bluuebunny/crossref_metadata_2025_split huggingface dataset:
MMAP: a cloud computing platform for mining the maximum accuracy of predicting phenotypes from genotypes
Authors: Huang Wei , Zheng Ping , Cui Zhenhai , Li Zhuo , Gao Yifeng , Yu Helong , Tang You , Yuan Xiaohui , Zhang Zhiwu 
Published: September 2020

Abstract

Accurately predicting phenotypes from genotypes holds great promise to improve health management in humans and animals, and breeding efficiency in animals and plants. Although many prediction methods have been developed, the optimal method differs across datasets due to multiple factors, including species, environments, populations and traits of interest. Studies have demonstrated that the number of genes underlying a trait and its heritability are the two key factors that determine which method fits the trait the best. In many cases, however, these two factors are unknown for the traits of interest. We developed a cloud computing platform for Mining the Maximum Accuracy of Predicting phenotypes from genotypes (MMAP) using unsupervised learning on publicly available real data and simulated data. MMAP provides a user interface to upload input data, manage projects and analyses and download the output results. The platform is free for the public to conduct computations for predicting phenotypes and genetic merit using the best prediction method optimized from many available ones, including Ridge Regression, gBLUP, compressed BLUP, Bayesian LASSO, Bayes A, B, Cpi and many more. Users can also use the platform to conduct data analyses with any methods of their choice. It is expected that extensive usage of MMAP would enrich the training data, which in turn results in continual improvement of the identification of the best method for use with particular traits.

Availability and implementation
The MMAP user manual, tutorials and example datasets are available at http://zzlab.net/MMAP.

Supplementary information
Supplementary data are available at Bioinformatics online.
Spectral Power in Marmoset Frontal Motor Cortex during Natural Locomotor Behavior
Authors: Tia Banty , Takemi Mitsuaki , Kosugi Akito , Castagnola Elisa , Ricci Davide , Ushiba Junichi , Fadiga Luciano , Iriki Atsushi 
Published: September 2020

Abstract
During primate arboreal locomotion, substrate orientation modifies body axis orientation and biomechanical contribution of fore- and hindlimbs. To characterize the role of cortical oscillations in integrating these locomotor demands, we recorded electrocorticographic activity from left dorsal premotor, primary motor, and supplementary motor cortices of three common marmosets moving across a branch-like small-diameter pole, fixed horizontally or vertically. Animals displayed behavioral adjustments to the task, namely, the horizontal condition mainly induced quadrupedal walk with pronated/neutral forelimb postures, whereas the vertical condition induced walk and bound gaits with supinated/neutral postures. Examination of cortical activity suggests that β (16–35 Hz) and γ (75–100 Hz) oscillations could reflect different processes in locomotor adjustments. During task, modulation of γ ERS by substrate orientation (horizontal/vertical) and epoch (preparation/execution) suggests close tuning to movement dynamics and biomechanical demands. β ERD was essentially modulated by gait (walk/bound), which could illustrate contribution to movement sequence and coordination. At rest, modulation of β power by substrate orientation underlines its role in sensorimotor processes for postural maintenance.
Risk factors for severity of COVID-19 in chronic dialysis patients from a multicentre French cohort
Authors: Lano Guillaume , Braconnier Antoine , Bataille Stanislas , Cavaille Guilhem , Moussi-Frances Julie , Gondouin Bertrand , Bindi Pascal , Nakhla Magued , Mansour Janette , Halin Pascale , Levy Bénédicte , Canivet Eric , Gaha Khaled , Kazes Isabelle , Noel Natacha , Wynckel Alain , Debrumetz Alexandre , Jourde-Chiche Noemie , Moal Valerie , Vial Romain , Scarfoglière Violaine , Bobot Mickael , Gully Marion , Legris Tristan , Pelletier Marion , Sallee Marion , Burtey Stephane , Brunet Philippe , Robert Thomas , Rieu Philippe 
Published: September 2020

