bluuebunny/crossref_metadata_2025_split huggingface dataset:
The draft genome sequence of cork oak
Authors: Ramos António Marcos , Usié Ana , Barbosa Pedro , Barros Pedro M. , Capote Tiago , Chaves Inês , Simões Fernanda , Abreu Isabl , Carrasquinho Isabel , Faro Carlos , Guimarães Joana B. , Mendonça Diogo , Nóbrega Filomena , Rodrigues Leandra , Saibo Nelson J. M. , Varela Maria Carolina , Egas Conceição , Matos José , Miguel Célia M. , Oliveira M. Margarida , Ricardo Cândido P. , Gonçalves Sónia 
Published: May 2018

AbstractCork oak (Quercus suber) is native to southwest Europe and northwest Africa where it plays a crucial environmental and economical role. To tackle the cork oak production and industrial challenges, advanced research is imperative but dependent on the availability of a sequenced genome. To address this, we produced the first draft version of the cork oak genome. We followed a de novo assembly strategy based on high-throughput sequence data, which generated a draft genome comprising 23,347 scaffolds and 953.3 Mb in size. A total of 79,752 genes and 83,814 transcripts were predicted, including 33,658 high-confidence genes. An InterPro signature assignment was detected for 69,218 transcripts, which represented 82.6% of the total. Validation studies demonstrated the genome assembly and annotation completeness and highlighted the usefulness of the draft genome for read mapping of high-throughput sequence data generated using different protocols. All data generated is available through the public databases where it was deposited, being therefore ready to use by the academic and industry communities working on cork oak and/or related species.
Gridded birth and pregnancy datasets for Africa, Latin America and the Caribbean
Authors: James W.H.M. , Tejedor-Garavito N. , Hanspal S.E. , Campbell-Sutton A. , Hornby G.M. , Pezzulo C. , Nilsen K. , Sorichetta A. , Ruktanonchai C.W. , Carioli A. , Kerr D. , Matthews Z. , Tatem A.J. 
Published: May 2018

AbstractUnderstanding the fine scale spatial distribution of births and pregnancies is crucial for informing planning decisions related to public health. This is especially important in lower income countries where infectious disease is a major concern for pregnant women and new-borns, as highlighted by the recent Zika virus epidemic. Despite this, the spatial detail of basic data on the numbers and distribution of births and pregnancies is often of a coarse resolution and difficult to obtain, with no co-ordination between countries and organisations to create one consistent set of subnational estimates. To begin to address this issue, under the framework of the WorldPop program, an open access archive of high resolution gridded birth and pregnancy distribution datasets for all African, Latin America and Caribbean countries has been created. Datasets were produced using the most recent and finest level census and official population estimate data available and are at a resolution of 30 arc seconds (approximately 1 km at the equator). All products are available through WorldPop.
Moved by Reading in a Spanish-Speaking, Dual Language Learner Population
Authors: Adams Ashley M. , Glenberg Arthur M. , Restrepo Ma Adelaida 
Published: May 2018

Purpose
The aim of this study was to evaluate the effectiveness of an English-only version and a Spanish-support version of an embodied reading comprehension intervention (Moved by Reading) consisting of 3 stages (physical manipulation, imagined manipulation, and transfer) for Spanish–English dual language learners.

Method
Sixty-one dual language learners in Arizona were randomly assigned to 4 groups (Spanish-support control, Spanish-support intervention, English-only control, and English-only intervention). Analyses of variance were used to compare control and intervention groups and to compare groups according to the language of the intervention.

Results
Children in the Spanish-support intervention group significantly outperformed both control groups during the physical manipulation stage, whereas children in the English-only intervention group outperformed both control groups in the imagined manipulation stage, but there was little transfer to a new, unrelated text.

