bluuebunny/crossref_metadata_2025_split huggingface dataset:
HaploTypo: a variant-calling pipeline for phased genomes
Authors: Pegueroles Cinta , Mixão Verónica , Carreté Laia , Molina Manu , Gabaldón Toni 
Published: December 2019

Abstract

Summary
An increasing number of phased (i.e. with resolved haplotypes) reference genomes are available. However, the most genetic variant calling tools do not explicitly account for haplotype structure. Here, we present HaploTypo, a pipeline tailored to resolve haplotypes in genetic variation analyses. HaploTypo infers the haplotype correspondence for each heterozygous variant called on a phased reference genome.

Availability and implementation
HaploTypo is implemented in Python 2.7 and Python 3.5, and is freely available at https://github.com/gabaldonlab/haplotypo, and as a Docker image.

Supplementary information
Supplementary data are available at Bioinformatics online.
Subthalamic Nucleus Activity Influences Sensory and Motor Cortex during Force Transduction
Authors: Alhourani Ahmad , Korzeniewska Anna , Wozny Thomas A , Lipski Witold J , Kondylis Efstathios D , Ghuman Avniel S , Crone Nathan E , Crammond Donald J , Turner Robert S , Richardson R Mark 
Published: December 2019

Abstract
The subthalamic nucleus (STN) is proposed to participate in pausing, or alternately, in dynamic scaling of behavioral responses, roles that have conflicting implications for understanding STN function in the context of deep brain stimulation (DBS) therapy. To examine the nature of event-related STN activity and subthalamic-cortical dynamics, we performed primary motor and somatosensory electrocorticography while subjects (n = 10) performed a grip force task during DBS implantation surgery. Phase-locking analyses demonstrated periods of STN-cortical coherence that bracketed force transduction, in both beta and gamma ranges. Event-related causality measures demonstrated that both STN beta and gamma activity predicted motor cortical beta and gamma activity not only during force generation but also prior to movement onset. These findings are consistent with the idea that the STN participates in motor planning, in addition to the modulation of ongoing movement. We also demonstrated bidirectional information flow between the STN and somatosensory cortex in both beta and gamma range frequencies, suggesting robust STN participation in somatosensory integration. In fact, interactions in beta activity between the STN and somatosensory cortex, and not between STN and motor cortex, predicted PD symptom severity. Thus, the STN contributes to multiple aspects of sensorimotor behavior dynamically across time.
Lipoprotein receptor signalling in atherosclerosis
Authors: Mineo Chieko 
Published: December 2019

AbstractThe founding member of the lipoprotein receptor family, low-density lipoprotein receptor (LDLR) plays a major role in the atherogenesis through the receptor-mediated endocytosis of LDL particles and regulation of cholesterol homeostasis. Since the discovery of the LDLR, many other structurally and functionally related receptors have been identified, which include low-density lipoprotein receptor-related protein (LRP)1, LRP5, LRP6, very low-density lipoprotein receptor, and apolipoprotein E receptor 2. The scavenger receptor family members, on the other hand, constitute a family of pattern recognition proteins that are structurally diverse and recognize a wide array of ligands, including oxidized LDL. Among these are cluster of differentiation 36, scavenger receptor class B type I and lectin-like oxidized low-density lipoprotein receptor-1. In addition to the initially assigned role as a mediator of the uptake of macromolecules into the cell, a large number of studies in cultured cells and in in vivo animal models have revealed that these lipoprotein receptors participate in signal transduction to modulate cellular functions. This review highlights the signalling pathways by which these receptors influence the process of atherosclerosis development, focusing on their roles in the vascular cells, such as macrophages, endothelial cells, smooth muscle cells, and platelets. Human genetics of the receptors is also discussed to further provide the relevance to cardiovascular disease risks in humans. Further knowledge of the vascular biology of the lipoprotein receptors and their ligands will potentially enhance our ability to harness the mechanism to develop novel prophylactic and therapeutic strategies against cardiovascular diseases.
Safety and outcome of very high-power short-duration ablation using 70 W for pulmonary vein isolation in patients with paroxysmal atrial fibrillation
Authors: Kottmaier Marc , Popa Miruna , Bourier Felix , Reents Tilko , Cifuentes Jairo , Semmler Verena , Telishevska Martha , Otgonbayar Ulamnemekh , Koch-Büttner Katharina , Lennerz Carsten , Bartkowiak Marcin , Kornmayer Marielouise , Rousseva Elena , Brkic Amir , Grebmer Christian , Kolb Christoph , Hessling Gabriele , Deisenhofer Isabel 
Published: December 2019