AbstractBackgroundCoronavirus disease 2019 (COVID-19) is an emerging infectious disease, related to severe acute respiratory syndrome coronavirus 2 infection. Few data are available in patients with end-stage renal disease (ESRD).MethodsWe conducted an observational cohort study of COVID-19 patients at 11 dialysis centres in two distinct districts of France to examine the epidemiological and clinical characteristics of COVID-19 in this population, and to determine risk factors of disease severity (defined as a composite outcome including intensive care unit admission or death) and mortality.ResultsAmong the 2336 patients enrolled, 5.5% had confirmed COVID-19 diagnosis. Of the 122 patients with a follow-up superior to 28 days, 37% reached the composite outcome and 28% died. Multivariate analysis showed that oxygen therapy on diagnosis and a decrease in lymphocyte count were independent risk factors associated with disease severity and with mortality. Chronic use of angiotensin II receptor blockers (ARBs) (18% of patients) was associated with a protective effect on mortality. Treatment with azithromycin and hydroxychloroquine (AZT/HCQ) (46% of patients) were not associated with the composite outcome and with death in univariate and multivariate analyses.ConclusionsCOVID-19 is a severe disease with poor prognosis in patients with ESRD. Usual treatment with ARBs seems to be protective of critical evolution and mortality. There is no evidence of clinical benefit with the combination of AZT/HCQ.
Safety and feasibility of minimally invasive esophagectomy for elderly esophageal cancer patients
Authors: Sugita Y , Nakamura T , Sawada R , Takiguchi G , Urakawa N , Hasegawa H , Yamamoto M , Kanaji S , Matsuda Y , Yamashita K , Matsuda T , Oshikiri T , Suzuki S , Kakeji Y 
Published: September 2020

Summary
The number of elderly patients with esophageal cancer has increased in recent years. The use of thoracoscopic esophagectomy has also increased, and its minimal invasiveness is believed to contribute to postoperative outcomes. However, the short- and long-term outcomes in elderly patients remain unclear. This study aimed to elucidate the safety and feasibility of minimally invasive esophagectomy in elderly patients. This retrospective study included 207 patients who underwent radical thoracoscopic esophagectomy for thoracic esophageal squamous cell carcinoma at Kobe University Hospital between 2005 and 2014. Patients were divided into non-elderly (&lt;75 years) and elderly (≥75 years) groups. A propensity score matching analysis was performed for sex and clinical T and N stage, with a total of 29 matched pairs. General preoperative data, surgical procedures, intraoperative data, postoperative complications, in-hospital death, cancer-specific survival, and overall survival were compared between groups. The elderly group was characterized by lower preoperative serum albumin levels and higher American Society of Anesthesiologists grade. Intraoperative data and postoperative complications did not differ between the groups. The in-hospital death rate was 4% in the elderly group, which did not significantly differ from the non-elderly group. Cancer-specific survival was similar between the two groups. Although overall survival tended to be poor in the elderly group, it was not significantly worse than that of the non-elderly group. In conclusion, the short- and long-term outcomes of minimally invasive esophagectomy in elderly versus non-elderly patients were acceptable. Minimally invasive esophagectomy is a safe and feasible modality for elderly patients with appropriate indications.
Predictors of left ventricular reverse remodelling after coarctation of aorta intervention
Authors: Egbe Alexander C , Miranda William R , Connolly Heidi M 
Published: September 2020

Abstract

Aims
Several coarctation of aorta (COA) severity indices are used for timing of COA intervention, and to define severity of residual coarctation post-intervention. However, it is unclear how many of these COA indices are required in order to recommend intervention, and what degree of residual coarctation results in suboptimal recovery of the left ventricle (LV). Our aim was to assess the correlation between different COA indices and effects of chronic LV pressure overload (LV hypertrophy, diastolic, and systolic dysfunction), and to determine the effect of residual coarctation on LV reverse remodelling after COA intervention.

Methods and results
COA severity indices were defined as Doppler COA gradient, systolic blood pressure (SBP, upper-to-lower-extremity SBP gradient, aortic isthmus ratio. LV remodelling indices were defined as LV mass index (LVMI), LV global longitudinal strain (LVGLS), e′ and E/e′. LV reverse remodelling was defined as the difference between indices obtained pre-intervention and 5-year post-intervention (delta LVMI, e′, E/e′, LVGLS).
Of the COA indices analysed in 546 adult COA patients, aortic isthmus ratio had the strongest correlation with LVMI (β ± standard error −28.3 ± 14.1, P &lt; 0.001), LVGLS (1.51 ± 0.42, P = 0.005), e′ (3.11 ± 1.10, P = 0.014), and E/e′ (−13.4 ± 6.67, P = 0.008). Residual aortic isthmus ratio also had the strongest correlation with LV reverse remodelling, and residual aortic isthmus ratio &lt;0.7 was predictive of suboptimal LV reverse remodelling post-intervention.