Conclusions
The Moved by Reading intervention, in both its English-only and Spanish-support versions, improved performance on comprehension questions, but in different stages of the intervention. The Spanish-support version of the intervention was most effective in the physical manipulation stage, whereas the English-only version was more effective in the imagined manipulation stage. Neither version was effective in producing significant transfer effects.
Internal and External Factors That Support Children's Minority First Language and English
Authors: Pham Giang , Tipton Timothy 
Published: May 2018

PurposeSequential bilingual children in the United States often speak 2 languages that have different social statuses (minority–majority) and separate contexts for learning (home–school). Thus, distinct factors may support the development of each language. This study examined which child internal and external factors were related to vocabulary skills in a minority language versus English.MethodParticipants included 69 children, aged 5–8 years, who lived in Southern California, spoke Vietnamese as the home language, and received school instruction in English. All participants had at least 1 foreign-born parent, and most mothers reported limited English proficiency. Parents completed a telephone survey, and children completed measures of receptive and expressive vocabulary in each language. Using correlations and stepwise regression, we examined predictors of vocabulary skills in each language that were internal to the child (age, gender, analytical reasoning, phonological memory) or that pertained to the surrounding environment (cumulative exposure, quantity and quality of input/output).ResultsVietnamese vocabulary outcomes were related to multiple external factors, of which input and enrichment activities were the best predictors. In contrast, English vocabulary outcomes were related to internal factors, of which age and phonological memory were the best predictors. Parental use of Vietnamese contributed to children's Vietnamese vocabulary outcomes but was not related to children's English vocabulary outcomes.ConclusionsVietnamese exposure does not hinder English development. Children from immigrant families are learning English with or without familial support. Rich and frequent exposure and opportunities for practice are essential for the continued development of a minority first language.
Spielersperren in Deutschland: Stand der gesetzlichen Glücksspielregelungen und ihre Umsetzung
Authors: Motka Franziska , Grüne Bettina , Braun Barbara , Kraus Ludwig 
Published: May 2018

ZusammenfassungSpielersperren stellen eine Maßnahme des Spielerschutzes dar. Ziel der vorliegenden Arbeit ist die Darstellung der derzeitigen Gesetzesgrundlage von Spielersperren in Deutschland und den Bundesländern und beispielhaft ihrer Nutzung in Bayern. Während auf Basis des Glücksspielstaatsvertrags für das staatliche Glücksspiel eine bundesweite Sperrdatei existiert, werden Spielersperren für das gewerbliche Glücksspiel länderspezifisch organisiert. Aufgrund der uneinheitlichen Gesetzeslage besteht trotz einer ausgesprochenen Spielersperre die Möglichkeit, auf andere Spielformen oder Spielstätten auszuweichen. Diese Gegebenheiten sollten im Beratungs- oder Behandlungskontext aufgegriffen werden, um betroffenen Glücksspielenden eine Abstinenz zu erleichtern. Für eine breite Nutzung von Spielersperren sind strukturelle Veränderungen der derzeitigen Organisation von Spielersperren nötig. Zum einem bedarf es unter Einbeziehung des gewerblichen Glücksspiels einer einheitlichen Regelung mit einer übergreifenden Sperrdatei. Zum anderen könnte über den Abbau von Barrieren und die Einführung transparenter Kriterien für die Entsperrung die Akzeptanz von Spielersperren erhöht werden.
Ambulant praktizierende Ärzte in Deutschland unzureichend auf Ebolafieber vorbereitet
Authors: Brekle Verena , Weiß Christel , Kolobaric Zvonimir , Schulz-Weidhaas Claudia , Vogelmann Roger 
Published: May 2018

