bluuebunny/crossref_metadata_2025_split huggingface dataset:
Survey of allele specific expression in bovine muscle
Authors: Guillocheau Gabriel M. , El Hou Abdelmajid , Meersseman Cédric , Esquerré Diane , Rebours Emmanuelle , Letaief Rabia , Simao Morgane , Hypolite Nicolas , Bourneuf Emmanuelle , Bruneau Nicolas , Vaiman Anne , Vander Jagt Christy J. , Chamberlain Amanda J. , Rocha Dominique 
Published: March 2019

AbstractAllelic imbalance is a common phenomenon in mammals that plays an important role in gene regulation. An Allele Specific Expression (ASE) approach can be used to detect variants with acis-regulatory effect on gene expression. In cattle, this type of study has only been done once in Holstein. In our study we performed a genome-wide analysis of ASE in 19 Limousine muscle samples. We identified 5,658 ASE SNPs (Single Nucleotide Polymorphisms showing allele specific expression) in 13% of genes with detectable expression in theLongissimus thoracimuscle. Interestingly we found allelic imbalance inAOX1,PALLDandCASTgenes. We also found 2,107 ASE SNPs located within genomic regions associated with meat or carcass traits. In order to identify causativecis-regulatory variants explaining ASE we searched for SNPs altering binding sites of transcription factors or microRNAs. We identified one SNP in the 3’UTR region ofPRNPthat could be a causal regulatory variant modifying binding sites of several miRNAs. We showed that ASE is frequent within our muscle samples. Our data could be used to elucidate the molecular mechanisms underlying gene expression imbalance.
Cytotoxicity of Ag, Au and Ag-Au bimetallic nanoparticles prepared using golden rod (Solidago canadensis) plant extract
Authors: Botha Tarryn L. , Elemike Elias E. , Horn Suranie , Onwudiwe Damian C. , Giesy John P. , Wepener Victor 
Published: March 2019

AbstractProduction and use of metallic nanoparticles have increased dramatically over the past few years and design of nanomaterials has been developed to minimize their toxic potencies. Traditional chemical methods of production are potentially harmful to the environment and greener methods for synthesis are being developed in order to address this. Thus far phytosynthesis have been found to yield nanomaterials of lesser toxicities, compared to materials synthesized by use of chemical methods. In this study nanoparticles were synthesized from an extract of leaves of golden rod (Solidago canadensis). Silver (Ag), gold (Au) and Ag-Au bimetallic nanoparticles (BNPs), synthesized by use of this “green” method, were evaluated for cytotoxic potency. Cytotoxicity of nanomaterials to H4IIE-luc (rat hepatoma) cells and HuTu-80 (human intestinal) cells were determined by use of the xCELLigence real time cell analyzer. Greatest concentrations (50 µg/mL) of Ag and Ag-Au bimetallic were toxic to both H4IIE-luc and HuTu-80 cells but Au nanoparticles were not toxic. BNPs exhibited the greatest toxic potency to these two types of cells and since AuNPs caused no toxicity; the Au functional portion of the bimetallic material could be assisting in uptake of particles across the cell membrane thereby increasing the toxicity.
Staphylococcal Superantigen-like protein 11 mediates neutrophil adhesion and motility arrest, a unique bacterial toxin action
Authors: Chen Chen , Yang Chen , Barbieri Joseph T. 
Published: March 2019

