bluuebunny/crossref_metadata_2025_split huggingface dataset:
Investigating the effect of sexual behaviour on oropharyngeal cancer risk: a methodological assessment of Mendelian randomization
Authors: Gormley Mark , Dudding Tom , Kachuri Linda , Burrows Kimberley , Chong Amanda HW , Martin Richard M , Thomas Steven , Tyrrell Jessica , Ness Andrew R , Brennan Paul , Munafò Marcus R , Pring Miranda , Boccia Stefania , Olshan Andrew F , Diergaarde Brenda , Hung Rayjean J , Liu Geoffrey , Tajara Eloiza , Severino Patricia , Toporcov Tatiana N , Lacko Martin , Waterboer Tim , Brenner Nicole , Smith George Davey , Vincent Emma E , Richmond Rebecca C 
Published: June 2021

AbstractHuman papilloma virus infection is known to influence oropharyngeal cancer (OPC) risk, likely via sexual transmission. However, sexual behaviour has been correlated with other risk factors including smoking and alcohol, meaning independent effects are difficult to establish. Here we evaluate aspects of sexual behaviour in relation to the risk of OPC (2,641 cases and 6,585 controls), using genetic variants associated with age at first sex (AFS) and number of sexual partners (NSP) to perform Mendelian randomization (MR) analyses. While univariable MR showed a causal effect of both later AFS and increasing NSP on OPC, results attenuated in the multivariable models (AFS IVW OR 0.7, 95%CI 0.4, 1.2,p=0.21; NSP IVW OR 0.9, 95%CI 0.5 1.7,p=0.76). We also found evidence for correlated pleiotropy in the genetic instruments for sexual behaviour, emphasising the need for multivariable approaches when performing MR of complex behavioural traits and the triangulation of evidence.
Sound level context modulates neural activity in the human brainstem
Authors: Herrmann Björn , Yasmin Sonia , Araz Kurdo , Purcell David W. , Johnsrude Ingrid S. 
Published: June 2021

AbstractOptimal perception requires adaptation to sounds in the environment. Adaptation involves representing the acoustic stimulation history in neural response patterns, for example, by altering response magnitude or latency as sound-level context change. Neurons in the auditory brainstem of rodents are sensitive to acoustic stimulation history and sound-level context (often referred to as sensitivity to stimulus statistics), but the degree to which the human brainstem exhibits such neural adaptation is unclear. In six electroencephalography experiments with over 125 participants, we demonstrate that the response latency of the human brainstem is sensitive to the history of acoustic stimulation over a few tens of milliseconds. We further show that human brainstem responses adapt to sound-level context in, at least, the last 44 ms, but that neural sensitivity to sound-level context decreases when the time window over which acoustic stimuli need to be integrated becomes wider. Our study thus provides evidence of adaptation to sound-level context in the human brainstem and of the timescale over which sound-level information affects neural responses to sound. The research delivers an important link to studies on neural adaptation in non-human animals.
Identification of antigenic epitopes on the F and G glycoproteins of bovine respiratory syncytial virus and in vitro assessment of their synthetic peptide vaccine potential
Authors: Lemon J. , Douglas A. , Power U. , McMenamy MJ. 
Published: June 2021

AbstractGlobally, bovine respiratory disease (BRD) remains the principal reason for mortality of calves over one month of age despite the availability of various vaccines on the UK market. Bovine respiratory syncytial virus (BRSV) was first discovered in the 1970s and is now considered a principal pathogen implicated in the disease complex. Outbreaks occur annually and re-infections are common even in the presence of maternal antibodies. Difficulties have arisen from using both live-attenuated and inactivated vaccines and recent efforts have focused on the development of sub-unit vaccines that are suitable for use in neonatal calves with maternally-derived circulating antibodies. This study was undertaken to identify antigenic epitopes on two of the surface glycoproteins of BRSV, the fusion (F) and attachment (G) proteins, the major surface viral antigens, for inclusion into a novel subunit peptide vaccine. Sequencing and antigenicity prediction of the F and G genes of BRSV revealed 21 areas of potential antigenicity; of which genuine peptide/antisera binding occurred with 4 peptides. Identification of the antigenic components of a vaccine is an important first step in the development of novel BRSV vaccines and this data, therefore, provides the basis for the generation of such vaccines.
The developmental transcriptome of Parhyale hawaiensis: microRNAs and mRNAs show different expression dynamics during the maternal-zygotic transition
Authors: Calvo Llilians , Birgaoanu Maria , Pettini Tom , Ronshaugen Matthew , Griffiths-Jones Sam 
Published: June 2021