Abstract

Aims
Pulmonary vein isolation (PVI) using radiofrequency ablation (RFA) in patients with paroxysmal atrial fibrillation (PAF) is effective but hampered by pulmonary vein reconnection due to insufficient ablation lesions. High-power delivery over a short period of time (HPSD) in RFA is stated to create more efficient lesions. The aim of this study was to compare intraprocedural safety and outcome of HPSD ablation to conventional power settings in patients undergoing PVI for PAF.

Methods and results
We included 197 patients with PAF that were scheduled for PVI. An ablation protocol with 70 W and a duration cut-off of 7 s at the anterior left atrium (LA) and 5 s at the posterior LA (HPSD group; n = 97) was compared to a conventional power protocol with 30–40 W for 20–40 s (standard group; n = 100) in terms of periprocedural complications and a 1-year outcome. The HPSD group showed significantly less arrhythmia recurrence during 1-year follow-up with 83.1% of patients free from atrial fibrillation compared to 65.1% in the standard group (P &lt; 0.013). No pericardial tamponade, periprocedural thromboembolic complications, or atrio-oesophageal fistula occurred in either group. Mean radiofrequency time (12.4 ± 3.4 min vs. 35.6 ± 12.1 min) and procedural time (89.5 ± 23.9 min vs. 111.15 ± 27.9 min) were significantly shorter in the HPSD group compared to the standard group (both P &lt; 0.001).

Conclusion
High-power short-duration ablation demonstrated a comparable safety profile to conventional ablation. High-power short-duration ablation using 70 W for 5–7 s leads to significantly less arrhythmia recurrences after 1 year. Radiofrequency and procedural time were significantly shortened.
Weight gain in early years and subsequent body mass index trajectories across birth weight groups: a prospective longitudinal study
Authors: Lu Yi , Pearce Anna , Li Leah 
Published: December 2019

Abstract

Background
Rapid weight gain (RWG) in early-life is associated with increased risk of childhood obesity and is common among low-birth weight infants. Few studies have compared body mass index (BMI) trajectories of children experienced RWG to those who did not, across birth weight groups. We investigated the association between RWG in early-life and subsequent BMI trajectory and whether the association differs by birth weight.

Methods
We included term singletons from the UK Millennium Cohort Study (n = 10 637). RWG was defined as an increase in weight z-scores (derived using UK–WHO growth reference) between birth and 3 years &gt;0.67. Mixed-effect fractional polynomial models were applied to examine the association between RWG and BMI trajectories (5–14 years). Models were further adjusted for confounders and stratified by birth weight-for-gestational-age group.

Results
Mean BMI trajectories were higher in children who experienced RWG in early-life, compared with their non-RWG counterparts. RWG was associated with higher BMI at five years [by 0.76 kg/m2 (95% CI: 0.67–0.85) in boys and 0.87 kg/m2 (0.76–0.97) in girls]; the difference persisted into adolescence [1.37 kg/m2 (1.17–1.58) and 1.75 kg/m2 (1.52–1.99) at 14 years, respectively]. Differences remained after adjustment and were particularly greater for children born large-for-gestational-age than those born small- and appropriate-for-gestational-age. Mean BMI trajectories for large-for-gestational-age children with RWG exceeded international reference curves for overweight (for obesity at some ages in girls).

Conclusions
RWG was associated with higher BMI trajectories throughout childhood and adolescence, especially in large-for-gestational-age children. Strategies for obesity prevention need to address factors during and before infancy and preventing excessive weight gain among infants who have already had adequate growth in utero.
Genomic and gene expression evidence of nonribosomal peptide and polyketide production among ruminal bacteria: a potential role in niche colonization?
Authors: Moreira Sofia Magalhães , de Oliveira Mendes Tiago Antônio , Santanta Mateus Ferreira , Huws Sharon A , Creevey Christopher J , Mantovani Hilário C 
Published: December 2019

