling for the purpose of measuring free oligosaccharides in a real sample set. We have identified 13 oligosaccharides that vary significantly by breed, with most structures being more abundant in the milk of Jersey cattle. The abundances of several oligosaccharides were increased in second-parity cows, and correlations between the abundances of oligosaccharide pairs were identified, potentially indicating similarities in their synthetic pathways. Fucosylated oligosaccharide structures were widely identified among both breeds. Improving our understanding of oligosaccharide production will aid in developing strategies to recover these compounds from processing streams and may enable their use as a functional ingredient in foods for infants and adults.
Molecular characterization and epidemiology of Streptococcus pneumoniae serotype 24F in Denmark
Authors: Kavalari Ioanna Drakaki , Fuursted Kurt , Krogfelt Karen A. , Slotved H.-C. 
Published: April 2019

AbstractSince 2012, have we in Denmark observed an increase of invasive pneumococcal infections (IPD) due to Streptococcus pneumoniae serotype 24F. We here present epidemiological data on 24F IPD cases, and characterization of 48 24F clinical isolates based on clonal relationship, antimicrobial resistance (AMR) determinants and virulence factors. IPD surveillance data from (1999–2016) were used to calculate the incidence and age-distribution of serotype 24F IPD and the effect of pneumococcal conjugated vaccines (PCV). Characterization of forty-eight 24F isolates (14.7% of all 24F isolates from the period) was based on whole-genome sequencing analysis (WGS). The IPD cases of serotype 24F showed a significant increase (p < 0.05) for all age groups after the PCV-13 introduction in 2010. The majority of tested 24F isolates consisted of two MLST types, i.e. the ST72 and the ST162. Serotype 24F IPD increased in Denmark after the PCV-13 introduction in parallel with an increase of the ST162 clone. The genotypic penicillin binding protein (PBP) profile agreed with the phenotypical penicillin susceptibility. The virulence genes lytA, ply, piaA, piaB, piaC, rspB and the cpsA/wzg were detected in all 24F isolates, while the pspA and zmpC genes were absent.
Molecular and Structural Characterization of MHC Class II β Genes Reveals High Diversity in the Cold-Adapted Icefish Chionodraco hamatus
Authors: Gerdol Marco , Lucente Daniela , Buonocore Francesco , Poerio Elia , Scapigliati Giuseppe , Mattiucci Simonetta , Pallavicini Alberto , Cimmaruta Roberta 
Published: April 2019

AbstractThis study reports the presence of two distinct MHC class II β genes in the Antarctic icefish Chionodraco hamatus, belonging to the classical (ChhaDAB) and nonclassical (ChhaDBB) evolutionary lineages. By the application of targeted sequencing approach, a remarkable molecular diversity in the exon 2 sequence of the highly expressed gene ChhaDAB has been observed, resulting in an estimate of 92 different variants translated in 87 different peptides from 54 analysed icefish individuals. A highly conservative estimate, based on a 95% sequence identity threshold clustering, translate this variability in 41 different peptide clusters belonging to four different clades and showing the signature of different kinds of selection. In stark contrast, the poorly expressed ChhaDBB gene displayed a very low level of molecular diversity within exon 2, in agreement with expectations for a nonclassical MHC class II β gene.
Novel avian paramyxovirus-based vaccine vectors expressing the Ebola virus glycoprotein elicit mucosal and humoral immune responses in guinea pigs
Authors: Yoshida Asuka , Kim Shin-Hee , Manoharan Vinoth K. , Varghese Berin P. , Paldurai Anandan , Samal Siba K. 
Published: April 2019

