bluuebunny/crossref_metadata_2025_split huggingface dataset:
Development of the Wheat Practical Haplotype Graph database as a resource for genotyping data storage and genotype imputation
Authors: Jordan Katherine W , Bradbury Peter J , Miller Zachary R , Nyine Moses , He Fei , Fraser Max , Anderson Jim , Mason Esten , Katz Andrew , Pearce Stephen , Carter Arron H , Prather Samuel , Pumphrey Michael , Chen Jianli , Cook Jason , Liu Shuyu , Rudd Jackie C , Wang Zhen , Chu Chenggen , Ibrahim Amir M H , Turkus Jonathan , Olson Eric , Nagarajan Ragupathi , Carver Brett , Yan Liuling , Taagen Ellie , Sorrells Mark , Ward Brian , Ren Jie , Akhunova Alina , Bai Guihua , Bowden Robert , Fiedler Jason , Faris Justin , Dubcovsky Jorge , Guttieri Mary , Brown-Guedira Gina , Buckler Ed , Jannink Jean-Luc , Akhunov Eduard D 
Published: November 2021

Abstract
To improve the efficiency of high-density genotype data storage and imputation in bread wheat (Triticum aestivum L.), we applied the Practical Haplotype Graph (PHG) tool. The Wheat PHG database was built using whole-exome capture sequencing data from a diverse set of 65 wheat accessions. Population haplotypes were inferred for the reference genome intervals defined by the boundaries of the high-quality gene models. Missing genotypes in the inference panels, composed of wheat cultivars or recombinant inbred lines genotyped by exome capture, genotyping-by-sequencing (GBS), or whole-genome skim-seq sequencing approaches, were imputed using the Wheat PHG database. Though imputation accuracy varied depending on the method of sequencing and coverage depth, we found 92% imputation accuracy with 0.01× sequence coverage, which was slightly lower than the accuracy obtained using the 0.5× sequence coverage (96.6%). Compared to Beagle, on average, PHG imputation was ∼3.5% (P-value &lt; 2 × 10−14) more accurate, and showed 27% higher accuracy at imputing a rare haplotype introgressed from a wild relative into wheat. We found reduced accuracy of imputation with independent 2× GBS data (88.6%), which increases to 89.2% with the inclusion of parental haplotypes in the database. The accuracy reduction with GBS is likely associated with the small overlap between GBS markers and the exome capture dataset, which was used for constructing PHG. The highest imputation accuracy was obtained with exome capture for the wheat D genome, which also showed the highest levels of linkage disequilibrium and proportion of identity-by-descent regions among accessions in the PHG database. We demonstrate that genetic mapping based on genotypes imputed using PHG identifies SNPs with a broader range of effect sizes that together explain a higher proportion of genetic variance for heading date and meiotic crossover rate compared to previous studies.
Development of community strategies supporting brief alcohol advice in three Latin American countries: a protocol
Authors: Solovei Adriana , Mercken Liesbeth , Jané-Llopis Eva , Bustamante Inés , Evers Silvia , Gual Antoni , Medina Perla , Mejía-Trujillo Juliana , Natera-Rey Guillermina , O’Donnell Amy , Pérez-Gómez Augusto , Piazza Marina , de Vries Hein , Anderson Peter 
Published: November 2021

Summary
Brief alcohol advice offered to patients was shown to be a clinically- and cost-effective intervention to prevent and manage alcohol-related health harm. However, this intervention is not yet optimally implemented in practice. A suggested strategy to improve the implementation of brief alcohol advice is through community actions which would enhance the environment in which primary healthcare providers must deliver the intervention. However, there has been scarce research conducted to date regarding which community actions have most influence on the adoption and implementation of brief alcohol advice. The current protocol presents the development of a package of community actions to be implemented in three Latin American municipalities, in Colombia, Mexico and Peru. The community actions were based on the Institute for Health Care Improvement’s framework for going to full scale, and include: (i) involvement of a Community Advisory Board, (ii) involvement of a project champion, (iii) adoption mechanisms, (iv) support systems and (v) a communication campaign. By presenting a protocol for developing community actions with input from local stakeholders, this article contributes to advancing the public health field of alcohol prevention by potentially stimulating the sustainable adoption and implementation of brief alcohol advice in routine practice.
Association of PLXND1 with a novel subtype of anomalous pulmonary venous return
Authors: Zhou Wei-Zhen , Zeng Ziyi , Shen Huayan , Chen Wen , Li Tianjiao , Ma Baihui , Sun Yang , Yang Fangfang , Zhang Yujing , Li Wenke , Han Bianmei , Liu Xuewen , Yuan Meng , Zhang Guangxin , Yang Yang , Liu Xiaoshuang , Pang Kun-Jing , Li Shou-Jun , Zhou Zhou 
Published: November 2021