AbstractParhyale hawaiensis has emerged as the crustacean model of choice due to its tractability, ease of imaging, sequenced genome, and development of CRISPR/Cas9 genome editing tools. However, transcriptomic datasets spanning embryonic development are lacking, and there is almost no annotation of non-protein-coding RNAs, including microRNAs. We have sequenced microRNAs, together with mRNAs and long non-coding RNAs, in Parhyale using paired size-selected RNA-seq libraries at seven time-points covering important transitions in embryonic development. Focussing on microRNAs, we annotate 175 loci in Parhyale, 85 of which have no known homologs. We use these data to annotate the microRNome of 37 crustacean genomes, and suggest a core crustacean microRNA set of around 61 sequence families. We examine the dynamic expression of microRNAs and mRNAs during the maternal-zygotic transition. Our data suggest that zygotic genome activation occurs in two waves in Parhyale with microRNAs transcribed almost exclusively in the second wave. Contrary to findings in other arthropods, we do not predict a general role for microRNAs in clearing maternal transcripts. These data significantly expand the available transcriptomics resources for Parhyale, and facilitate its use as a model organism for the study of small RNAs in processes ranging from embryonic development to regeneration.
PV-specific loss of the transcriptional coactivator PGC-1α slows down the evolution of epileptic activity in an acute ictogenic model
Authors: Parrish R. Ryley , Mackenzie-Gray-Scott Connie , Walsh Darren , Racca Claudia , Cowell Rita M. , Trevelyan Andrew J. 
Published: June 2021

AbstractThe transcriptional coactivator, PGC-1α (peroxisome proliferator activated receptor gamma coactivator 1α), plays a key role coordinating energy requirement within cells. Its importance is reflected in the growing number of psychiatric and neurological conditions that have been associated with reduced PGC-1α levels. In cortical networks, PGC-1α is required for the induction of parvalbumin (PV) expression in interneurons, and PGC-1α deficiency affects synchronous GABAergic release. It is unknown, however, how this affects cortical excitability. We show here that knocking down PGC-1α specifically in the PV-expressing cells (PGC-1αPV-/-), blocks the activity-dependent regulation of the synaptic proteins, SYT2 and CPLX1. More surprisingly, this cell-class specific knock-out of PGC-1α appears to have a novel anti-epileptic effect, as assayed in brain slices bathed in 0 Mg2+ media. The rate of pre-ictal discharges developed approximately equivalently in wild-type and PGC-1αPV-/- brain slices, but the intensity of these discharges was lower in PGC-1αPV-/- slices, as evident from the reduced power in the gamma range and reduced firing rates in both PV interneurons and pyramidal cells during these discharges. Reflecting this reduced intensity in the pre-ictal discharges, the PGC-1αPV-/- brain slices experienced many more discharges before transitioning into a seizure-like event. Consequently, there was a large increase in the latency to the first seizure-like event in brain slices lacking PGC-1α in PV interneurons. We conclude that knocking down PGC-1α limits the range of PV interneuron firing, and this slows the pathophysiological escalation during ictogenesis.
Single cell multi-omics analysis of chromothriptic medulloblastoma highlights genomic and transcriptomic consequences of genome instability
Authors: Parra R. Gonzalo , Przybilla Moritz J , Simovic Milena , Susak Hana , Ratnaparkhe Manasi , Wong John KL , Körber Verena , Mallm Philipp , Sill Martin , Kolb Thorsten , Kumar Rithu , Casiraghi Nicola , Norali Ghasemi David R , Maaß Kendra Korinna , Pajtler Kristian W , Jauch Anna , Korshunov Andrey , Höfer Thomas , Zapatka Marc , Pfister Stefan M , Stegle Oliver , Ernst Aurélie 
Published: June 2021

ABSTRACTChromothripsis is a form of genome instability, whereby a presumably single catastrophic event generates extensive genomic rearrangements of one or few chromosome(s). However, little is known about the heterogeneity of chromothripsis across different clones from the same tumor, as well as changes in response to treatment. We analyzed single-cell genomic and transcriptomic alterations linked with chromothripsis in human p53-deficient medulloblastoma (n=7). We reconstructed the order of somatic events, identified early alterations likely linked to chromothripsis and depicted the contribution of chromothripsis to malignancy. We characterized subclonal variation of chromothripsis and its effects on double-minute chromosomes, cancer drivers and putatively druggable targets. Furthermore, we highlighted the causative role and the fitness consequences of specific rearrangements in neural progenitors.Graphical Abstract
Functional divergence of the bag of marbles gene in the Drosophila melanogaster species group
Authors: Bubnell Jaclyn E. , Ulbing Cynthia K.S. , Begne Paula Fernandez , Aquadro Charles F. 
Published: June 2021