AbstractParamyxovirus vaccine vectors based on human parainfluenza virus type 3 (HPIV-3) and Newcastle disease virus (NDV) have been previously evaluated against Ebola virus (EBOV) challenge. Although both the viral vectored vaccines efficiently induce protective immunity, some concerns remain to be solved. Since HPIV-3 is a common human pathogen, the human population has pre-existing immunity to HPIV-3, which may restrict the replication of the vaccine vector. For NDV, mesogenic (intermediate virulent) strain used in previous studies is currently classified as a Select Agent in the United States, thus making it unsuitable to be used as a vaccine vector. To overcome these concerns, we have developed a modified NDV vector based on a mesogenic NDV strain, in which the ectodomains of envelope glycoproteins were replaced with the corresponding ectodomains from avian paramyxovirus serotype 3 (APMV-3). The modified NDV vector was highly attenuated in chickens and was able to express the EBOV glycoprotein (GP) gene at high level. In addition, the recombinant APMV-3 was also evaluated as a vaccine vector to express the EBOV GP gene. Guinea pigs immunized with these two vector vaccines developed high levels of neutralizing GP-specific IgG and IgA antibodies.
Association of body composition with predicted hip bone strength among Chinese postmenopausal women: a longitudinal study
Authors: Shi Xin , Deng Yunyang , Kang Huili , Liu Meng , Chen Yu-Ming , Xiao Su-Mei 
Published: April 2019

AbstractBody composition and bone strength are closely associated. How lean mass (LM) and fat mass (FM) contribute to bone strength remains ambiguous. We investigated the associations of total body LM and FM with changes in predicted hip bone strength over a period of 3 years in 1,743 postmenopausal Chinese women from the communities of Guangzhou, China. The body compositions of the women were obtained with dual-energy X-ray absorptiometry. We used the hip structure analysis program to obtain the bone parameters at the femoral neck region, including the bone mineral density (BMD), cross-sectional area (CSA), cortical thickness (CT), section modulus (SM) and buckling ratio (BR). We found the FM and LM were positive predictors for hip bone strength (β > 0, P < 0.05). The LM had a larger contribution to the BMD, CSA, CT, SM and/or their annual percent changes (βLM > βFM), while the contribution of FM to the BR and its annual percent change was higher than LM (|βFM| > |βLM|). Further analysis found that the associations of FM and LM with bone parameters were stronger in the underweight and normal weight participants (|βBMI1| > |βBMI2|). Overall, FM and LM had positive but differential effects on predicted hip bone strength, with a higher impact in the thinner participants.
Identifying a BRCA2 c.5722_5723del mutation in a Han-Chinese family with breast cancer
Authors: Guo Yi , Wang Peng , Li Xiaorong , Zhu Shaihong , Xu Hongbo , Li Shizhou , Deng Hao , Yuan Lamei 
Published: April 2019

Abstract
Breast cancer (BC) is the most common female cancer found worldwide. It is responsible for 25% of all cancer patients in females. Hereditary BC accounts for about 5–10% of all BC cases. The breast cancer 1 gene (BRCA1) and the breast cancer 2 gene (BRCA2) are the two most-studied BC susceptibility genes. Genetic testing for disease-causing mutations in BRCA1, BRCA2, and other BC susceptibility genes is strongly recommended for members of families having a BC family history. The present study found a heterozygous c.5722_5723del mutation in the BRCA2 exon 11 of a large Han-Chinese BC family using whole exome sequencing and Sanger sequencing. It may cause DNA double-strand breaks repair dysfunction by disturbing homologous recombination, further resulting in BC. The study findings may help supplement and further improve genetic testing strategies and BC risk estimation methodologies in China.
Anti-depressant effects of oil from fructus gardeniae via PKA-CREB-BDNF signaling
Authors: Ruan Jie , Liu Li , Shan Xin , Xia Baomei , Fu Qiang 
Published: April 2019

Abstract
The dried ripe fruit of Gardenia jasminoides Ellis was usually applied as an herb medicine in Traditional Chinese Medicine. It was suggested that the Gardenia jasminoides oil extract (oil from Fructus Gardeniae [OFG]) might serve as a potential treatment for depression, whereas its pathogenesis still remained not fully understood. The present research was conducted to evaluate the anti-depressive effect of OFG in mice and explore its potential mechanism. The OFG and ketamine (KET) were intragastrically and intraperitoneally treated, respectively. Thereafter, the animals were subjected to the behavior tests. The expressions of protein kinase A (PKA), brain derived neurotrophic factor (BDNF), cAMP response element-binding protein (CREB) in hippocampus were detected by Western blot. The selective PKA inhibitor H-89 was also applied to confirm the mechanism. As a result, OFG and KET treatment improved the behavior performance. Furthermore, the administrations of OFG effectively enhanced the expressions of PKA, p-CREB, and BDNF. With the application of selective PKA inhibitor H-89, the ameliorated effects caused by OFG were blocked, but not by KET. In conclusion, the presented work indicated that OFG-exerted protective effect on depression through PKA-CREB-BDNF signaling.
Rotationally driven VHE emission from the Vela pulsar
Authors: Osmanov Z. , Rieger F. M. 
Published: April 2019