Abstract
Anomalous pulmonary venous return (APVR) is a potentially lethal congenital heart disease. Elucidating the genetic etiology is crucial for understanding its pathogenesis and improving clinical practice, whereas its genetic basis remains largely unknown because of complex genetic etiology. We thus performed whole-exome sequencing for 144 APVR patients and 1636 healthy controls and report a comprehensive atlas of APVR-related rare genetic variants. Novel singleton, loss-of-function and deleterious missense variants (DVars) were enriched in patients, particularly for genes highly expressed in the developing human heart at the critical time point for pulmonary veins draining into the left atrium. Notably, PLXND1, encoding a receptor for semaphorins, represents a strong candidate gene of APVR (adjusted P = 1.1e-03, odds ratio: 10.9–69.3), accounting for 4.17% of APVR. We further validated this finding in an independent cohort consisting of 82 case–control pairs. In these two cohorts, eight DVars were identified in different patients, which convergently disrupt the GTPase-activating protein-related domain of PLXND1. All variant carriers displayed strikingly similar clinical features, in that all anomalous drainage of pulmonary vein(s) occurred on the right side and incorrectly connected to the right atrium, which may represent a novel subtype of APVR for molecular diagnosis. Studies in Plxnd1 knockout mice further revealed the effects of PLXND1 deficiency on severe heart and lung defects and cellular abnormalities related to APVR such as abnormal migration and vascular formation of vascular endothelial cells. These findings indicate the important role of PLXND1 in APVR pathogenesis, providing novel insights into the genetic etiology and molecular subtyping for APVR.
Translating Results from VARSITY to Real World: Adalimumab vs Vedolizumab as First-line Biological in Moderate to Severe IBD
Authors: Moens Annick , Verstockt Bram , Alsoud Dahham , Sabino João , Ferrante Marc , Vermeire Séverine 
Published: November 2021

Abstract

Background
Selecting a first-line therapy remains challenging in IBD. Adalimumab (ADM) and vedolizumab (VDZ) effectively lead to endoscopic remission in moderate to severe IBD. The VARSITY trial showed superiority of VDZ over ADM in ulcerative colitis (UC) regarding clinical remission and endoscopic improvement at week 52. We explored these results in a real-world setting of UC and Crohn’s disease (CD).

Methods
This retrospective study followed a cohort of biologic-naïve patients starting ADM or VDZ from 2015-2019. Patients had moderate to severe disease (endoscopic Mayo score ≥2 for UC, presence of ulcerations for CD) prior to therapy initiation. For UC, endoscopic remission (endoscopic Mayo score 0) and improvement (endoscopic Mayo score ≤1) at week 52 were assessed. For CD, endoscopic remission (absence of ulcerations) and improvement (markedly better endoscopy despite ulcerations) at weeks 26-52 were studied. Treatment persistence was also evaluated.

Results
In total, 195 biologic-naïve patients (109 UC; 86 CD) were included. In UC, VDZ was superior to ADM regarding endoscopic remission (29% vs 11%, P = .03), endoscopic improvement (51% vs 26%, P = .01) at week 52, and treatment persistence (P = .04). In CD, no differences in endoscopic remission (VDZ 48% vs ADM 60%; P=0.37), improvement (VDZ 76% vs ADM 77%; P = 1.00), or treatment persistence (P=0.43) at weeks 26-52 were seen. Safety profiles were similar in UC and CD.