AbstractMethicillin resistant Staphylococcus aureus (MRSA) is a major human pathogen, which causes superficial to lethal clinical infections. Neutrophils are the most abundant leukocytes in the blood and are the first defense mechanism against S. aureus infections. Here we show Staphylococcal Superantigen-Like protein 11 (SSL11) from MRSA USA300_FPR3757 mediated differentiated human neutrophil-like cells (dHL60) motility arrest by inducing cell adhesion and “locking” cells in adhesion stage, without inducing oxidative burst. Pre-incubation of SSL11 with the glycan Sialyl Lewis X blocked SSL11 function and de-glycosylation of dHL60 cells by PNGase F abolished SSL11 binding, suggesting that SSL11 functions via interacting with glycans. This is the first description of a bacterial toxin inhibiting neutrophil motility by inducing adhesion and “locking” cells in an adhesion stage. Therefore, this study might provide a new target against S. aureus infections.
PTMselect: optimization of protein modifications discovery by mass spectrometry
Authors: Perchey Renaud T. , Tonini Laure , Tosolini Marie , Fournié Jean-Jacques , Lopez Frédéric , Besson Arnaud , Pont Frédéric 
Published: March 2019

AbstractDiscovery of protein modification sites relies on protein digestion by proteases and mass spectrometry (MS) identification of the modified peptides. Depending on proteases used and target protein sequence, this method yields highly variable coverage of modification sites. We introduce PTMselect, a digestion-simulating software which tailors the optimal set of proteases for discovery of global or targeted modification from any single or multiple proteins.
Investigation of natural environmental radioactivity concentration in soil of coastaline area of Ado-Odo/Ota Nigeria and its radiological implications
Authors: Joel E. S. , Maxwell O. , Adewoyin O. O. , Olawole O. C. , Arijaje T. E. , Embong Z. , Saeed M. A. 
Published: March 2019

AbstractNatural radioactivity in coastaline area soil of Ado-Odo/Ota has been carried out to ascertain the presence of radionuclides using gamma-ray spectroscopy (HPGe detector). The result showed that U-238, Th-232 and K-40 ranged from 24 ± 7–49 ± 10; 67 ± 6–120 ± 9 and 88 ± 17–139 ± 20 Bqkg−1 respectively. The radium equivalent for the samples ranged from 132.51 to 230.91 Bqkg−1 with mean value of 185.89 Bqkg−1. The mean value for the gamma dose rate for the soil samples was estimated to be 81.32 nGyh−1. The estimated values of annual effective dose equivalent ranged from 0.61 to 1.07 mSv y−1. The estimation of alpha index representative (Iα) ranged from 0.12 to 0.24 with mean value of 0.21 while the gamma representative index ranged between 0.465 and 0.810. The activity utilization index of the soil samples ranged from 1.09 to 1.89 with mean value of 1.53. The radiological implication in the study area has shown that the soil samples with gamma dose rate value of 89.99 nGyh−1, 94.39 nGyh−1, 97.40 nGyh−1 and 101.04 nGyh−1 respectively are higher than the recommended value of 80 nGyh−1 and may pose health implication for long term exposure.
A comparison between the abdominal and femoral adipose tissue proteome of overweight and obese women
Authors: Vogel M. A. A. , Wang P. , Bouwman F. G. , Hoebers N. , Blaak E. E. , Renes J. , Mariman E. C. , Goossens G. H. 
Published: March 2019

AbstractBody fat distribution is an important determinant of cardiometabolic health. Lower-body adipose tissue (AT) has protective characteristics as compared to upper-body fat, but the underlying depot-differences remain to be elucidated. Here, we compared the proteome and morphology of abdominal and femoral AT. Paired biopsies from abdominal and femoral subcutaneous AT were taken from eight overweight/obese (BMI ≥ 28 kg/m2) women with impaired glucose metabolism after an overnight fast. Proteins were isolated and quantified using liquid chromatography-mass spectrometry, and protein expression in abdominal and femoral subcutaneous AT was compared. Moreover, correlations between fat cell size and the proteome of both AT depots were determined. In total, 651 proteins were identified, of which 22 proteins tended to be differentially expressed between abdominal and femoral AT after removal of blood protein signals (p < 0.05). Proteins involved in cell structure organization and energy metabolism were differently expressed between AT depots. Fat cell size, which was higher in femoral AT, was significantly correlated with ADH1B, POSTN and LCP1. These findings suggest that there are only slight differences in protein expression between abdominal and femoral subcutaneous AT. It remains to be determined whether these differences, as well as differences in protein activity, contribute to functional and/or morphological differences between these fat depots.
Characterization of the rumen and fecal microbiome in bloated and non-bloated cattle grazing alfalfa pastures and subjected to bloat prevention strategies
Authors: Azad E. , Derakhshani H. , Forster R. J. , Gruninger R. J. , Acharya S. , McAllister T. A. , Khafipour E. 
Published: March 2019