AbstractIn Drosophila melanogaster, a key germline stem cell (GSC) differentiation factor, bag of marbles (bam) shows rapid bursts of amino acid fixations between sibling species D. melanogaster and D. simulans, but not in the outgroup species D. ananassae. Here, we test the null hypothesis that bam’s differentiation function is conserved between D. melanogaster and four additional Drosophila species in the melanogaster species group spanning approximately 30 million years of divergence. Surprisingly, we demonstrate that bam is not necessary for oogenesis or spermatogenesis in D. teissieri nor is bam necessary for spermatogenesis in D. ananassae. Remarkably bam function may change on a relatively short time scale. We further report tests of neutral sequence evolution at bam in additional species of Drosophila and find a positive, but not perfect, correlation between evidence for positive selection at bam and its essential role in GSC regulation and fertility for both males and females. Further characterization of bam function in more divergent lineages will be necessary to distinguish between bam’s critical gametogenesis role being newly derived in D. melanogaster, D. simulans, D. yakuba, and D. ananassae females or it being basal to the genus and subsequently lost in numerous lineages.
ETV2 primes hematoendothelial gene enhancers prior to hematoendothelial fate commitment
Authors: Steimle Jeffrey D. , Kim Chul , Nadadur Rangarajan D. , Wang Zhezhen , Hoffmann Andrew D. , Hanson Erika , Kweon Junghun , Sinha Tanvi , Choi Kyunghee , Black Brian L. , Cunningham John M. , Ikegami Kohta , Moskowitz Ivan P. 
Published: June 2021

SUMMARYThe lineage-determining transcription factor ETV2 is necessary and sufficient for hematoendothelial fate commitment. We investigated how ETV2-driven gene regulatory networks promote hematoendothelial fate commitment. We resolved the sequential determination steps of hematoendothelial versus cardiac differentiation from mouse embryonic stem cells.Etv2was strongly induced and bound to the enhancers of hematoendothelial genes in a common cardiomyocyte-hematoendothelial mesoderm progenitor. However, onlyEtv2itself andTal1, not other ETV2-bound genes, were induced. Despite ETV2 genomic binding andEtv2andTal1expression, cardiomyogenic fate potential was maintained. A second wave of ETV2-bound target genes was up-regulated during the transition from the common cardiomyocyte-hematoendothelial progenitor to the committed hematoendothelial population. A third wave of ETV-bound genes were subsequently expressed in the committed hematoendothelial population for sub-lineage differentiation. The shift from ETV2 binding to productive transcription, not ETV2 binding to target gene enhancers, drove hematoendothelial fate commitment. This work identifies mechanistic phases of ETV2-dependent gene expression that distinguish hematoendothelial specification, commitment, and differentiation.HIGHLIGHTSThe hematoendothelial master TF ETV2 is expressed in a multipotent mesoderm progenitor.ETV2 binds to target genes in the mesoderm progenitor without target gene activation.ETV2 binding in the mesoderm progenitor does not diminish alternative cardiac fate potential.ETV2-bound target genes are activated upon hematoendothelial fate commitment.GRAPHICAL ABSTRACT
Simulation study evaluating the ability of two statistical approaches to identify variance quantitative trait loci Arabidopsis and maize
Authors: Murphy Matthew D. , Fernandes Samuel B. , Morota Gota , Lipka Alexander E. 
Published: June 2021

