bluuebunny/crossref_metadata_2025_split huggingface dataset:
How Clean Is the Linen at My Hospital? The Mucorales on Unclean Linen Discovery Study of Large United States Transplant and Cancer Centers
Authors: Sundermann Alexander J , Clancy Cornelius J , Pasculle A William , Liu Guojun , Cumbie Richard B , Driscoll Eileen , Ayres Ashley , Donahue Lisa , Pergam Steven A , Abbo Lilian , Andes David R , Chandrasekar Pranatharthi , Galdys Alison L , Hanson Kimberly E , Marr Kieren A , Mayer Jeanmarie , Mehta Seema , Morris Michele I , Perfect John , Revankar Sanjay G , Smith Becky , Swaminathan Sankar , Thompson George R , Varghese Merin , Vazquez Jose , Whimbey Estella , Wingard John R , Nguyen M Hong 
Published: September 2018

Abstract
Mucormycosis outbreaks have been linked to contaminated linen. We performed fungal cultures on freshly-laundered linens at 15 transplant and cancer hospitals. At 33% of hospitals, the linens were visibly unclean. At 20%, Mucorales were recovered from >10% of linens. Studies are needed to understand the clinical significance of our findings.
Protective Efficacy and Long-Term Immunogenicity in Cynomolgus Macaques by Ebola Virus Glycoprotein Synthetic DNA Vaccines
Authors: Patel Ami , Reuschel Emma L , Kraynyak Kimberly A , Racine Trina , Park Daniel H , Scott Veronica L , Audet Jonathan , Amante Dinah , Wise Megan C , Keaton Amelia A , Wong Gary , Villarreal Daniel O , Walters Jewell , Muthumani Kar , Shedlock Devon J , de La Vega Marc-Antoine , Plyler Ross , Boyer Jean , Broderick Kate E , Yan Jian , Khan Amir S , Jones Shane , Bello Alexander , Soule Geoff , Tran Kaylie N , He Shihua , Tierney Kevin , Qiu Xiangguo , Kobinger Gary P , Sardesai Niranjan Y , Weiner David B 
Published: September 2018

Abstract

Background
There remains an important need for prophylactic anti-Ebola virus vaccine candidates that elicit long-lasting immune responses and can be delivered to vulnerable populations that are unable to receive live-attenuated or viral vector vaccines.

Methods
We designed novel synthetic anti-Ebola virus glycoprotein (EBOV-GP) DNA vaccines as a strategy to expand protective breadth against diverse EBOV strains and evaluated the impact of vaccine dosing and route of administration on protection against lethal EBOV-Makona challenge in cynomolgus macaques. Long-term immunogenicity was monitored in nonhuman primates for &gt;1 year, followed by a 12-month boost.

Results
Multiple-injection regimens of the EBOV-GP DNA vaccine, delivered by intramuscular administration followed by electroporation, were 100% protective against lethal EBOV-Makona challenge. Impressively, 2 injections of a simple, more tolerable, and dose-sparing intradermal administration followed by electroporation generated strong immunogenicity and was 100% protective against lethal challenge. In parallel, we observed that EBOV-GP DNA vaccination induced long-term immune responses in macaques that were detectable for at least 1 year after final vaccination and generated a strong recall response after the final boost.

Conclusions
These data support that this simple intradermal-administered, serology-independent approach is likely important for additional study towards the goal of induction of anti-EBOV immunity in multiple at-risk populations.
Gaia DR2 in 6D: searching for the fastest stars in the Galaxy
Authors: Marchetti T , Rossi E M , Brown A G A 
Published: September 2018