Zusammenfassung
Hintergrund Globalisierung, zunehmende Mobilität und Klimawandel erhöhen die Gefahr des globalen Auftretens von Erkrankungen durch hochpathogene Erreger. Ziel der Arbeit: Anhand der Ebolafieber-Epidemie in Westafrika wurde untersucht, ob ambulant praktizierende Mediziner als Primärversorger vorbereitet sind, den Ernstfall zu erkennen, richtig zu bewerten und fachgerecht zu handeln.
Methodik In 2 anonym durchgeführten Befragungen von ambulant praktizierenden Medizinern (n=166 bzw. 129) wurden u. a. der objektive Wissensstand, die subjektive Einschätzung zum eigenen Wissen und die praktische Umsetzung in den Alltag erhoben und mit dem von 14 STAKOB-Experten (Ständiger Arbeitskreis der Kompetenz- und Behandlungszentren für Krankheiten durch hochpathogene Erreger) als erforderlich definierten Mindeststandard verglichen.
Ergebnisse Der Wissensstand der Teilnehmer blieb signifikant hinter dem in Experteninterviews definierten Standard zurück. Von 8 gestellten Wissensfragen wurden im Durchschnitt nur 5 korrekt beantwortet. Auch die subjektive Wissenseinschätzung stellte sich als weniger gut dar. Obwohl 56% der Teilnehmer Handlungsanweisungen erhalten hatten, setzten 64% diese nicht in ihrer Praxis um. Ebolafieber-spezifische Fortbildungen waren von etwa 22% der Befragten in Anspruch genommen worden, wobei die Teilnahme zu einer signifikant besseren subjektiven Wissenseinschätzung führte.
Schlussfolgerung Entgegen der landesweit offiziell kommunizierten fachlichen Einschätzung, dass Deutschland gut auf das Auftreten von Erkrankungen durch hochpathogene Erreger vorbereitet sei, legen die Ergebnisse der vorliegenden Studie diesbezüglich existierende Defizite nahe. Trotz eines umfangreich zur Verfügung stehenden Informationsangebots war das relevante Detailwissen nicht immer im erforderlichen Umfang bei der Zielgruppe abrufbar. Und das obwohl knapp die Hälfte das Risiko einer Einschleppung als wahrscheinlich oder sehr wahrscheinlich angab. Welche Konsequenzen daraus für die Informationsvermittlung und weitere Forschungsansätze gezogen werden könnten, zeigt die Studie auf.
Ein webbasierter Farbsehtest als Tool zur qualitativen Bewertung von pseudoisochromatischen Pflüger-Haken-Farbtafeln
Authors: Kuchenbecker Joern 
Published: May 2018

Zusammenfassung
Einleitung Pseudoisochromatische Farbtafeln werden nach bestimmten Prinzipien konstruiert und können von der Qualität sehr unterschiedlich sein. Um die diagnostische Qualität zu prüfen, müssen sie an einer größeren Anzahl von Probanden getestet werden, was jedoch mit großem Zeit- und Kostenaufwand verbunden ist. Hier bietet sich der Einsatz eines standardisierten webbasierten Tests an.
Methodik Es wurden 8 Pflüger-Haken-Farbtafeln (inkl. 1 Demotafel) nach Velhagen aus der Auflage von 1980 digitalisiert und in einen webbasierten Farbsehtest (www.farbsehtest.de) eingefügt. Nach visueller Bildschirmkalibrierung und 2-maliger Präsentation der Demotafel (Nr. 1) zur Prüfung des Verständnisses des Testablaufes wurden 7 Rot-Grün-Tafeln (Nr. 3, 4, 10, 11, 12, 13, 16) in randomisierter Reihenfolge in 3 verschiedenen randomisierten Positionen für je 10 s präsentiert. Der Benutzer musste die Öffnung des Pflüger-Hakens per Mausklick oder Pfeiltasten angeben.
Ergebnisse In die Auswertung wurden so 6360 Bewertungen von allen Tafeln von 2120 zufällig ausgewählten Probanden einbezogen. Ohne Fehler lagen die Erkennungsraten der Tafeln zwischen 72,2% (Tafel 1) und 90,7% (Tafel 7; n = 6360). Bei einer Fehleranzahl von 7 Fehlern pro Test lagen die Erkennungsraten der Tafeln zwischen 21,6% (Tafel 1) und 67,7% (Tafel 7; n = 1556). Wird eine Fehleranzahl von 14 Fehlern zugrunde gelegt, lagen die Erkennungsraten der Tafeln zwischen 10,9% (Tafel 4) und 40,1% (Tafel 7; n = 606). Die Tafel Nr. 16 zeigte bei null Fehler die höchste Erkennungsrate, bei der Fehleranzahl von 7 und 14 ebenfalls, sodass die Qualität dieser Tafel am geringsten einzustufen ist und eine Verbesserung der kolorimetrischen Daten vorgenommen wurde. Danach lag die Erkennungsrate in einem deutlich niedrigeren Bereich.
Zusammenfassung Die unterschiedliche Qualität von pseudoisochromatischen Pflüger-Haken-Farbtafeln kann per webbasierten Test ohne großen Aufwand getestet werden, sodass eine Optimierung einer qualitativ weniger guten Tafel anschließend erfolgen konnte.
Reduction of myocardial ischaemia–reperfusion injury by inactivating oxidized phospholipids
Authors: Yeang Calvin , Hasanally Devin , Que Xuchu , Hung Ming-Yow , Stamenkovic Aleksandra , Chan David , Chaudhary Rakesh , Margulets Victoria , Edel Andrea L , Hoshijima Masahiko , Gu Yusu , Bradford William , Dalton Nancy , Miu Phuong , Cheung David Yc , Jassal Davinder S , Pierce Grant N , Peterson Kirk L , Kirshenbaum Lorrie A , Witztum Joseph L , Tsimikas Sotirios , Ravandi Amir 
Published: May 2018