Conclusions
This real-world cohort study of biologic-naïve IBD patients found VDZ to be superior to ADM as first-line treatment for patients with UC—but not CD—regarding endoscopic remission at week 52 and treatment persistence.
Open thoracoabdominal aortic aneurysm repair in a patient with myasthenia gravis
Authors: Uehara Kyokun , Fujiwara Yasue , Morishima Manabu , Iwakura Atsushi 
Published: November 2021

Abstract
Myasthenia gravis (MG) is an autoimmune neuromuscular junction disorder and rarely coexists with aortic aneurysms requiring open repair. A 66-year-old patient with MG underwent extended thoraco-abdominal aortic aneurysm (TAAA) repair 16 years after onset of type-B acute aortic dissection. At 62 years, the patient was diagnosed with MG (MGFA class IIIa) from positive anti-acetylcholine receptor antibody without thymoma. Preoperatively, MG was well-controlled by prednisolone, cyclosporin and pyridostigmine. Extent II TAAA repair was performed under general anaesthesia maintained by total intravenous anaesthesia. Transcranial motor-evoked potential and somatosensory-evoked potential were applied to monitor intraoperative spinal cord ischaemia and muscle weakness. Amplitudes of motor-evoked potential and somatosensory-evoked potential attenuated intraoperatively but normalized after reperfusion from the reconstructed tube graft. Perioperative steroid coverage was given against surgical stress. The patient was weaned from mechanical ventilatory support on postoperative day 7. No signs of spinal cord ischaemia or muscle weakness were seen.
Group BStreptococcusCapsular Serotype Alters Vaginal Colonization Fitness
Authors: Dammann Allison N , Chamby Anna B , Gonzalez Francisco J , Sharp Molly E , Flores Karina , Shahi Ifrah , Dongas Sophia , Hooven Thomas A , Ratner Adam J 
Published: November 2021

AbstractBackgroundGroup B Streptococcus (GBS) remains a leading cause of infant morbidity and mortality. A candidate vaccine targets 6 GBS serotypes, offering a potential alternative to intrapartum antibiotic prophylaxis to reduce disease burden. However, our understanding of the contributions of specific capsule types to GBS colonization and disease remains limited.MethodsUsing allelic exchange, we generated isogenic GBS strains differing only in the serotype-determining region in 2 genetic backgrounds, including the hypervirulent clonal complex (CC) 17. Using a murine model of vaginal cocolonization, we evaluated the roles of the presence of capsule and of expression of specific capsular types in GBS vaginal colonization fitness independent of other genetic factors.ResultsEncapsulated wild-type strains COH1 (CC17, serotype III) and A909 (non-CC17, serotype Ia) outcompeted isogenic acapsular mutants in murine vaginal cocolonization. COH1 wild type outcompeted A909. Notably, expression of type Ia capsule conferred an advantage over type III capsule in both genetic backgrounds.ConclusionsSpecific capsule types may provide an advantage in GBS vaginal colonization in vivo. However, success of certain GBS lineages, including CC17, likely involves both capsule and noncapsule genetic elements. Capsule switching in GBS, a potential outcome of conjugate vaccine programs, may alter colonization fitness or pathogenesis.
Estimation of SARS-CoV-2 Infection Fatality Rate by Age and Comorbidity Status Using Antibody Screening of Blood Donors During the COVID-19 Epidemic in Denmark
Authors: Kaspersen Kathrine Agergård , Hindhede Lotte , Boldsen Jens Kjærgaard , Mikkelsen Susan , Vestergaard Lasse Skafte , Berthelsen Ann-Sofie Nicole , Moustsen-Helms Ida Rask , Holm Dorte Kinggaard , Nilsson Anna Christine , Sækmose Susanne Gjørup , Sørensen Erik , Harritshøj Lene Holm , Aagaard Bitten , Hjalgrim Henrik , Lillevang Søren Thue , Jørgensen Charlotte Sværke , Krause Tyra Grove , Ullum Henrik , Pedersen Ole Birger Vestager , Ostrowski Sisse Rye , Erikstrup Christian 
Published: November 2021

Abstract

Background
Studies presenting severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection fatality rate (IFR) for healthy individuals are warranted. We estimate IFR by age and comorbidity status using data from a large serosurvey among Danish blood donors and nationwide data on coronavirus disease 2019 (COVID-19) mortality.

Methods
Danish blood donors aged 17–69 years donating blood October 2020–February 2021 were tested with a commercial SARS-CoV-2 total antibody assay. IFR was estimated for weeks 11 to 42, 2020 and week 43, 2020 to week 6, 2021, representing the first 2 waves of COVID-19 epidemic in Denmark.