ABSTRACT
Genomic and transcriptomic analyses were performed to investigate nonribosomal peptide synthetases (NRPS) and polyketide synthases (PKS) in 310 genomes of ruminal/fecal microorganisms. A total of 119 biosynthetic genes potentially encoding distinct nonribosomal peptides (NRPs) and polyketides (PKs) were predicted in the ruminal microbial genomes and functional annotation separated these genes into 19 functional categories. The phylogenetic reconstruction of the 16S rRNA sequences coupled to the distribution of the three ‘backbone’ genes involved in NRPS and PKS biosyntheses suggested that these genes were not acquired through horizontal gene transfer. Metatranscriptomic analyses revealed that the predominant genes involved in the synthesis of NRPs and PKs were more abundant in sheep rumen datasets. Reads mapping to the NRPS and PKS biosynthetic genes were represented in the active ruminal microbial community, with transcripts being highly expressed in the bacterial community attached to perennial ryegrass, and following the main changes occurring between primary and secondary colonization of the forage incubated with ruminal fluid. This study is the first comprehensive characterization demonstrating the rich genetic capacity for NRPS and PKS biosyntheses within rumen bacterial genomes, which highlights the potential functional roles of secondary metabolites in the rumen ecosystem.
Transnationalism, Subjectivities and Spatial Relations in Jane Katjavivi’s Undisciplined Heart
Authors: Mlambo Nelson 
Published: December 2019

Abstract
This article explores the literary representations of the ‘unsaid’ and intangible connections of humanity across cultures as represented in Undisciplined Heart (2010), the memoir of the Namibian writer Jane Katjavivi. The central concerns are to examine how the author, through the act of writing, ascertains a new female identity within a culturally transforming Africa; how the fictionalization of her life is a revolutionary way of abdicating the role of silent white-female spectator in Africa; and how her story is a voice that matters in as much as it demonstrates the salient cultural relatedness and connectedness in Africa. The issues and concerns around transnational families, transculturalism, female subjectivity, agency, transnationality and multiculturalism are therefore central in this article.
The guiding principles of this essay are Ubuntu (ubuntuism) and Afro-transnationalism in order to explore the sense of ‘rainbowism’ as articulated within a transnational, multiracial and multicultural literary text, Undisciplined Heart. The article brings to the fore the often overlooked presence of ‘white’ writing in postcolonial and post-independence Africa and provides some nuanced insights into the racial and cultural patterns of connectedness – the harmonious cross-cultural sense of being in an Africa that is both culturally and spatially diverse. The article also interrogates as well as problematizes the elusive and constantly changing issues of identity and belonging.
Class Analysis and the Killing of the Newborn Child: Manchester, 1790–1860
Authors: Beattie Ian 
Published: December 2019

Abstract
This article explores the practice of neonaticide – the killing of an infant at the moment of birth – in Manchester during the first decades of the industrial revolution. Using a set of previously unexamined pre-trial witness statements, the author makes the case that newborn-killing was practised by working-class women in the town as a known and even accepted form of birth control. There is quite suggestive evidence that women had a language for this practice, shielded other women from having it reported, and in certain circumstances, assisted one another in carrying it out. This finding resonates with similar moral frameworks that have been studied from high-medieval England to early colonial Mexico. Nonetheless, it has also been well established that middle-class people throughout the nineteenth century in Britain abhorred infant killing, associated it strongly with stigmatized stereotypes of working-class maternity, and sought to suppress it using the punitive weight of the law. Period diaries and publications show that this ‘moral panic’ was as potent in Manchester as anywhere else. Taking these contrary patterns together, the author suggests that neonaticide and practices like it allow historians to observe the profound cultural divisions and frictions along class lines which structured life in the early industrial city.
Early Induction of Cross-Reactive CD8+ T-Cell Responses in Tonsils After Live-Attenuated Influenza Vaccination in Children
Authors: Mohn K G-I , Brokstad K A , Islam S , Oftung F , Tøndel C , Aarstad H J , Cox R J 
Published: December 2019

