bluuebunny/crossref_metadata_2025_split huggingface dataset:
Dysarthria in Adults With Cerebral Palsy: Clinical Presentation and Impacts on Communication
Authors: Schölderle Theresa , Staiger Anja , Lampe Renée , Strecker Katrin , Ziegler Wolfram 
Published: April 2016

Purpose
Although dysarthria affects the large majority of individuals with cerebral palsy (CP) and can substantially complicate everyday communication, previous research has provided an incomplete picture of its clinical features. We aimed to comprehensively describe characteristics of dysarthria in adults with CP and to elucidate the impact of dysarthric symptoms on parameters relevant for communication.

Method
Forty-two adults with CP underwent speech assessment by means of standardized auditory rating scales. Listening experiments were conducted to obtain communication-related parameters—that is, intelligibility and naturalness—as well as age and gender estimates.

Results
The majority of adults with CP showed moderate to severe dysarthria with symptoms on all dimensions of speech, most prominently voice quality, respiration, and prosody. Regression analyses revealed that articulatory, respiratory, and prosodic features were the strongest predictors of intelligibility and naturalness of speech. Listeners' estimates of the speakers' age and gender were predominantly determined by voice parameters.

Conclusion
This study provides an overview on the clinical presentation of dysarthria in a convenience sample of adults with CP. The complexity of the functional impairment described and the consequences on the individuals' communication call for a stronger consideration of dysarthria in CP both in clinical care and in research.
Mapping physiological G protein-coupled receptor signaling pathways reveals a role for receptor phosphorylation in airway contraction
Authors: Bradley Sophie J. , Wiegman Coen H. , Iglesias Max Maza , Kong Kok Choi , Butcher Adrian J. , Plouffe Bianca , Goupil Eugénie , Bourgognon Julie-Myrtille , Macedo-Hatch Timothy , LeGouill Christian , Russell Kirsty , Laporte Stéphane A. , König Gabriele M. , Kostenis Evi , Bouvier Michel , Chung Kian Fan , Amrani Yassine , Tobin Andrew B. 
Published: April 2016

SignificanceStudies in transfected cells have established that G protein-coupled receptors (GPCRs) activate a number of intracellular signaling pathways; however, which of these pathways are physiologically important is unclear. Here, we use a genetically engineered mouse to demonstrate a novel role for M3-muscarinic acetylcholine receptor (M3-mAChR) phosphorylation in airway constriction, with implications for human respiratory disease, including asthma and chronic obstructive pulmonary disease. Combining this finding with other M3-mAChR physiological responses, we generate a map of responses that are downstream of G protein-dependent signaling or receptor phosphorylation-dependent signaling. Such a map predicts the outcome of biased GPCR drugs designed to drive receptor signaling preferentially toward pathways that improve therapeutic efficacy while minimizing toxic/adverse outcomes and provides a fundamental approach to the rational design of next-generation GPCR-based therapies.
Unique techniques developed in Israel for short- and long-term storage of table grapes
Authors: Lichter Amnon , Kaplunov Tatiana , Zutahy Yohanan , Lurie Susan 
Published: April 2016

Gray mold caused byBotrytis cinereaand rachis browning due to desiccation are the two main factors that reduce table grape quality after harvest. For over 90 years treatments with the gas sulfur dioxide (SO2) have been in use to control decay. In Israel, two methods have been developed for grape storage: one for short-term storage and shipping, and one for extended storage of late ripening cultivars. The first is based on storage in cardboard boxes without liners, which shortens the forced air cooling time due to the reduction in packaging material. After cooling the pallets are wrapped around with linear low density polyethylene to contain the SO2and the humidity. The second method involves storage in plastic boxes with modification of commercially available dual release SO2pads, so that the pads release a continuous low rate of SO2for a long period of over 4 months in cold storage. In this case as well, the pallet is wrapped on all sides in order to maintain the level of SO2and high humidity. Moreover, for late season grapes, we established the efficacy of a postharvest disinfection treatment with ethanol in order to reduce the inoculum load before extended storage and to clean the grapes from accumulation of dust particles. These techniques allow prolonged storage for more than 3 months with minimal decay development combined with retention of grape quality.
The dominance of quenching through cosmic times
Authors: Renzini Alvio 
Published: April 2016