Results
In total, 84944 blood donors were tested for antibodies. The seroprevalence was 2% in October 2020 and 7% in February 2021. Among 3898039 Danish residents aged 17–69 years, 249 deaths were recorded. The IFR was low for people &lt;51 years without comorbidity during the 2 waves (combined IFR=3.36 per 100000 infections). The IFR was below 3‰ for people aged 61–69 years without comorbidity. IFR increased with age and comorbidity but declined from the first to second wave.

Conclusions
In this nationwide study, the IFR was very low among people &lt;51 years without comorbidity.
Interruption of initial patient assessment in the emergency department and its effect on patient perception of care quality
Authors: Johnson Kimberly D , Lindsell Christopher J , Froehle Craig , Gillespie Gordon Lee 
Published: November 2021

Abstract

Background
Triage is a critical first step in appropriately caring for patients in the emergency department (ED). Patients’ assumptions of the care they will receive can be established in triage. Interruptions to this process can disrupt patient flow, cause errors and lead to patient dissatisfaction.

Objective
The purpose of this study was to determine how the frequency and duration of interruptions during triage are associated with errors, patient satisfaction and patient’s perception of the care they received.

Methods
Prospective, observational, cohort study conducted in the ED of a Level 1 trauma center. Interruptions were measured using time-and-motion observations of triage interviews performed by nurses and physicians. Patients were surveyed immediately after triage interviews were complete.

Results
Surveys were completed for 178 observations. In total, 62.9% of the observations were interrupted between 1 and 5 times. While interruptions did not significantly influence patient satisfaction directly, interruptions positively influenced triage duration, which was negatively associated with patient satisfaction. Increased errors were associated with increasing frequency of triage interruptions. Triage interruptions were not associated with either patient satisfaction or perceived caregiver competence. Overall, the majority (76.6%) of patients were satisfied with their care; patient satisfaction was associated with the perceived competency of caregivers but was not associated with errors.

Conclusion
Interruptions are associated with increased errors and delays in patient care. Although increased triage duration adversely affected patient satisfaction, patients’ perceptions were not influenced by interruptions. While patient satisfaction is essential, a lack of association between patient satisfaction and errors suggests that using patient satisfaction as a measure of care quality may omit important safety information.
BSAC Vanguard Series: Antimicrobial resistance and the future of diagnostic testing
Authors: Hayward Gail , Turner Philip 
Published: November 2021

Abstract
In the UK around 80% of all antibiotics are prescribed by GP surgeries and in other community settings. Diagnostic technology has the potential to enable transformative change to antimicrobial stewardship in these settings. Current diagnostics are limited in terms of the information they can provide prescribers and the speed they can provide it. We need to develop diagnostics that are cheap enough for mass application, rapid enough to change prescribing decisions and able to detect bacteria which are causing disease rather than simply resident in the host. To be successful in creating change these diagnostics need to be appropriately funded and embedded in practice in ways which encourage change in prescribing behaviours. Collaboration between academia and industry is key in developing tests which are fit for purpose, well evidenced and appropriately funded in these settings.
Advances in the Use of Electrospun Nanofibrous Polymeric Matrix for Dermal Healing at the Donor Site After the Split-Thickness Skin Graft Excision: A Prospective, Randomized, Controlled, Open-Label, Multicenter Study
Authors: Haik Josef , Ullman Yehuda , Gur Eyal , Ad-El Dean , Egozi Dana , Kruchevsky Dani , Zissman Sivan , Biros Erik , Nir Rony-Reuven , Kornhaber Rachel , Cleary Michelle , Harats Moti 
Published: November 2021