AbstractBackgroundLive-attenuated influenza vaccine (LAIV) was licensed for prophylaxis of children 2–17 years old in Europe in 2012 and is administered as a nasal spray. Live-attenuated influenza vaccine induces both mucosal and systemic antibodies and systemic T-cell responses. Tonsils are the lymph nodes serving the upper respiratory tract, acting as both induction and effector site for mucosal immunity.MethodsHere, we have studied the early tonsillar T-cell responses induced in children after LAIV. Thirty-nine children were immunized with trivalent LAIV (containing A/H1N1, A/H3N2, and B viruses) at days 3, 7, and 14 before tonsillectomy. Nonvaccinated controls were included for comparison. Tonsils and peripheral blood (pre- and postvaccination) were collected to study T-cell responses.ResultsTonsillar and systemic T-cell responses differed between influenza strains, and both were found against H3N2 and B viruses, whereas only systemic responses were observed against A/H1N1. A significant increase in cross-reactive tonsillar CD8+ T cells recognizing conserved epitopes from a broad range of seasonal and pandemic viruses occurred at day 14. Tonsillar T cells showed significant cytokine responses (Th1, Th2, and granulocyte-macrophage colony-stimulating factor).ConclusionsOur findings support the use of LAIV in children to elicit broadly cross-reactive T cells, which are not induced by traditional inactivated influenza vaccines and may provide protection to novel virus strains.
Case-Control Study of the Immune Status of Humans Infected With Zoonotic Gorilla Simian Foamy Viruses
Authors: Gessain Antoine , Montange Thomas , Betsem Edouard , Bilounga Ndongo Chanceline , Njouom Richard , Buseyne Florence 
Published: December 2019

AbstractBackgroundZoonotic simian foamy viruses (SFVs) establish persistent infections in humans, for whom the long-term consequences for health are poorly described. In this study, we aimed to characterize blood-cell phenotypes and plasma biomarkers associated with gorilla SFV infection in humans.MethodsWe used a case-control design to compare 15 Cameroonian hunters infected with gorilla SFV (cases) to 15 controls matched for age and ethnicity. A flow cytometry-based phenotypic study and quantification of plasma immune biomarkers were carried out on blood samples from all participants. Wilcoxon signed-rank tests were used to compare cases and controls.ResultsCases had a significantly higher percentage of CD8 T lymphocytes than controls (median, 17.6% vs 13.7%; P = .03) but similar levels of B, natural killer, and CD4 T lymphocytes. Cases also had a lower proportion of recent CD4 thymic emigrants (10.9% vs 18.6%, P = .05), a higher proportion of programmed death receptor 1 (PD-1) expressing memory CD4 T lymphocytes (31.7% vs 24.7%, P = .01), and higher plasma levels of the soluble CD163 scavenger receptor (0.84 vs .59 µg/mL, P = .003) than controls.ConclusionsWe show, for the first time, that chronic infection with SFV is associated with T lymphocyte differentiation and monocyte activation.
Study reporting quality among interventions to reduce antibiotic use is a barrier to evidence-informed policymaking on antimicrobial resistance: systematic review
Authors: Rogers Van Katwyk S , Grimshaw J M , Nkangu M , Mendelson M , Taljaard M , Hoffman S J 
Published: December 2019

Abstract

Background
Countries are currently seeking evidence-informed policy options to address antimicrobial resistance (AMR). While rigorous evaluations of AMR interventions are the ideal, they are far from the current reality. Additionally, poor reporting and documentation of AMR interventions impede efforts to use evidence to inform future evaluations and policy interventions.

Objectives
To critically evaluate reporting quality gaps in AMR intervention research.

Methods
To evaluate the reporting quality of studies, we conducted a descriptive synthesis and comparative analysis of studies that were included in a recent systematic review of government policy interventions aiming to reduce human antimicrobial use. Reporting quality was assessed using the SQUIRE 2.0 checklist of 18 items for reporting system-level interventions to improve healthcare. Two reviewers independently applied the checklist to 66 studies identified in the systematic review.

Results
None of the studies included complete information on all 18 SQUIRE items (median score = 10, IQR = 8–11). Reporting quality varied across SQUIRE items, with 3% to 100% of studies reporting the recommended information for each SQUIRE item. Only 20% of studies reported the elements of the intervention in sufficient detail for replication and only 24% reported the mechanism through which the intervention was expected to work.