Abstract
The evolution with cosmic time of the star formation rate density (SFRD) and of the main-sequence star formation rate–stellar mass relations are two well-established observational facts. In this Letter, the implications of these two relations combined are analytically explored, showing that quenching of star formation must start already at very early cosmic times and the quenched fraction then dominates ever since over the star-forming one. Thus, a simple picture of the cosmic evolution of the global SFRD is derived, in terms of the interplay between star formation and its quenching.
Inferring the distances of fast radio bursts through associated 21-cm absorption
Authors: Margalit Ben , Loeb Abraham 
Published: April 2016

Abstract
The distances of fast radio burst (FRB) sources are currently unknown. We show that the 21-cm absorption line of hydrogen can be used to infer the redshifts of FRB sources, and determine whether they are Galactic or extragalactic. We calculate a probability of ∼10 per cent for the host galaxy of an FRB to exhibit a 21-cm absorption feature of equivalent width ≳10 km s−1. Arecibo, along with several future radio observatories, should be capable of detecting such associated 21-cm absorption signals for strong bursts of ≳several Jy peak flux densities.
Comparison of Clustering Methods for High-Dimensional Single-Cell Flow and Mass Cytometry Data
Authors: Weber Lukas M. , Robinson Mark D. 
Published: April 2016

AbstractRecent technological developments in high-dimensional flow cytometry and mass cytometry (CyTOF) have made it possible to detect expression levels of dozens of protein markers in thousands of cells per second, allowing cell populations to be characterized in unprecedented detail. Traditional data analysis by “manual gating” can be inefficient and unreliable in these high-dimensional settings, which has led to the development of a large number of automated analysis methods. Methods designed for unsupervised analysis use specialized clustering algorithms to detect and define cell populations for further downstream analysis. Here, we have performed an up-to-date, extensible performance comparison of clustering methods for high-dimensional flow and mass cytometry data. We evaluated methods using several publicly available data sets from experiments in immunology, containing both major and rare cell populations, with cell population identities from expert manual gating as the reference standard. Several methods performed well, includingFlowSOM, X-shift, PhenoGraph, Rclusterpp, andflowMeans. Among these,FlowSOMhad extremely fast runtimes, making this method well-suited for interactive, exploratory analysis of large, high-dimensional data sets on a standard laptop or desktop computer. These results extend previously published comparisons by focusing on high-dimensional data and including new methods developed for CyTOF data. R scripts to reproduce all analyses are available from GitHub (https://github.com/lmweber/cytometry-clustering-comparison), and pre-processed data files are available from FlowRepository (FR-FCM-ZZPH), allowing our comparisons to be extended to include new clustering methods and reference data sets.
Fate of glair glands and spawning behaviour in unmated crayfish: a comparison between gonochoristic slough crayfish and parthenogenetic marbled crayfish
Authors: Vogt Günter 
Published: April 2016