AbstractFrothy bloat is an often fatal digestive disorder of cattle grazing alfalfa pastures. The aim of this study was to investigate ruminal and fecal microbiota dynamics associated with development of alfalfa-induced frothy bloat and to further explore how bloat prevention strategies influence the composition of these microbial communities. In a 3 × 3 crossover experiment, twelve rumen-cannulated steers were sequentially subjected to: (1) pure alfalfa pasture, (2) pure alfalfa pasture supplemented with the pluronic detergent ALFASURE, and (3) alfalfa – sainfoin mixed pasture. Eleven out of 12 steers in pure alfalfa pasture developed clinical bloat, whereas ALFASURE treatment prevented the development of bloat in all 12 steers and alfalfa – sainfoin prevented bloat in 5 out of 11 steers. Development of bloat was associated with considerable shifts in the microbiota profile of rumen contents. In particular, the microbiota of solid rumen contents from bloated steers contained higher species richness and diversity. Streptococcus, Succinivibrio and unclassified Myxococcales were enriched in the rumen microbiota of bloated steers, whereas Fibrobacter and Ruminococcus were overrepresented in the rumen contents of non-bloated steers. Our results provide novel insights into bloat-associated shifts in the composition and predicted functional properties of the rumen microbiota of cattle grazing alfalfa pasture.
Deep structural brain lesions associated with consciousness impairment early after hemorrhagic stroke
Authors: Rohaut Benjamin , Doyle Kevin W. , Reynolds Alexandra S. , Igwe Kay , Couch Caroline , Matory Adu , Rizvi Batool , Roh David , Velazquez Angela , Megjhani Murad , Park Soojin , Agarwal Sachin , Mauro Christine M. , Li Gen , Eliseyev Andrey , Perlbarg Vincent , Connolly Sander , Brickman Adam M. , Claassen Jan 
Published: March 2019

AbstractThe purpose of this study was to determine the significance of deep structural lesions for impairment of consciousness following hemorrhagic stroke and recovery at ICU discharge. Our study focused on deep lesions that previously were implicated in studies of disorders of consciousness. We analyzed MRI measures obtained within the first week of the bleed and command following throughout the ICU stay. A machine learning approach was applied to identify MRI findings that best predicted the level consciousness. From 158 intracerebral hemorrhage patients that underwent MRI, one third was unconscious at the time of MRI and half of these patients recovered consciousness by ICU discharge. Deep structural lesions predicted both, impairment and recovery of consciousness, together with established measures of mass effect. Lesions in the midbrain peduncle and pontine tegmentum alongside the caudate nucleus were implicated as critical structures. Unconscious patients predicted to recover consciousness by ICU discharge had better long-term functional outcomes than those predicted to remain unconscious.
Contrasting in vitro and in vivo methanol oxidation activities of lanthanide-dependent alcohol dehydrogenases XoxF1 and ExaF from Methylobacterium extorquens AM1
Authors: Good Nathan M. , Moore Riley S. , Suriano Carly J. , Martinez-Gomez N. Cecilia 
Published: March 2019