Context. The recent detection of pulsedγ-ray emission from the Vela pulsar in the ∼10 to 100 GeV range by H.E.S.S. promises important potential to probe into the very high energy (VHE) radiation mechanisms of pulsars.Aims. A combined analysis of H.E.S.S. andFermi-LAT data suggests that the leading wing of the P2 peak shows a new, hard gamma-ray component (with photon index as hard as Γ ∼ 3.5), setting in above 50 GeV and extending beyond 100 GeV. We study these findings in the context of rotationally driven (centrifugal) particle acceleration.Methods. We analyze achievable particle energies in the magnetosphere of the Vela pulsar and calculate the resultant emission properties.Results. Inverse Compton up-scattering of thermal photons from the surface of the star is shown to lead a pulsed VHE contribution reaching into the TeV regime with spectral characteristics compatible with current findings. If confirmed by further observations this could be the second case where rotationally driven processes turn out to be important to understand the VHE emission in young pulsars.
Ophthalmologische Abbildungstechnik vor 200 Jahren – der Atlas von Antoine Pierre Demours als Grundlage der Rostocker Kunstaugensammlung
Authors: Schubert Daniel , Niemeyer Günter , Guthoff Rudolf F. 
Published: April 2019

ZusammenfassungNeue Nachforschungen haben ergeben, dass die vor ca. 150 Jahren angefertigte „Rostocker Kunstaugensammlung“ mit 132 in Glas modellierten Vorderabschnittspathologien zum großen Teil auf die
Abbildungen des von Antoine Pierre Demours 1818 veröffentlichten Atlas der Augenheilkunde zurückgeht. Schwerpunkt dieses Beitrages bildet die Analyse der Abbildungstechniken des o. g.
Bildwerkes. Nach gegenwärtigem Kenntnisstand verwendete der Autor unterschiedliche Farbradierungskonzepte, die z. T. individuell nachkoloriert wurden. Die Abbildungen des Demoursʼschen
Atlasʼ stellen nach dem Urteil der Zeitgenossen den Gipfel der wissenschaftlichen Abbildungskunst dar und auch 100 Jahre später wird es in der Fachliteratur als ein bedeutendes illustratives
Werk für die Augenheilkunde beschrieben.
Neurodevelopmental Disorders and Array-Based Comparative Genomic Hybridization: Sensitivity and Specificity using a Criteria Checklist for Genetic Test Performance
Authors: Amado-Puentes Alfonso , Reparaz-Andrade Alfredo , Del Campo-García Aida , Blanco-Barca Manuel , Salgado-Barreira Ángel , Del Campo-Pérez Víctor , Fernández-Lorenzo José 
Published: April 2019

Background Array-based comparative genomic hybridization (aCGH) is a molecular analysis method for identifying chromosomal anomalies or copy number variants (CNVs) correlating with clinical phenotypes. The aim of our study was to identify the most significant clinical variables associated with a positive outcome of aCGH analyses to develop a simple predictive clinical score.
Methods We conducted a cross-sectional study in a tertiary center comparing the genotype and phenotype of the cases. A score was developed using multivariate logistic regression. The best score cutoff point, sensitivity, specificity, positive and negative predictive values, and area under the curve were calculated with the receiver operating characteristic curve.
Results aCGH identified structural chromosomal alterations responsible for the disorder in 13.7% (95% confidence interval [CI]: 10.9–16.5) of our sample (570 patients analyzed by aCGH). Based on the most frequent phenotypic characteristics among patients with a pathogenic CNV, we have created a checklist with the following items: alteration of the cranial perimeter, stature < percentile (p) 3, weight < p3, presence of brain malformations, ophthalmological malformations, two or more dysmorphic features in the same patient, and autism spectrum disorder diagnosis. Using a score ≥1.5 as the cutoff point for the test, we obtained a sensitivity of 82.4% (95% CI: 73.1–91.8) and a specificity of 54.2% (95% CI: 49.7–58.7).
Conclusion All individuals with a score of 1.5 or higher should be genetically screened by aCGH. This approach can improve clinical indications for aCGH in patients with neurodevelopmental disorders, but the scoring system should be validated in an external group.
Needs assessment of youths in residential child care in Portugal / Evaluación de necesidades de jóvenes en acogimiento residencial en Portugal / Evaluación de necesidades de jóvenes en acogimiento residencial en Portugal
Authors: Tavares-Rodrigues André , González-García Carla , Bravo Amaia , F. Del Valle Jorge 
Published: April 2019