Abstract

Aims
Myocardial ischaemia followed by reperfusion (IR) causes an oxidative burst resulting in cellular dysfunction. Little is known about the impact of oxidative stress on cardiomyocyte lipids and their role in cardiac cell death. Our goal was to identify oxidized phosphatidylcholine-containing phospholipids (OxPL) generated during IR, and to determine their impact on cell viability and myocardial infarct size.

Methods and results
OxPL were quantitated in isolated rat cardiomyocytes using mass spectrophotometry following 24 h of IR. Cardiomyocyte cell death was quantitated following exogenously added OxPL and in the absence or presence of E06, a ‘natural’ murine monoclonal antibody that binds to the PC headgroup of OxPL. The impact of OxPL on mitochondria in cardiomyocytes was also determined using cell fractionation and Bnip expression. Transgenic Ldlr−/− mice, overexpressing a single-chain variable fragment of E06 (Ldlr−/−-E06-scFv-Tg) were used to assess the effect of inactivating endogenously generated OxPL in vivo on myocardial infarct size. Following IR in vitro, isolated rat cardiomyocytes showed a significant increase in the specific OxPLs PONPC, POVPC, PAzPC, and PGPC (P < 0.05 to P < 0.001 for all). Exogenously added OxPLs resulted in significant death of rat cardiomyocytes, an effect inhibited by E06 (percent cell death with added POVPC was 22.6 ± 4.14% and with PONPC was 25.3 ± 3.4% compared to 8.0 ± 1.6% and 6.4 ± 1.0%, respectively, with the addition of E06, P < 0.05 for both). IR increased mitochondrial content of OxPL in rat cardiomyocytes and also increased expression of Bcl-2 death protein 3 (Bnip3), which was inhibited in presence of E06. Notably cardiomyocytes with Bnip3 knock-down were protected against cytotoxic effects of OxPL. In mice exposed to myocardial IR in vivo, compared to Ldlr−/− mice, Ldlr−/−-E06-scFv-Tg mice had significantly smaller myocardial infarct size normalized to area at risk (72.4 ± 21.9% vs. 47.7 ± 17.6%, P = 0.023).