AbstractLanthanide (Ln) elements are utilized as cofactors for catalysis by XoxF-type methanol dehydrogenases (MDHs). A primary assumption is that XoxF enzymes produce formate from methanol oxidation, which could impact organisms that require formaldehyde for assimilation. We report genetic and phenotypic evidence showing that XoxF1 (MexAM1_1740) from Methylobacterium extorquens AM1 produces formaldehyde, and not formate, during growth with methanol. Enzyme purified with lanthanum or neodymium oxidizes formaldehyde. However, formaldehyde oxidation via 2,6-dichlorophenol-indophenol (DCPIP) reduction is not detected in cell-free extracts from wild-type strain methanol- and lanthanum-grown cultures. Formaldehyde activating enzyme (Fae) is required for Ln methylotrophic growth, demonstrating that XoxF1-mediated production of formaldehyde is essential. Addition of exogenous lanthanum increases growth rate with methanol by 9–12% but does not correlate with changes to methanol consumption or formaldehyde accumulation. Transcriptomics analysis of lanthanum methanol growth shows upregulation of xox1 and downregulation of mxa genes, consistent with the Ln-switch, no differential expression of formaldehyde conversion genes, downregulation of pyrroloquinoline quinone (PQQ) biosynthesis genes, and upregulation of fdh4 formate dehydrogenase (FDH) genes. Additionally, the Ln-dependent ethanol dehydrogenase ExaF reduces methanol sensitivity in the fae mutant strain when lanthanides are present, providing evidence for the capacity of an auxiliary role for ExaF during Ln-dependent methylotrophy.
Carbon replicas reveal double stranded structure of tight junctions in phase-contrast electron microscopy
Authors: Krystofiak Evan S. , Heymann J. Bernard , Kachar Bechara 
Published: March 2019

AbstractReplica-based freeze-fracture and freeze-etching electron microscopy methods provide surface topography information, particularly suited to studying membrane protein complexes in their native context. The fidelity and resolution of metal replicas is limited by the inherent property of metal atoms to crystallize. To overcome the limitations of metal replicas, we combined amorphous carbon replicas with phase-contrast electron microscopy. Using this approach, tight junction intramembrane fibrils were shown to have a double stranded morphology.
The Relationship Between Operational Competency, Buy-In, and Augmentative and Alternative Communication Use in School-Age Children With Autism
Authors: DeCarlo Jenna , Bean Allison , Lyle Samantha , Paden Miller Cargill Lindsey 
Published: March 2019

Purpose
The objective of this study was to investigate the relationship between 2 variables that influence augmentative and alternative communication (AAC) use, caregiver operational competency (i.e., the ability to navigate, customize, and program the device), and AAC system buy-in (i.e., understanding that the device acts as the child's voice and should be treated as an extension of his or her physical body), to determine if there was a relationship between these variables and device use at home and at school in school-age children with autism who use AAC.

Method

The device use of 29 school-age children (
M
age
= 7.82 years) with an educational diagnosis of autism who use AAC was tracked using the logging feature on the participants' AAC devices. Participants' parents (
n
= 29) and teachers (
n
= 14, some teachers reported on multiple students) completed a questionnaire assessing caregiver operational competency and AAC system buy-in. Minutes of data use were extracted from each participant's AAC device (
Cross & Segalman, 2016
) and averaged across three randomly selected dates.

Results
The parents and teachers reported high rates of operational competency and buy-in. However, only 10 of the children used their devices at home during the weekends. Despite high rates of parent- and teacher-reported operational competency, participants did not use their devices at high rates.

Conclusion
Speech-language pathologists may also need to focus on other aspects of parent and teacher training, such as creating communication opportunities for students who use AAC to increase device use at home and at school.
Growth Effects on Velopharyngeal Anatomy From Childhood to Adulthood
Authors: Perry Jamie L. , Kollara Lakshmi , Sutton Bradley P. , Kuehn David P. , Fang Xiangming 
Published: March 2019