ABSTRACT
We search for the fastest stars in the subset of stars with radial velocity measurements of the second data release (DR2) of the European Space Agency mission Gaia. Starting from the observed positions, parallaxes, proper motions, and radial velocities, we construct the distance and total velocity distribution of more than 7 million stars in our Milky Way, deriving the full 6D phase space information in Galactocentric coordinates. These information are shared in a catalogue, publicly available at http://home.strw.leidenuniv.nl/~marchetti/research.html. To search for unbound stars, we then focus on stars with a probability greater than $50 $ per cent of being unbound from the Milky Way. This cut results in a clean sample of 125 sources with reliable astrometric parameters and radial velocities. Of these, 20 stars have probabilities greater than 80 per cent of being unbound from the Galaxy. On this latter subsample, we perform orbit integration to characterize the stars’ orbital parameter distributions. As expected given the relatively small sample size of bright stars, we find no hypervelocity star candidates, stars that are moving on orbits consistent with coming from the Galactic Centre. Instead, we find seven hyperrunaway star candidates, coming from the Galactic disc. Surprisingly, the remaining 13 unbound stars cannot be traced back to the Galaxy, including two of the fastest stars (around 700 km s−1). If conformed, these may constitute the tip of the iceberg of a large extragalactic population or the extreme velocity tail of stellar streams.
Crust or core? Insights from the slow rise of large glitches in the Crab pulsar
Authors: Haskell B , Khomenko V , Antonelli M , Antonopoulou D 
Published: September 2018

ABSTRACT
Pulsar glitches are attributed to the sudden recoupling of weakly coupled superfluid components in the neutron star interior. The transfer of angular momentum between the components is regulated by mutual friction, whose strength defines the spin-up time-scale of a glitch. Hence, observations of glitch rises can be used to shed light on the dominant microphysical interactions at work in the interior of the star. We present a model which naturally produces a fast spin-up followed by a more gradual rise, as observed in large glitches of the Crab pulsar, including the largest recent glitch of 2017. Our model is then used to determine whether the glitch driving region is located in the crust or core of the star. To do this, we compare our results to observations of large glitches in the Crab and Vela pulsars and obtain constraints on the mutual friction parameters that govern the coupling between the superfluid and the crust. Our results are consistent with theoretical estimates for mutual friction in the core for the Vela, but with estimates for the crust in the Crab. This suggests a crustal origin for Crab glitches, but an outer core contribution for Vela glitches.
Two-dimensional translation-invariant probability distributions: approximations, characterizations and no-go theorems
Authors: Wang Zizhu , Navascués Miguel 
Published: September 2018

We study the properties of the set of marginal distributions of infinite translation-invariant systems in the two-dimensional square lattice. In cases where the local variables can only take a small number
d
of possible values, we completely solve the marginal or membership problem for nearest-neighbours distributions (
d
= 2, 3) and nearest and next-to-nearest neighbours distributions (
d
= 2). Remarkably, all these sets form convex polytopes in probability space. This allows us to devise an algorithm to compute the minimum energy per site of any TI Hamiltonian in these scenarios exactly. We also devise a simple algorithm to approximate the minimum energy per site up to arbitrary accuracy for the cases not covered above. For variables of a higher (but finite) dimensionality, we prove two no-go results. To begin, the exact computation of the energy per site of arbitrary TI Hamiltonians with only nearest-neighbour interactions is an undecidable problem. In addition, in scenarios with
d
≥2947, the boundary of the set of nearest-neighbour marginal distributions contains both flat and smoothly curved surfaces and the set itself is not semi-algebraic. This implies, in particular, that it cannot be characterized via semidefinite programming, even if we allow the input of the programme to include polynomials of nearest-neighbour probabilities.
Disease heritability enrichment of regulatory elements is concentrated in elements with ancient sequence age and conserved function across species
Authors: Hujoel Margaux L.A. , Gazal Steven , Hormozdiari Farhad , van de Geijn Bryce , Price Alkes L. 
Published: September 2018

AbstractRegulatory elements, e.g. enhancers and promoters, have been widely reported to be enriched for disease and complex trait heritability. We investigated how this enrichment varies with the age of the underlying genome sequence, the conservation of regulatory function across species, and the target gene of the regulatory element. We estimated heritability enrichment by applying stratified LD score regression to summary statistics from 41 independent diseases and complex traits (averageN=320K) and meta-analyzing results across traits. Enrichment of human enhancers and promoters was larger in elements with older sequence age, assessed via alignment with other species irrespective of conserved functionality: enhancer elements with ancient sequence age (older than the split between marsupial and placental mammals) were 8.8x enriched (vs. 2.5x for all enhancers; p = 3e-14), and promoter elements with ancient sequence age were 13.5x enriched (vs. 5.1x for all promoters; p = 5e-16). Enrichment of human enhancers and promoters was also larger in elements whose regulatory function was conserved across species, e.g. human enhancers that were enhancers in ≥5 of 9 other mammals were 4.6x enriched (p = 5e-12 vs. all enhancers). Enrichment of human promoters was larger in promoters of loss-of-function intolerant genes: 12.0x enrichment (p = 8e-15 vs. all promoters). The mean value of several measures of negative selection within these genomic annotations mirrored all of these findings. Notably, the annotations with these excess heritability enrichments were jointly significant conditional on each other and on our baseline-LD model, which includes a broad set of coding, conserved, regulatory and LD-related annotations.
Tissue-expression profiles unveils the gene interaction of hepatopancreas, eyestalk, and ovary in precocious female Chinese mitten crab,Eriocheir sinensis
Authors: Chen Xiaowen , Wang Jun , Hou Xin , Yue Wucheng , Huang Shu , Wang Chenghui 
Published: September 2018