Conclusions
OxPL are generated within cardiomyocytes during IR and have detrimental effects on cardiomyocyte viability. Inactivation of OxPL in vivo results in a reduction of infarct size.
ASaiM: a Galaxy-based framework to analyze microbiota data
Authors: Batut Bérénice , Gravouil Kévin , Defois Clémence , Hiltemann Saskia , Brugère Jean-François , Peyretaillade Eric , Peyret Pierre 
Published: May 2018

Abstract

Background
New generations of sequencing platforms coupled to numerous bioinformatics tools have led to rapid technological progress in metagenomics and metatranscriptomics to investigate complex microorganism communities. Nevertheless, a combination of different bioinformatic tools remains necessary to draw conclusions out of microbiota studies. Modular and user-friendly tools would greatly improve such studies.

Findings
We therefore developed ASaiM, an Open-Source Galaxy-based framework dedicated to microbiota data analyses. ASaiM provides an extensive collection of tools to assemble, extract, explore, and visualize microbiota information from raw metataxonomic, metagenomic, or metatranscriptomic sequences. To guide the analyses, several customizable workflows are included and are supported by tutorials and Galaxy interactive tours, which guide users through the analyses step by step. ASaiM is implemented as a Galaxy Docker flavour. It is scalable to thousands of datasets but also can be used on a normal PC. The associated source code is available under Apache 2 license at https://github.com/ASaiM/framework and documentation can be found online (http://asaim.readthedocs.io).

Conclusions
Based on the Galaxy framework, ASaiM offers a sophisticated environment with a variety of tools, workflows, documentation, and training to scientists working on complex microorganism communities. It makes analysis and exploration analyses of microbiota data easy, quick, transparent, reproducible, and shareable.
Transplantation of CCR5∆32 Homozygous Umbilical Cord Blood in a Child With Acute Lymphoblastic Leukemia and Perinatally Acquired HIV Infection
Authors: Rothenberger Meghan , Wagner John E , Haase Ashley , Richman Douglas , Grzywacz Bartosz , Strain Matthew , Lada Steven , Estes Jacob , Fletcher Courtney V , Podany Anthony T , Anderson Jodi , Schmidt Thomas , Wietgrefe Steve , Schacker Timothy , Verneris Michael R 
Published: May 2018

Abstract

Background
Allogeneic hematopoietic cell transplantation (allo-HCT) in a CCR5∆32 homozygous donor resulted in HIV cure. Understanding how allo-HCT impacts the HIV reservoir will inform cure strategies.

Methods
A 12-year-old with perinatally acquired, CCR5-tropic HIV and acute lymphoblastic leukemia underwent myeloablative conditioning and umbilical cord blood (UCB) transplantation from a CCR5∆32 homozygous donor. Peripheral blood mononuclear cells (PBMCs) and the rectum were sampled pre- and post-transplant. The brain, lung, lymph node (LN), stomach, duodenum, ileum, and colon were sampled 73 days after transplantation (day +73), when the patient died from graft-vs-host disease. Droplet digital polymerase chain reaction (ddPCR) and in situ hybridization (ISH) were used detect the HIV reservoir in tissues. CCR5 and CD3 expression in the LN was assessed using immunohistochemistry (IHC).

Results
HIV DNA (vDNA) was detected in PBMCs by ddPCR pretransplant but not post-transplant. vDNA was detected by ISH in the rectum at days –8 and +22, and in the LN, colon, lung, and brain day +73. vDNA was also detected in the lung by ddPCR. IHC revealed CCR5+CD3+ cells in the LN postmortem.

Conclusions
HIV was detected in multiple tissues 73 days after CCR5∆32 homozygous UCB allo-HCT despite myeloablative conditioning and complete donor marrow engraftment. These results highlight the importance of analyzing tissue during HIV cure interventions and inform the choice of assay used to detect HIV in tissue reservoirs.
JC Virus Granule Cell Neuronopathy and Lymphoma
Authors: Demas Alexis , Bennani Omar , Vandendriessche Anne , de Menibus Laurence Hellouin , Langlois Vincent , Gasnault Jacques 
Published: May 2018