Residential child care in Portugal is the most common protection measure in cases of family separation, since family foster care is still very rare. However, little is known about the needs of these children and young people. The purpose of this study is to describe the profile of adolescents close to legal adulthood who are in residential care, comparing it with a Spanish sample. The sample is composed of 345 young people aged 16 to 17 on whom information has been collected regarding their history of protection, family background, schooling, mental health and offending behaviour. A Spanish sample was selected as a comparison group ( N = 384). The results reveal the complexity and special seriousness of the profile of young people in residential care in Portugal compared to a Spanish sample, highlighting a high presence of mental health problems and especially suicidal behaviours. Given these results, efforts should be focused on developing specialized residential care programmes adapted to the specific needs of these young people.
HLA*LA—HLA typing from linearly projected graph alignments
Authors: Dilthey Alexander T , Mentzer Alexander J , Carapito Raphael , Cutland Clare , Cereb Nezih , Madhi Shabir A , Rhie Arang , Koren Sergey , Bahram Seiamak , McVean Gil , Phillippy Adam M 
Published: April 2019

Abstract

Summary
HLA*LA implements a new graph alignment model for human leukocyte antigen (HLA) type inference, based on the projection of linear alignments onto a variation graph. It enables accurate HLA type inference from whole-genome (99% accuracy) and whole-exome (93% accuracy) Illumina data; from long-read Oxford Nanopore and Pacific Biosciences data (98% accuracy for whole-genome and targeted data) and from genome assemblies. Computational requirements for a typical sample vary between 0.7 and 14 CPU hours per sample.

Availability and implementation
HLA*LA is implemented in C++ and Perl and freely available as a bioconda package or from https://github.com/DiltheyLab/HLA-LA (GPL v3).

Supplementary information
Supplementary data are available at Bioinformatics online.
scRNAss: a single-cell RNA-seq assembler via imputing dropouts and combing junctions
Authors: Liu Juntao , Liu Xiangyu , Ren Xianwen , Li Guojun 
Published: April 2019

Abstract

Motivation
Full-length transcript reconstruction is essential for single-cell RNA-seq data analysis, but dropout events, which can cause transcripts discarded completely or broken into pieces, pose great challenges for transcript assembly. Currently available RNA-seq assemblers are generally designed for bulk RNA sequencing. To fill the gap, we introduce single-cell RNA-seq assembler, a method that applies explicit strategies to impute lost information caused by dropout events and a combing strategy to infer transcripts using scRNA-seq.

Results
Extensive evaluations on both simulated and biological datasets demonstrated its superiority over the state-of-the-art RNA-seq assemblers including StringTie, Cufflinks and CLASS2. In particular, it showed a remarkable capability of recovering unknown ‘novel’ isoforms and highly computational efficiency compared to other tools.

Availability and implementation
scRNAss is free, open-source software available from https://sourceforge.net/projects/single-cell-rna-seq-assembly/files/.