AbstractSexual precocity is a serious and common biological phenomenon in animal species. Large amount of precocity individuals was identified in Chinese mitten crab,Eriocheir sinensis, which caused huge economical loss every year. However, the underlying genetic basis of precocity inE. sinensisis still lack. In this study, histology observation, comparative transcriptome was conducted among different stages of precocious one-year old and normal two-year oldE. sinensis, tissue-expression profiles of ovary, hepatopancreas, and eyestalk tissues were presented and compared. Genes associated with lipid metabolic process, lipid transport, vitelline membrane formation, vitelline synthesis and neuropeptide hormone related genes were upregulated in the ovary, hepatopancreas and eyestalk of precociousE. sinensis. Our results indicated eyestalk involved in neuroendocrine system providing neuropeptide hormone that may induce vitellogenesis in hepatopancreas and further stimulate ovary development. Hepatopancreas is a site for energy storage, vitellogenin synthesis and may assist to induce oogenesis through lipid transport in precociousE. sinensis. The genetic basis of precocity inE. sinensisis an integrated gene regulatory network of eyestalk, hepatopancreas, and ovary tissues. Our study provides effective convenient phenotype measurement method for identification of potential precociousE. sinensisdetection, and valuable genetic resources and novel insights into the research of molecular mechanism of precocity inE. sinensis.
Impact of specimen age on its DNA quality for Formalin-Fixed Paraffin-Embedded HPV specimens
Authors: Park James Yeongjun 
Published: September 2018

AbstractFormalin fixation and paraffin embedding (FFPE) allows the storage of diagnostic and surplus tissue in archival banks. Therefore, FFPE is now a standard method for long-term preservation of tissue biopsies as FFPE of samples preserves the morphology of tissue. Unfortunately, the FFPE process engenders chemical changes and degradation in tissue macromolecules that can pose threats to reliable subsequent analysis. DNA, while more resistant to FFPE in comparison to RNA and protein, is also subject to such chemical formations and degradation. This study provides robust findings about the relationship between DNA quality and specimen age from 10252 FFPE HPV specimens. This paper suggests that there is a perceptible degrading effect in DNA quality as specimens age. This study suggests that the biospecimen may begin to take on new characteristics after certain storage years, and such changes may result in inaccurate determinations of the molecular characteristics of the biospecimen during analysis. Results from this study demonstrate that older HPV specimens are more inclined to be tested negative or inadequate from commercial HPV genotyping assays. Same findings are conferred when multiple genotyping assays are involved with HPV testing. Also, older HPV samples typify fewer HPV types compared to younger HPV samples. The results from this study will be useful to enhance potential scope for next fixation methods such as ethanol fixation that may be equally useful for both molecular profiling and histology as FFPE.
Information and communication technology, mobile devices, and medical education
Authors: Rodríguez-Ríos Andrea , Espinoza-Téllez Gerardo , Martínez-Ezquerro José Darío , Rendón-Macías Mario Enrique 
Published: September 2018