Abstract
Dressings used to manage donor site wounds (DSWs) have up to 40% of patients experiencing complications that may cause suboptimal scarring. We evaluated the efficacy and safety of a portable electrospun nanofibrous matrix that provides contactless management of DSWs compared with standard dressing techniques. This study included adult patients who underwent an excised split-thickness skin graft (STSG) with a DSW area of 10 to 200 cm2. Patients were allocated into two groups; ie, the nanofiber group managed with a nanofibrous polymer-based matrix, and the control group managed using the standard of care such as Jelonet® or Biatain® Ibu dressing. Primary outcomes were postoperative dermal healing efficacy assessed by Draize scores. The time to complete re-epithelialization was also recorded. Secondary outcomes included postoperative adverse events, pain, and infections during the first 21 days and extended 12-month follow-up. The itching and scarring were recorded during the extended follow-up (months 1, 3, 6, 9, and 12) using Numerical-Analogue-Score and Vancouver scores, respectively. The nanofiber and control groups included 21 and 20 patients, respectively. The Draize dermal irritation scores were significantly lower in the nanofiber vs control group (Z = −2.509; P = .028) on the first postoperative day but became similar afterward (Z ≥ −1.62; P ≥ .198). In addition, the average time to re-epithelialization was similar in the nanofiber (17.9 ± 4.4 days) and control group (18.3 ± 4.5 days; Z = −0.299; P = .764), so were postoperative adverse events, pain, and infection incidence, itching and scarring. The safety and efficacy of electrospun nanofibrous matrix are similar to standard wound care allowing its use as an alternative donor site dressing following the STSG excision.
Eruptions of the Sacred in a South Indian Fishing Village
Authors: Nuckolls Charles W 
Published: November 2021

AbstractEliade invented the term ‘hierophany’ to refer to a physical manifestation of the sacred. For Eliade, all hierophanies are prefigurations of the one great manifestation, the incarnation of Christ. One can dispense with this limiting feature, and instead make use of Eliade’s more tractable theory—namely, that hierophanies are composite structures, made up of elements in contradiction with each other. Here, the hierophany to be examined is a ‘snake mound’ that suddenly appeared in a residential structure in Jalaripet, a fishing caste village in southeastern India. This article argues that the mound is a response to mutually exclusive kinship ideals, one focused on patrilineal solidarity in the form of fraternal unity and the other focuses on fraternal separation and the breakdown of patrilineal solidarity. The mound represents both ideals at a particular moment in the course of family development when the opposition between the two is most intense.
‘Hit and Miss’? Access to Legal Assistance in Immigration Detention
Authors: Lindley Anna 
Published: November 2021

Abstract
In the context of significant cuts to legal aid in the last decade in the UK, immigration detention remains in scope: indeed the argument that detention is legitimate rests partly on the claim that people can challenge it. Drawing on interviews with legal professionals combined with published data and reports, this article concludes that while the publicly funded Detention Duty Advice Scheme delivers advice and representation to many people held in detention, variations in access and quality give grounds for concern. Many people are also forced to rely on private solicitors, pro-bono provision and their own legal capabilities, raising questions regarding effective remedy and equality of access to justice. The article reviews the limited information available on representation types and rates, outcomes, and the wider impact of access to legal representation or the lack of it. The conclusion summarizes key points and explores ways forward.
Mink (Neovison vison) fecal microbiomes are influenced by sex, temperature, and time postdefecation
Authors: Lafferty Diana J R , Gillman Sierra J , Jeakle Lane K , Roell Brian J , McKenney Erin A 
Published: November 2021

Abstract
Gut microbiomes encode myriad metabolic functions critical to mammalian ecology and evolution. While fresh fecal samples provide an efficient, noninvasive method of sampling gut microbiomes, collecting fresh feces from elusive species is logistically challenging. Nonfresh feces, however, may not accurately represent the gut microbiome of the host due to succession of gut microbial consortia postdefecation as well as colonization by microbes from the surrounding environment. Using American mink (Neovison vison) as a model species, we examined postdefecation microbial community succession to learn how ambient temperature and temporal sampling constraints influence the reliability of nonfresh feces to represent host gut microbiomes. To achieve our goal, we analyzed fresh mink feces (n = 5 females; n = 5 males) collected at the time of defecation from captive mink at a farm in the Upper Peninsula of Michigan and we subsequently subsampled each fecal specimen to investigate microbial community succession over five days, under both warm (21°C) and cold (–17°C to –1°C) temperature treatments. We found that both temperature and time influenced fecal microbiome composition; and we also detected significant sexual dimorphism in microbial community structures, with female mink microbiomes exhibiting significantly greater variation than males’ when exposed to the warm temperature treatment. Our results demonstrate that feces from unknown individuals can be a powerful tool for examining carnivore gut microbiomes, though rigorous study design is required because sex, ambient temperature, and time since defecation drive significant microbial variation and the sample size requirements necessary for detecting statistically significant differences between target populations is an important consideration for future ecologically meaningful research.