PurposeThe observed sexual dimorphism of velopharyngeal structures among adult populations has not been observed in the young child (4- to 9-year-old) population. The purpose of this study was to examine the age at which sexual dimorphism of velopharyngeal structures become apparent and to examine how growth trends vary between boys and girls.MethodStatic 3-dimensional magnetic resonance imaging velopharyngeal data were collected among 202 participants ranging from 4 to 21 years of age. Participants were divided into 3 groups based on age, including Group 1: 4–10 years of age, Group 2: 11–17 years of age, and Group 3: 18–21 years of age. Nine velopharyngeal measures were obtained and compared between groups.ResultsSignificant sex effects were evident for levator length (p= .011), origin to origin (p= .018), and velopharyngeal ratio (p= .036) for those in Group 2 (11–17 years of age). Sex effects became increasingly apparent with age, with 7 of 9 variables becoming significantly different between male and female participants in Group 3. Boys, in general, displayed a delayed growth peak in velopharyngeal growth compared to girls.ConclusionResults from this study demonstrate the growth of velopharyngeal anatomy with sexual dimorphism becoming apparent predominantly after 18 years of age. However, velopharyngeal variables displayed variable growth trends with some variables presenting sexual dimorphism at an earlier age compared to other velopharyngeal variables.
Akzeptanz des fäkalen Mikrobiota-Transfers (Stuhltransplantation) als alternative Therapie bei Patienten mit Colitis ulcerosa
Authors: Roggenbrod Sebastian , Schuler Constantin , Haller Bernhard , Sohn Maximilian , Storr Martin , Schepp Wolfgang , Gundling Felix 
Published: March 2019

Zusammenfassung
Einleitung Die Stuhltransplantation (Fäkaler Mikrobiota-Transfer, FMT) stellt eine mögliche Behandlungsoption für die rezidivierende pseudomembranöse Colitis dar. Zusätzlich gibt es Hinweise, dass die FMT auch in der Behandlung der Colitis ulcerosa wirksam ist. Ziel dieser Studie ist die Untersuchung hinsichtlich Akzeptanz auf Patientenseite anhand eines Fragebogens.
Methodik Ein standardisierter Fragebogen aus 27 geschlossenen Fragen wurde an eine Patientenkohorte von 262 Patienten mit Colitis ulcerosa versendet. Inhalt waren Fragen u. a. zu Ablauf der FMT, Spendern sowie möglichen Bedenken. Zusätzlich wurden Aspekte des sozialen Hintergrunds sowie zur Krankheitsaktivität der Colitis ulcerosa evaluiert.
Ergebnis Die Rücklaufrate der Fragebögen lag bei 31,3 % (n = 82). 48 (58,5 %) der Patienten war die FMT bekannt. 46 (56,1 %) gaben an, bei entsprechender Indikation eine FMT durchführen zu lassen. Als Hauptmotivation wurde von 33 Patienten (40,2 %) die (vorausgesetzte) Wirksamkeit des Verfahrens sowie von 14 (17,1 %) Patienten ein Versagen aller anderen Therapien (17,1 %) genannt. Bedenken bestanden im Hinblick auf die mangelnde Testung des Transplantats hinsichtlich möglicher Infektionserreger (22, 28,9 %) sowie eine potenzielle Kontamination des Transplantats mit Gefahr einer möglichen (nachteiligen) Beeinflussung des aktuellen Krankheitsverlaufs (17, 20,7 %).Als Verabreichungsform bevorzugten 55 Patienten (67,1 %) die FMT in Tablettenform, gefolgt von einer koloskopischen Applikation (36, 43,9 %). Als Spender wurde die vom behandelnden Arzt vorgeschlagene Person (43, 52,4 %) favorisiert. Die Bereitschaft zur FMT unterschied sich bei beiden Geschlechtern nicht signifikant (56,4 % bei ♀ vs. 57,1 % bei ♂). Bei Rauchern (88,9 %), Patienten, die auf Fernsehkonsum verzichten (77,8 %) sowie Patienten mit privater Krankenversicherung (70,6 %) war die Akzeptanz der FMT besonders hoch.
Schlussfolgerung Die FMT stellt für die Mehrheit der durch uns befragten Patienten mit Colitis ulcerosa eine erwägenswerte Therapieform mit bereits hohem Bekanntheitsgrad dar. Knapp die Hälfte der Befragten würden unter bestimmten Voraussetzungen trotz mindestens zufriedenstellenden Ansprechens auf die bisherige (konventionelle) Therapie eine FMT als alternative Behandlung erwägen. Erwartungsgemäß bestehen Bedenken im Hinblick auf die Übertragung möglicher Krankheitserreger sowie hinsichtlich der hygienekonformen Durchführung des Verfahrens.
Thiadiazoloquinoxalines
Authors: Hu Ben-Lin , Baumgarten Martin 
Published: March 2019