AbstractIntroductionInformation and communication technologies (ICT) are practical and highly available tools. In medical education, ICTs allow physicians to update their knowledge and remember the necessary information within reach of current mobile devices. ICTs as preparation tools for medical education have not been reported for medical students in Mexico.MethodologyTo assess the use of mobile devices as ICTs with medical education purposes, we distributed a questionnaire through an online survey management system to all the medical students (n=180) from a private university in Mexico City, 100% agreed to participate. We developed a questionnaire based on previous surveys and adapted it to our university.ResultsAll participants reported possession of an electronic mobile device, and 95% used it regularly for learning purposes. Regardless of the school year, the most frequent usage given to these devices was the search and reading of medical articles, the use of medical calculators, and taking notes. As the levels in career advances, there was a reduction in the use of electronic devices. According to the students, the main barriers towards using mobile devices for learning purposes were both the lack of access to the Internet and permission from the professor to use them.ConclusionMost medical students use mobile devices for learning purposes, but usage changes during their education. It is convenient to encourage the use of mobile devices and the development of ICT skills as tools for educational purposes rather than banning their use in schools and hospitals.
Cancer3D 2.0: interactive analysis of 3D patterns of cancer mutations in cancer subsets
Authors: Sedova Mayya , Iyer Mallika , Li Zhanwen , Jaroszewski Lukasz , Post Kai W. , Hrabe Thomas , Porta-Pardo Eduard , Godzik Adam 
Published: September 2018

ABSTRACTOur knowledge of cancer genomics exploded in last several years, providing us with detailed knowledge of genetic alterations in almost all cancer types. Analysis of this data gave us new insights into molecular aspects of cancer, most important being the amazing diversity of molecular abnormalities in individual cancers. The most important question in cancer research today is how to classify this diversity to identify subtypes that are most relevant for treatment and outcome prediction for individual patients. The Cancer3D database athttp://www.cancer3d.orggives an open and user-friendly way to analyze cancer missense mutations in the context of structures of proteins they are found in and in relation to patients’ clinical data. This approach allows users to find novel candidate driver regions for specific subgroups, that often cannot be found when similar analyses are done on the whole gene level and for large, diverse cohorts. Interactive interface allows user to visualize the distribution of mutations is subgroups defined by cancer type and stage, gender and age brackets, patient’s ethnicity, or vice versa find dominant cancer type, gender or age groups for specific three-dimensional mutation patterns.
Over-expression of Hsp83 in grossly depletedhsrωlncRNA background causes synthetic lethality andl(2)glphenocopy inDrosophila
Authors: Ray Mukulika , Acharya Sundaram , Shambhavi Sakshi , Lakhotia Subhash C. 
Published: September 2018

AbstractWe examined interactions between Hsp83 andhsrωlncRNAs inhsrω66Hsp90GFPhomozygotes, which almost completely lackhsrωlncRNAs but over-express Hsp83. All+/+; hsrω66Hsp90GFPprogeny died before third instar. RareSp/CyO; hsrω66Hsp90GFPreached third instar stage but phenocopiedl(2)glmutants, dying after prolonged larval life, becoming progressively bulbous and transparent with enlarged brain. Additionally, ventral ganglia were elongated. However,hsrω66Hsp90GFP/TM6Bheterozygotes, carrying+/+orSp/CyOsecond chromosomes, developed normally. Total RNA sequencing (+/+, +/+;hsrω66/hsrω66,Sp/CyO; hsrω66/hsrω66,+/+; Hsp90GFP/Hsp90GFP, andSp/CyO; hsrω66Hsp90GFP/hsrω66Hsp90GFPlate third instar larvae) revealed similar effects on many genes inhsrω66andHsp90GFPhomozygotes. Besides additive effect on many of them, numerous additional genes were affected inSp/CyO; hsrω66Hsp90GFPlarvae, withl(2)gland several genes regulating CNS being highly down-regulated in survivingSp/CyO; hsrω66Hsp90GFPlarvae, but not inhsrω66orHsp90GFPsingle mutants. Hsp83 binds at these gene promoters. Several omega speckle associated hnRNPs too may bind with these genes and transcripts. Hsp83-hnRNP interactions are also known. Thus, elevated Hsp83 in altered hnRNP distribution and dynamics, following absence of hsrωlncRNAs and omega speckles, background can severely perturb regulatory circuits with unexpected consequences, including down-regulation of tumor suppressor gene likel(2)gl.
Bleaching-independent, whole-cell, 3D and multi-color STED imaging with exchangeable fluorophores
Authors: Spahn Christoph , Grimm Jonathan B. , Lavis Luke D. , Lampe Marko , Heilemann Mike 
Published: September 2018