AbstractIn the period before spawning, freshwater crayfish females develop glair glands on the underside of the pleon. These glands produce the mucus for a transient tent-like structure in which the eggs are fertilized and attached to the pleopods. Long-term observation of females of the bisexually reproducing slough crayfish,Procambarus fallax, kept in captivity revealed that glair glands developed in late winter and late summer of each year independent of the presence of males. However, in contrast to mated females unmated females did neither form a fertilization tent nor spawn. Their glair glands persisted for an unusually long period of time and disappeared only during the next moult. Apparently, females use information on sperm availability to either reproduce or save the resources. Marbled crayfish,Procambarus virginalis, a parthenogenetic descendant of slough crayfish, developed glair glands in approximately the same periods of the year but spawned despite of the absence of mating. These findings indicate that on their way from gonochorism to parthenogenesis regulation of glair gland activity and spawning has been decoupled from mating. Therefore, the species pairProcambarus fallax/Procambarus virginalisseems to be particularly suitable to investigate the physiological, molecular and genetic mechanisms underlying spawning in freshwater crayfish.
PALADIN:Protein Alignment for Functional Profiling Whole Metagenome Shotgun Data
Authors: Westbrook Anthony , Ramsdell Jordan , Aggarwal Taruna , Normington Louisa , Bergeron R. Daniel , Thomas W. Kelley , MacManes Matthew 
Published: April 2016

AbstractWhole metagenome shotgun sequencing is a powerful approach for assaying the functional potential of microbial communities. Presently, we lack tools that efficiently and accurately align DNA reads against protein references, the technique necessary for constructing a functional profile. Here, we present PALADIN—a novel modification of Burrows-Wheeler Aligner that provides more accurate alignment and orders-of-magnitude improved efficiency by directly mapping in protein space.
A Transcriptional Lineage of the EarlyC. elegansEmbryo
Authors: Tintori Sophia C. , Nishimura Erin Osborne , Golden Patrick , Lieb Jason D. , Goldstein Bob 
Published: April 2016

HIGHLIGHTS‒RNA-seq on each cell of the earlyC. elegansembryo complements the known lineage‒We measured the zygotic activation specific to each unique cell of the embryo‒We identified genes that are functionally redundant and critical for development‒We created an interactive online data visualization tool for exploring the dataeTOC BLURBC. elegansis a powerful model for development, with an invariant and completely described cell lineage. To enrich this resource, we performed single-cell RNA-seq on each cell of the embryo through the 16-cell stage. Zygotic genome activation is differential between cell types. We identified hundreds of candidates for partially redundant genes, and verified one such set as critical for development. We created an interactive online data visualization tool to invite others to explore our dataset.SUMMARYDuring embryonic development, cells must establish fates, morphologies and behaviors in coordination with one another to form a functional body. A prevalent hypothesis for how this coordination is achieved is that each cell’s fate and behavior is determined by a defined mixture of RNAs. Only recently has it become possible to measure the full suite of transcripts in a single cell. Here we quantify the abundance of every mRNA transcript in each cell of theC. elegansembryo up to the 16-cell stage. We describe spatially dynamic expression, quantify cell-specific differential activation of the zygotic genome, and identify critical developmental genes previously unappreciated because of their partial redundancy. We present an interactive data visualization tool that allows broad access to our dataset. This genome-wide single-cell map of mRNA abundance, alongside the well-studied life history and fates of each cell, describes at a cellular resolution the mRNA landscape that guides development.
Immune DNA signature of T-cell infiltration in breast tumor exomes
Authors: Levy Eric , Marty Rachel , Garate-Calderon Valentina , Woo Brian , Dow Michelle , Armisen Ricardo , Carter Hannah , Harismendy Olivier 
Published: April 2016

AbstractTumor infiltrating lymphocytes (TILs) have been associated with favorable prognosis in multiple tumor types. The Cancer Genome Atlas (TCGA) represents the largest collection of cancer molecular data, but lacks detailed information about the immune environment. Here, we show that exome reads mapping to the complementarity-determining-region 3 (CDR3) of mature T-cell receptor beta (TCRB) can be used as an immune DNA (iDNA) signature. Specifically, we propose a method to identify CDR3 reads in a breast tumor exome and validate it using deepTCRBsequencing. In 1,078 TCGA breast cancer exomes, the fraction of CDR3 reads was associated with TILs fraction, tumor purity, adaptive immunity gene expression signatures and improved survival in Her2+ patients. Only 2/839TCRBclonotypes were shared between patients and none associated with a specific HLA allele or somatic driver mutations. The iDNA biomarker enriches the comprehensive dataset collected through TCGA, revealing associations with other molecular features and clinical outcomes.
Coordinated Regulation of Species-Specific Hydroxycinnamic Acid Degradation and Siderophore Biosynthesis Pathways in Agrobacterium fabrum
Authors: Baude Jessica , Vial Ludovic , Villard Camille , Campillo Tony , Lavire Céline , Nesme Xavier , Hommais Florence 
Published: April 2016