In this account we summarized our work on the modification and extension of the thiadiazoloquinoxaline (TQ) as a strong acceptor unit for organic electronics. While also alternating conjugated copolymers with different donors were published, the focus here is the description of variation of the acceptor unit leading to many small molecules with different electronic properties as indicated from their optical absorptions, cyclic voltammetry (CV) data, density functional theory (DFT), and time-dependent (TD-DFT) calculations. The extension with ortho-diquinones seemed a promising way to enlarge the TQ molecules and further increase their electron affinity. At the end it is demonstrated how these units can be merged with other acceptors like naphthalenediimide (NDI) and be extended in an iterative way to extremely long condensed pyrene-fused heteroacenes with TQ end groups just by ring opening of the thiadiazole five-membered ring followed by further condensations in an iterative way.1	Introduction2	The Synthesis of TQ Cores3	The Extension of TQ3.1	The Extension at 4,9-Positions3.2	The Extension at 6,7-Positions3.3	The Extension on NDI3.4	The Extension with TQ for Endcapping (Bis TQ)4	Conclusions
Opening-Wedge High Tibial Osteotomy Using Autograft versus Allograft: A Systematic Review and Meta-analysis
Authors: Ren Yi-Ming , Duan Yuan-Hui , Sun Yun-Bo , Yang Tao , Hou Wei-Yu , Zhu Ru-Sen , Tian Meng-Qiang 
Published: March 2019

AbstractBone grafting is a good alternative for filling the inevitable void that is created following opening-wedge high tibial osteotomy (OWHTO). This systematic review and meta-analysis evaluated whether bone grafting is necessary for OWHTO and the successful outcomes of OWHTO using either autograft (AU) or allograft (AL). All analyzed studies were acquired from PubMed, Medline, Embase, CNKI, Google Scholar, and Cochrane Library. Data were independently extracted by two coauthors and were analyzed using RevMan5.3. Mean differences, odds ratios, and 95% confidence intervals were calculated. Cochrane Collaboration's Risk of Bias Tool and Newcastle–Ottawa Scale were used to assess the risk of bias. In total, 10 studies were assessed including three randomized controlled trials and seven observational studies. The methodological quality of the trials ranged from low to high. The overall estimate demonstrated that the difference between OWHTO using AU and AL groups and OWHTO using no filling group was not statistically significant for the loss of correction, and complications, but OWHTO using no filling group statistically showed better knee society score. Pooled results of reoperations, lateral cortex breaches, complications, and clinical function assessments showed no significant difference between AU and AL materials. Using AL statistically reduced the operative time compared with using AU. OWHTO with or without bone graft does not affect postoperative complications. No loss of correction was observed due to the lack of bone grafting. In addition, OWHTO without bone graft performs better for postoperative clinical function assessment. Complications and clinical results of medial OWHTO were similar using AL and AU and neither reported a median loss of correction of following OWHTO. Compared with using AU, using AL avoids harvest site complications and reduces operative time. To sum up, OWHTO without any bone graft is recommended for medial unicompartmental osteoarthritis of the knee. Further large-sample, multicenter, high-quality, randomized controlled trials are warranted to verify the outcomes of this meta-analysis.