Conclusions
Gaps in the reporting of impact evaluations pose challenges for interpreting and replicating study results. Failure to improve reporting practice of policy evaluations is likely to impede efforts to tackle the growing health, social and economic threats posed by AMR.
#1forEquality: The Story of an Unlikely Victorious Campaign in the Making
Authors: Casla Koldo 
Published: December 2019

AbstractThe UK government proudly affirms that the country has some of the strongest equalities legislation in the world, including the Equality Act 2010. For it to be true, however, the government should implement the legislation in its entirety, including the socio-economic duty (section 1 of the Act). That duty would require public authorities to actively consider how their decisions and policies of the highest strategic importance can increase or decrease inequalities of outcome. Regrettably, successive governments have failed to commence the duty, and therefore it is not technically binding on public authorities. It is encouraging that the duty was brought to life in Scotland in 2018 and the Welsh Government has announced they will follow suit in 2020. The socio-economic duty is potentially a useful lever to understand and address the structural causes of material inequalities and their negative effects on human rights and well-being. This article presents and draws conclusions from the strategic choices made by the people running #1forEquality, the national campaign to bring the socio-economic duty to life. The article introduces four key factors that contributed to making progress between 2017 and 2019, despite the limited resources available: a) the added value of merging advocacy and epistemic communities working on equality and on human rights; b) the engagement with political actors at key stages of the process; c) the combination of ‘naming and shaming’ and best practice; and d) the celebration of smaller victories along the way.
A new genus of vespertilionid bat: the end of a long journey for Joffre’s Pipistrelle (Chiroptera: Vespertilionidae)
Authors: Görföl Tamás , Kruskop Sergei V , Tu Vuong Tan , Estók Péter , Son Nguyen Truong , Csorba Gábor 
Published: December 2019

AbstractKnowledge as to the taxonomic status of enigmatic bat species often is hindered by limited availability of specimens. This is particularly true for aerial-hawking bats that are difficult to catch. One such species, “Hypsugo” joffrei, was originally described in Nyctalus due to its long and slender wings, but subsequently transferred to Pipistrellus, and most recently to Hypsugo, on the basis of morphology. Analysis of newly available material, which more than doubles the known specimens of this taxon, demonstrates that it is morphologically and genetically distinct from all other bat genera. We accordingly describe it as belonging to a new, monotypic genus. We provide a detailed description of its external and craniodental traits, measurements, and assessment of genetic relationships, including barcode sequences to facilitate its rapid identification in future. The new genus belongs to a group that includes the recently described Cassistrellus, as well as Tylonycteris, and its closest relative, Philetor. We also describe the echolocation calls emitted by members of the taxon in different situations, which may facilitate finding them in previously unsampled locations. Based on the new data, the species occurs from Nepal to North Vietnam and China, which suggests that it could be more widespread than previously thought.
Lack of Availability and Efficacy of Phase I and Basket Trials for Patients With Gastrointestinal Cancers
Authors: Agarwal Rajiv , Cangemi Nicholas A , Epstein Andrew S , Harding James , Reidy-Lagunes Diane , Saltz Leonard B 
Published: December 2019

Abstract
In the modern era of targeted and immune-based therapies, investigator and patient expectations of availability and efficacy in phase I trials have increased. We assessed availability of, and benefit from, early drug development trials, specifically in patients with gastrointestinal cancers. We reviewed computerized referral records of the Early Drug Development Service at our institution to identify patients internally referred from our Gastrointestinal Oncology Service in calendar year 2018. End points were treatment on a trial, 3- and 6-month progression-free survival (PFS), and any tumor shrinkage. Of 394 gastrointestinal cancer patients referred in 2018, 54 enrolled on a trial and 53 (13.5%) were treated (1 withdrew before treatment): 34 on immune-based and 19 on targeted (3 to phase II basket) studies. None of the 52 patients who had exhausted standard therapy achieved 6-month PFS, two (3.8%) met 3-month PFS with tumor growth below Response Evaluation Criteria in Solid Tumors progression at 3 months, and both came off study for progression at 4 months. One patient who was to receive an irinotecan-based regimen as standard therapy instead received irinotecan plus an investigational targeted agent and remained stable for 8 months. No patients achieved any degree of tumor shrinkage. The most common reasons for nonaccrual were lack of available protocol treatment openings and failure to meet eligibility criteria for specific trials. Thus, availability and benefit from investigational treatment in this treatment-refractory gastrointestinal cancer patient population was extremely modest. Expectations regarding both availability and efficacy of phase I investigational therapy in gastrointestinal cancer patients likely exceed what our experience suggests.