Abstract
Neurological opportunistic infections are going to increase. Clinicians should be aware of the neurological spectrum of JC virus manifestations, including granule cell neuronopathy. Detection of JC virus DNA by polymerase chain reaction in cerebrospinal fluid should be realized in the assessment of a progressive cerebellar ataxia in an immunocompromised patient.
Cellular Stress Response to Varicella-Zoster Virus Infection of Human Skin Includes Highly Elevated Interleukin-6 Expression
Authors: Jarosinski Keith W , Carpenter John E , Buckingham Erin M , Jackson Wallen , Knudtson Kevin , Moffat Jennifer F , Kita Hirohito , Grose Charles 
Published: May 2018

Abstract

Background
The infectious cycle of varicella-zoster virus (VZV) after reactivation from the dorsal root ganglia includes replication and assembly of complete enveloped virions in the human skin to cause the characteristic herpes zoster (shingles).

Methods
To pursue studies of innate immunity to VZV infection, we have adapted a fetal skin organ culture model to a human neonatal foreskin explant model.

Results
Abundant expression of VZV IE62, gE, and gC was visualized by confocal microscopy while numerous enveloped virions were observed by electron microscopy in infected skin organ cultures. Microarray experiments demonstrated that the patterns of upregulated transcripts differed between VZV-infected cells and VZV-infected skin explants. One result stood out, namely a &gt;30-fold elevated interleukin (IL)-6 level in the infected skin explant that was not present in the infected monolayer culture. The IL-6 results in the polyermase chain reaction (PCR) assay were reproduced by quantitative PCR testing with newly designed primers. To determine if increased transcription was accompanied by increased IL-6 expression, we quantitated the levels of IL-6 protein in the explant media at increasing intervals after infection. We found a statistically significant increase in IL-6 protein levels secreted into the media from VZV-infected skin explants as compared with mock-infected explants.

Conclusions
The cellular stress response to VZV infection in neonatal skin explants included highly elevated levels of IL-6 transcription and expression. This skin organ model could be adapted to other viruses with a skin tropism, such as herpes simplex virus.
Peritumoral Edema Relative to Meningioma Size Predicts Functional Outcomes after Resection in Older Patients
Authors: Loewenstern Joshua , Aggarwal Amit , Pain Margaret , Barthélemy Ernest , Costa Anthony , Bederson Joshua , Shrivastava Raj K 
Published: May 2018

Abstract

BACKGROUND
Resection of meningiomas in older adults is associated with increased complications and postoperative functional deficits. Extent of peritumoral edema (PTE), which has been associated with surgical prognosis, may represent a preoperative risk marker for poorer outcomes in older adults.

OBJECTIVE
To quantitatively evaluate the relationship between preoperative PTE and postresection outcomes in older meningioma patients.

METHODS
One hundred twelve older meningioma patients (age ≥ 60) with evidence of PTE on MRI were reviewed. Extent of PTE, measured as a ratio of edema to tumor volume (edema index, EI) using semiautomatic image-processing software, was correlated with postresection outcomes. Other preoperative factors were included as covariates in multivariate analyses. Results were compared to matched nonedema older patients. Receiver operating characteristic (ROC) curve analysis was performed to identify cut-off EI values to predict postoperative outcomes.

RESULTS
EI was associated with functional decline (as measured by Karnofsky Performance Status, KPS) at 6 mo, 1, 2 yr, and most recent follow-up (Ps < .05), but not among the nonedema matched patients. Seizure or prior stroke additionally trended towards increasing the likelihood of lower KPS at 2 yr (odds ratio = 3.06) and last follow-up (odds ratio = 5.55), respectively. ROC curve analysis found optimal cut-off values for EI ranging from 2.01 to 3.37 to predict lower KPS at each follow-up interval. Sensitivities ranged from 60% to 80%, specificities from 78% to 89%, and positive and negative predictive values from 38% to 58% and 80% to 97%.

CONCLUSION
Preoperative PTE may represent a significant marker of poor functional outcome risk in older adults and provides a quantitative measurement to incorporate into surgical decision-making.