ABSTRACTThe rhizosphere-inhabiting speciesAgrobacterium fabrum(genomospecies G8 of theAgrobacterium tumefaciensspecies complex) is known to degrade hydroxycinnamic acids (HCAs), especially ferulic acid andp-coumaric acid, via the novelA. fabrumHCA degradation pathway. Gene expression profiles ofA. fabrumstrain C58 were investigated in the presence of HCAs, using a C58 whole-genome oligoarray. Both ferulic acid andp-coumaric acid caused variations in the expression of more than 10% of the C58 genes. Genes of theA. fabrumHCA degradation pathway, together with the genes involved in iron acquisition, were among the most highly induced in the presence of HCAs. Two operons coding for the biosynthesis of a particular siderophore, as well as genes of theA. fabrumHCA degradation pathway, have been described as being specific to the species. We demonstrate here their coordinated expression, emphasizing the interdependence between the iron concentration in the growth medium and the rate at which ferulic acid is degraded by cells. The coordinated expression of these functions may be advantageous in HCA-rich but iron-starved environments in which microorganisms have to compete for both iron and carbon sources, such as in plant roots. The present results confirm that there is cooperation between theA. fabrum-specific genes, defining a particular ecological niche.IMPORTANCEWe previously identified seven genomic regions inAgrobacterium fabrumthat were specifically present in all of the members of this species only. Here we demonstrated that two of these regions, encoding the hydroxycinnamic acid degradation pathway and the iron acquisition pathway, were regulated in a coordinated manner. The coexpression of these functions may be advantageous in hydroxycinnamic acid-rich but iron-starved environments in which microorganisms have to compete for both iron and carbon sources, such as in plant roots. These data support the view that bacterial genomic species emerged from a bacterial population by acquiring specific functions that allowed them to outcompete their closest relatives. In conclusion, bacterial species could be defined not only as genomic species but also as ecological species.
Restructuring of the Aquatic Bacterial Community by Hydric Dynamics Associated with Superstorm Sandy
Authors: Ulrich Nikea , Rosenberger Abigail , Brislawn Colin , Wright Justin , Kessler Collin , Toole David , Solomon Caroline , Strutt Steven , McClure Erin , Lamendella Regina 
Published: April 2016

ABSTRACT

Bacterial community composition and longitudinal fluctuations were monitored in a riverine system during and after Superstorm Sandy to better characterize inter- and intracommunity responses associated with the disturbance associated with a 100-year storm event. High-throughput sequencing of the 16S rRNA gene was used to assess microbial community structure within water samples from Muddy Creek Run, a second-order stream in Huntingdon, PA, at 12 different time points during the storm event (29 October to 3 November 2012) and under seasonally matched baseline conditions. High-throughput sequencing of the 16S rRNA gene was used to track changes in bacterial community structure and divergence during and after Superstorm Sandy. Bacterial community dynamics were correlated to measured physicochemical parameters and fecal indicator bacteria (FIB) concentrations. Bioinformatics analyses of 2.1 million 16S rRNA gene sequences revealed a significant increase in bacterial diversity in samples taken during peak discharge of the storm. Beta-diversity analyses revealed longitudinal shifts in the bacterial community structure. Successional changes were observed, in which
Betaproteobacteria
and
Gammaproteobacteria
decreased in 16S rRNA gene relative abundance, while the relative abundance of members of the
Firmicutes
increased. Furthermore, 16S rRNA gene sequences matching pathogenic bacteria, including strains of
Legionella
,
Campylobacter
,
Arcobacter
, and
Helicobacter
, as well as bacteria of fecal origin (e.g.,
Bacteroides
), exhibited an increase in abundance after peak discharge of the storm. This study revealed a significant restructuring of in-stream bacterial community structure associated with hydric dynamics of a storm event.