AbstractGenomic loci that control the variance of agronomically important traits are increasingly important due to the profusion of unpredictable environments arising from climate change. The ability to identify such variance quantitative trait loci (vQTL) in association studies will be critical for future breeding efforts. Two statistical approaches that have already been used to detect vQTL are the Brown-Forsythe test (BFT) and the double generalized linear model (DGLM). To ensure that they are deployed to variance genome-wide association studies as effectively as possible, it is critical to study the factors that influence their ability to identify vQTL. We used genome-wide marker data in maize (Zea maysL.) andArabidopsis thalianato simulate traits controlled by variance quantitative trait nucleotides (vQTNs) and then quantified true and false positive detection rates of the BFT and DGLM. We observed that the DGLM yielded similar or higher true positive vQTN detection rates than the BFT, regardless of the effect size or minor allele frequency (MAF) of the vQTNs. Low true positive detection rates were noted for QTNs with low MAFs (~0.10), especially when tested on subsets ofn= 500 individuals. We recommend that larger data sets than those used in our study (i.e.,n> 2,532) be considered to overcome these low observed true positive detection rates. Such an undertaking should maximize the potential of the BFT and DGLM to highlight which vQTLs should be considered for further study.
Use of untargeted magnetic beads to capture Mycobacterium smegmatis and Mycobacterium avium paratuberculosis prior detection by mycobacteriophage D29 and Real-Time-PCR
Authors: Rojas-Ponce Gabriel , Sauvageau Dominic , Zemp Roger , Barkema Herman W. , Evoy Stephane 
Published: June 2021

ABSTRACTUntargeted magnetic beads were evaluated to capture Mycobacterium smegmatis and Mycobacterium avium subspecies paratuberculosis (MAP) from spiked feces, milk, and urine. Untargeted magnetic beads recovered more M. smegmatis cells from PBS suspension than the typical centrifugation method; 96.31% of 1.68 × 104 CFU/mL viable M. smegmatis were recovered by beads and 0% by centrifugation. Likewise, the F57-qPCR detection of MAP cells was different whether they were recovered by beads or centrifugation; cycle threshold (Ct) was lower (p<0.05) for the detection of MAP cells recovered by beads than centrifugation, indicative of higher sensitivity. Magnetic separation of MAP cells from milk, urine, and feces specimens were detected by F57 and IS900 sequences. Ct values demonstrated that beads captured no less than 109 CFU/mL from feces and no less than 104 CFU/mL from milk and urine suspensions. In another detection strategy, M. smegmatis coupled to magnetic beads were infected by mycobacteriophage D29. Plaque forming units were observed after 24 h of incubation from urine samples containing 2 × 105 and 2 × 103 CFU/mL M. smegmatis. The results of this study provide a promising tool for diagnosis of Johne’s disease and other mycobacterial diseases such as tuberculosis.
AwAlbBWolbachiatransinfection displays stable phenotypic effects across divergentAedes aegyptimosquito backgrounds
Authors: Ross Perran A. , Gu Xinyue , Robinson Katie L. , Yang Qiong , Cottingham Ellen , Zhang Yifan , Yeap Heng Lin , Xu Xuefen , Endersby-Harshman Nancy M. , Hoffmann Ary A. 
Published: June 2021

AbstractAedesmosquitoes harboring intracellularWolbachiabacteria are being released in arbovirus and mosquito control programs. With releases taking place around the world, understanding the contribution of host variation toWolbachiaphenotype is crucial. We generated aWolbachiatransinfection (wAlbBQ) inAedes aegyptiand performed backcrossing to introduce the infection into Australian or Malaysian nuclear backgrounds. WholeWolbachiagenome sequencing shows that thewAlbBQtransinfection is near-identical to the referencewAlbB genome, suggesting few changes since the infection was first introduced toAe. aegyptiover 15 years ago. However, these sequences were distinct from other availablewAlbB genome sequences, highlighting the potential diversity ofwAlbB in naturalAe. albopictuspopulations. Phenotypic comparisons demonstrate effects ofwAlbB infection on egg hatch and nuclear background on fecundity and body size, but no interactions betweenwAlbB infection and nuclear background for any trait. ThewAlbB infection was stable at high temperatures and showed perfect maternal transmission and cytoplasmic incompatibility regardless of host background. Our results demonstrate the stability ofwAlbB across host backgrounds and point to its long-term effectiveness for controlling arbovirus transmission and mosquito populations.
Successional Stages in Infant Gut Microbiota Maturation
Authors: Beller Leen , Deboutte Ward , Falony Gwen , Vieira-Silva Sara , Tito Raul Yhossef , Valles-Colomer Mireia , Rymenans Leen , Jansen Daan , Van Espen Lore , Papadaki Maria Ioanna , Shi Chenyan , Yinda Claude Kwe , Zeller Mark , Faust Karoline , Van Ranst Marc , Raes Jeroen , Matthijnssens Jelle 
Published: June 2021