Supplementary information
Supplementary data are available at Bioinformatics online.
The financial burden of non-communicable diseases in the European Union: a systematic review
Authors: Vandenberghe Désirée , Albrecht Johan 
Published: April 2019

AbstractBackgroundNon-communicable diseases (NCDs) impose a significant and growing burden on the health care system and overall economy of developed (and developing) countries. Nevertheless, an up-to-date assessment of this cost for the European Union (EU) is missing from the literature. Such an analysis could however have an important impact by motivating policymakers and by informing effective public health policies.MethodsFollowing the PRISMA protocol, we conduct a systematic review of electronic databases (PubMed/Medline, Embase, Web of Science Core Collection) and collect scientific articles that assess the direct (health care-related) and indirect (economic) costs of four major NCDs (cardiovascular disease, cancer, type-2 diabetes mellitus and chronic respiratory disease) in the EU, between 2008 and 2018. Data quality was assessed through the Newcastle–Ottawa Scale.ResultsWe find 28 studies that match our criteria for further analysis. From our review, we conclude that the four major NCDs in the EU claim a significant share of the total health care budget (at least 25% of health spending) and they impose an important economic loss (almost 2% of gross domestic product).ConclusionThe NCD burden forms a public health risk with a high financial impact; it puts significant pressure on current health care and economic systems, as shown by our analysis. We identify a further need for cost analyses of NCDs, in particular on the impact of comorbidities and other complications. Aside from cost estimations, future research should focus on assessing the mix of public health policies that will be most effective in tackling the NCD burden.
The role of democratic legitimacy in the recognition of governments in Africa since the end of the Cold War
Authors: de Wet Erika 
Published: April 2019

Abstract
This article explores whether recent institutional reforms within Africa have modified the traditional criterion of effective control as the decisive requirement for recognition of de jure governments in the region. It examines in particular whether measures adopted by the African Union (AU) for outlawing unconstitutional changes of government have elevated democratic legitimacy to an (additional) criterion for governmental recognition. The article illustrates that on the whole, the practice of the AU has been neither consistent in the condemnation of coup regimes nor keen to support popular movements that oppose authoritarian rule, or scrutinize the democratic pedigree of governments for the purposes of (continued) recognition. In essence, the AU’s institutional commitments to oppose unconstitutional changes of government amount to guiding principles, rather than binding obligations. While at times decisive, democratic legitimacy has not yet replaced effective control as the point of departure for governmental recognition.
Use of Intraoperative Indocyanine Green Angiography for Feeder Vessel Ligation and En Bloc Resection of Intramedullary Hemangioblastoma
Authors: Molina Camilo A , Pennington Zach , Ahmed A Karim , Westbroek Erick , Goodwin Matthew L , Tamargo Rafael , Sciubba Daniel M 
Published: April 2019

Abstract

BACKGROUND
As vascular tumors, intramedullary hemangioblastomas are associated with significant intraoperative blood loss, making them particularly challenging clinical entities. The use of intraoperative indocyanine green or other fluorescent dyes has previously been described to avoid breaching the tumor capsule, but improved surgical outcomes may result from identifying and ligating the feeder arteries and arterialized draining veins.

OBJECTIVE
To describe the use of combined preoperative angiography and intraoperative indocyanine green use for the identification of feeder arteries and arterialized draining veins to decrease blood loss in the resection of intramedullary hemangioblastomas.

METHODS
A patient with cervical myelopathy secondary to a large C3 hemangioblastoma and cervicothoracic syrinx underwent a C2-3 laminoplasty with resection of the lesion. To reduce intraoperative blood loss and facilitate safe lesion resection, the vascular architecture of the lesion was defined via preoperative digital subtraction angiography and intraoperative use of indocyanine green. The latter permitted ligation of the major and minor feeding arteries and arterialized veins prior to tumor breach, allowing for facile en bloc resection of the lesion.

RESULTS
The lesion was resected en bloc with minimal blood loss (approximately 100 mL) and without intraoperative neuromonitoring signal changes. The patient remained at neurological baseline throughout their stay.

CONCLUSION
We present a written and media illustration of a technique for intraoperative indocyanine green use in the en bloc resection of intramedullary hemangioblastoma.
REVIEW OF RADON AND THORON RESEARCH IN KENYA: 1997–2017
Authors: Chege M , Nyambura C 
Published: April 2019

Abstract
Six research studies involving radon and thoron in Kenya were carried out between 1997 and 2007. The studies were mainly small scale and involved a few areas scattered across Nairobi, Rift Valley, Coast and Western regions. The results were captured in seven online journal articles. This paper relooks at the journal articles with the view of underscoring the high radon and thoron areas in Kenya, raising awareness on the sources and risks of radon isotopes in indoor environments and highlighting the need for more research on the isotopes in the country.