IMPORTANCE
In order to better understand the microbial risks associated with freshwater environments during a storm event, a more comprehensive understanding of the variations in aquatic bacterial diversity is warranted. This study investigated the bacterial communities during and after Superstorm Sandy to provide fine time point resolution of dynamic changes in bacterial composition. This study adds to the current literature by revealing the variation in bacterial community structure during the course of a storm. This study employed high-throughput DNA sequencing, which generated a deep analysis of inter- and intracommunity responses during a significant storm event. This study has highlighted the utility of applying high-throughput sequencing for water quality monitoring purposes, as this approach enabled a more comprehensive investigation of the bacterial community structure. Altogether, these data suggest a drastic restructuring of the stream bacterial community during a storm event and highlight the potential of high-throughput sequencing approaches for assessing the microbiological quality of our environment.
Involvement of Vitamin B6Biosynthesis Pathways in the Insecticidal Activity of Photorhabdus luminescens
Authors: Sato Kazuki , Yoshiga Toyoshi , Hasegawa Koichi 
Published: April 2016

ABSTRACTPhotorhabdus luminescensis a Gram-negative entomopathogenic bacterium which symbiotically associates with the entomopathogenic nematodeHeterorhabditis bacteriophora.P. luminescensis highly virulent to many insects and nonsymbiotic nematodes, includingCaenorhabditis elegans. To understand the virulence mechanisms ofP. luminescens, we obtained virulence-deficient and -attenuated mutants againstC. elegansthrough a transposon-mutagenized library. From the genetic screening, we identified thepdxBgene, encoding erythronate-4-phosphate dehydrogenase, as required forde novovitamin B6biosynthesis. Mutation inpdxBcaused growth deficiency ofP. luminescensin nutrient-poor medium, which was restored under nutrient-rich conditions or by supplementation with pyridoxal 5′-phosphate (PLP), an active form of vitamin B6. Supplementation with three other B6vitamers (pyridoxal, pyridoxine, and pyridoxamine) also restored the growth of thepdxBmutant, suggesting the existence of a salvage pathway for vitamin B6biosynthesis inP. luminescens. Moreover, supplementation with PLP restored the virulence-deficient phenotype againstC. elegans. Combining these results with the fact thatpdxBmutation also caused attenuation of insecticidal activity, we concluded that the production of appropriate amounts of vitamin B6is critical forP. luminescenspathogenicity.IMPORTANCEThe Gram-negative entomopathogenic bacteriumPhotorhabdus luminescenssymbiotically associates with the entomopathogenic nematodeHeterorhabditis bacteriophora.P. luminescensis highly virulent to many insects and nonsymbiotic nematodes, includingCaenorhabditis elegans. We have obtained several virulence-deficient and -attenuatedP. luminescensmutants againstC. elegansthrough genetic screening. From the genetic analysis, we present the vitamin B6biosynthetic pathways inP. luminescensthat are important for its insecticidal activity. Mutation inpdxB, encoding erythronate-4-phosphate dehydrogenase and required for thede novovitamin B6biosynthesis pathway, caused virulence deficiency againstC. elegansand growth deficiency ofP. luminescensin nutrient-poor medium. Because such phenotypes were restored under nutrient-rich conditions or by supplementation with B6vitamers, we showed the presence of the two vitamin B6synthetic pathways (de novoand salvage) inP. luminescensand also showed that the ability to produce an appropriate amount of vitamin B6is critical forP. luminescenspathogenicity.