ABSTRACTBackgroundDisturbances in the primary colonization of the infant gut can result in life-long consequences and have been associated with a range of host conditions. Although early life factors have been shown to affect the infant gut microbiota development, our current understanding of the human gut colonization in early life remains limited.To gain more insights in the unique dynamics of this rapidly evolving ecosystem, we investigated the microbiota over the first year of life in eight densely sampled infants (total number of samples, n=303). To evaluate gut microbiota maturation transition towards an adult configuration, we compared the microbiome composition of the infants to the Flemish Gut Flora Project population (n=1,106).ResultsWe observed the infant gut microbiota to mature through three distinct, conserved stages of ecosystem development. Across these successional gut microbiota maturation stages, genus predominance was observed to shift fromEscherichiaoverBifidobacteriumtoBacteroides. Both disease and antibiotic treatment were observed to be associated occasionally with gut microbiota maturation stage regression, a transient setback in microbiota maturation dynamics. Although the studied microbiota trajectories evolved to more adult-like constellations, microbiome community typing against the background of the Flemish Gut Flora Project (FGFP) cohort clustered all infant samples within the (in adults) potentially dysbiotic Bact2 enterotype.ConclusionWe confirmed similarities between infant gut microbial colonization and adult dysbiosis. A profound knowledge about the primary gut colonization process in infants might provide crucial insights into how the secondary colonization of a dysbiotic adult gut can be redirected.
Undergraduate teaching assistantships: exploring career readiness and relationality among Emirati students
Authors: Patka Mazna , Bukhash Maryam Fuad , Jogia Jigar , Barbato Mariapaola , Moussa Mona 
Published: June 2021

PurposeThe purpose of this study was to pilot an undergraduate teaching assistantship for Emirati students, an area of scholarship underexplored in the Middle East. The teaching assistantship was developed to better prepare students for the workforce, amidst the push for Emiratization.Design/methodology/approachOver the course of one semester, four undergraduate teaching assistants documented their experience through reflexive journals that were analysed using a reflexive thematic analysis.FindingsUndergraduate teaching assistants characterised their experience as providing professional development and learning to connect with student learners. Findings suggest that relationality may be an important factor in student engagement and learning.Practical implicationsUnderstanding the experience of undergraduate teaching assistants can help develop targeted opportunities to enhance career readiness. Exploring the role of relationality could be important in the training and development of the Emirati workforce and help address some of the gaps in skills. Understanding the way in which undergraduate teaching assistants perceive their teaching experience can also provide faculty with insight into their teaching practices.Originality/valueThis exploratory study shows that students are able to acquire skills that may be applied in a variety of work settings (e.g. balancing multiple responsibilities). However, undergraduate teaching assistants expressed wanting to connect with student learners; this may be more culturally rooted and is less explored within the Emirati context. Given the socio-cultural context of the United Arab Emirates (UAE), female Emiratis may benefit from work-type opportunities, which to the authors’ knowledge has not been explored previously.
A cause for celebration! A psychographic typology of attendees at a benefit concert
Authors: Kruger Martinette , Viljoen Adam 
Published: June 2021

Purpose
This exploratory study aims to show that events can create awareness and facilitate behavioural change among attendees. Festivals and events can use the United Nations sustainable development goals as drivers of societal change and business growth. Unfortunately, the attendees to a benefit concert have not been investigated to date. This study fills this gap by segmenting attendees to a benefit concert aimed at eradicating poverty.

Design/methodology/approach
A quantitative destination-based survey was undertaken at the Mandela 100: Global Citizen Festival in Johannesburg, South Africa, in 2018. A simple random sampling method was used within a stratified sampling method, and 408 questionnaires were obtained.

Findings
Three psychographic segmentation variables were used: motives for attending the event (novelty, escape and socialization and cause advocating); behavioural intentions and change as a result of attending the event (cognition and awareness, loyalty-related behaviour, active engagement and travel-related behaviour); and global causes aimed at eradicating poverty that attendees regard as important to support (social, sustainability, fiscal, fundamental and elevated prosperity). The results revealed three distinct segments, proposing that an AID-typology applies to benefit concert attendees: advocates, inspirers and discoverers. Each group has either a high, moderate or low level of commitment towards the festival’s and other global causes.

Practical implications
Practical implications are suggested as guidelines to encourage advocacy and active involvement for global causes.

Originality/value
This study was conducted from a developing country’s perspective and contextualizes the role that events can play in advocating for specific causes and encouraging citizens to get involved.