AbstractWe demonstrate bleaching-independent STED microscopy using fluorogenic labels that reversibly bind to their target structure. A constant exchange of labels guarantees the removal of photobleached fluorophores and their replacement by intact fluorophores, thereby circumventing bleaching-related limitations of STED super-resolution imaging in fixed and living cells. Foremost, we achieve a constant labeling density and demonstrate a fluorescence signal for long and theoretically unlimited acquisition times. Using this concept, we demonstrate whole-cell, 3D, multi-color and live cell STED microscopy with up to 100 min acquisition time.
Pervasive selection against microRNA target sites in human populations
Authors: Hatlen Andrea , Marco Antonio 
Published: September 2018

ABSTRACTMicroRNA target sites are often conserved during evolution and purifying selection to maintain such sites is expected. On the other hand, comparative analyses identified a paucity of microRNA target sites in co-expressed transcripts, and novel target sites can potentially be deleterious. We proposed that selection against novel target sites pervasive. The analysis of derived allele frequencies revealed that, when the derived allele is a target site, the proportion of non-target sites is higher than expected, particularly for highly expressed microRNAs. Thus, new alleles generating novel microRNA target sites can be deleterious and selected against. When we analysed ancestral target sites the derived (non-target) allele frequency does not show statistical support for microRNA target allele conservation. We investigated the joint effects of microRNA conservation and expression and found that selection against microRNA target sites depends mostly on the expression level of the microRNA. We identified microRNA target sites with relatively high levels of population differentiation. However, when we analyse separately target sites in which the target allele is ancestral to the population, the proportion of SNPs with high Fst significantly increases. These findings support population differentiation is more likely in target sites that are lost than in the gain of new target sites. Our results indicate that selection against novel microRNA target sites is prevalent and, although individual sites may have a weak selective pressure, the overall effect across untranslated regions is not negligible and should be accounted when studying the evolution of genomic sequences.
Multiple Toll-Spätzle Pathways in Drosophila melanogaster Immunity
Authors: Chowdhury Munmun , Li Chun-Feng , He Zhen , Lu Yuzhen , Liu Xusheng , Wang Yufeng , Ip Y. Tony , Strand Michael R. , Yu Xiao-Qiang 
Published: September 2018

AbstractThe Drosophila melanogaster Toll-Spätzle pathway plays an important role in development and immunity. Drosophila genome encodes nine Toll receptors and six Spätzle (Spz) proteins, and only the canonical Toll-Spz (Toll-1-Spz-1) pathway has been well investigated. In this study, we compared the nine Drosophila Tolls and showed that similarly to Toll, Toll-7 also strongly activated drosomycin promoter. Importantly, we showed that both Toll and Toll-7 interacted with Spz, Spz-2 and Spz-5, and co-expression of Toll or Toll-7 with Spz, Spz-2 and Spz-5 activated the drosomycin promoter. Furthermore, Toll and Toll-7 both recognized vesicular stomatitis virus (VSV) by binding to the VSV glycoprotein. Septic infection in Toll and Toll-7 mutant flies suggested that Toll and Toll-7 differentially affected defense responses in adult males and females after systemic infection by Enterococcus faecalis, Pseudomonas aeruginosa, Candida albicans or VSV. Our results suggest multiple Toll family members activate the expression of antimicrobial peptides. Our results also provide evidence that Toll and Toll-7 bind multiple Spätzle proteins and differentially affect immune defense against different pathogens in adult male and female flies.
A new statistic for efficient detection of repetitive sequences
Authors: Chen Sijie , Sun Fengzhu , Waterman Michael S. , Zhang Xuegong 
Published: September 2018

ABSTRACTDetecting sequences containing repetitive regions is a basic bioinformatics task with many applications. Several methods have been developed for various types of repeat detection tasks. An efficient generic method for detecting all types of repetitive sequences is still desirable.Inspired by the excellent properties and successful applications of the D2 family of statistics in comparative analyses of genomic sequences, we developed a new statistic that can efficiently discriminate sequences with or without repetitive regions. Using the statistic, we developed an algorithm of linear complexity in both computation time and memory usage for detecting all types of repetitive sequences in multiple scenarios, including finding candidate CRISPR regions from bacterial genomic or metagenomics sequences. Simulation and real data experiments showed that the method works well on both assembled sequences and unassembled short reads.