Conclusion
Considering the known prognostic implications of LV remodelling and reverse remodelling in response to pressure overload, these results support the use of aortic isthmus ratio for timing of COA intervention, and for prognostication post-intervention.
The role of HIF-1α in nicotine-induced root and bone resorption during orthodontic tooth movement
Authors: Ullrich Niklas , Schröder Agnes , Bauer Maria , Spanier Gerrit , Jantsch Jonathan , Deschner James , Proff Peter , Kirschneck Christian 
Published: September 2020

Summary

Background
In orthodontic tooth movement (OTM), pseudo-inflammatory processes occur that are similar to those of nicotine-induced periodontitis. Previous studies have shown that nicotine accelerates OTM, but induces periodontal bone loss and dental root resorption via synergistically increased osteoclastogenesis. This study aimed to investigate the role of hypoxia-inducible factor 1 alpha (HIF-1α) in nicotine-induced osteoclastogenesis during OTM.

Materials/Methods
Male Fischer-344 rats were treated with l-Nicotine (1.89 mg/kg/day s.c., N = 10) or NaCl solution (N = 10). After a week of premedication, a NiTi spring was inserted to mesialize the first upper left molar. The extent of dental root resorption, osteoclastogenesis, and HIF-1α protein expression was determined by (immuno)histology, as well as bone volume (BV/TV) and trabecular thickness (TbTh) using µCT. Receptor activator of nuclear factor of activated B-cells ligand (RANK-L), osteoprotegerin (OPG), and HIF-1α expression were examined at the protein level in periodontal ligament fibroblasts (PDLF) exposed to pressure, nicotine and/or hypoxia, as well as PDLF-induced osteoclastogenesis in co-culture experiments with osteoclast progenitor cells.

Results
Nicotine favoured dental root resorptions and osteoclastogenesis during OTM, while BV/TV and TbTh were only influenced by force. This nicotine-induced increase does not appear to be mediated by HIF-1α, since HIF-1α was stabilized by force application and hypoxia, but not by nicotine. The in vitro data showed that the hypoxia-induced increase in RANK-L/OPG expression ratio and PDLF-mediated osteoclastogenesis was less pronounced than the nicotine-induced increase.

Conclusions
Study results indicate that the nicotine-induced increase in osteoclastogenesis and periodontal bone resorption during OTM may not be mediated by hypoxic effects or HIF-1α stabilization in the context of nicotine-induced vasoconstriction, but rather by an alternative mechanism.
Reconstructing the Invasion Route of the P-Element inDrosophila melanogasterUsing Extant Population Samples
Authors: Weilguny Lukas , Vlachos Christos , Selvaraju Divya , Kofler Robert 
Published: September 2020

AbstractThe P-element, one of the best understood eukaryotic transposable elements, spread in natural Drosophila melanogaster populations in the last century. It invaded American populations first and later spread to the Old World. Inferring this invasion route was made possible by a unique resource available in D. melanogaster: Many strains sampled from different locations over the course of the last century. Here, we test the hypothesis that the invasion route of the P-element may be reconstructed from extant population samples using internal deletions (IDs) as markers. These IDs arise at a high rate when DNA transposons, such as the P-element, are active. We suggest that inferring invasion routes is possible as: 1) the fraction of IDs increases in successively invaded populations, which also explains the striking differences in the ID content between American and European populations, and 2) successively invaded populations end up with similar sets of IDs. This approach allowed us to reconstruct the invasion route of the P-element with reasonable accuracy. Our approach also sheds light on the unknown timing of the invasion in African populations: We suggest that African populations were invaded after American but before European populations. Simulations of TE invasions in spatially distributed populations confirm that IDs may allow us to infer invasion routes. Our approach might be applicable to other DNA transposons in different host species.
Seismic discontinuities in the lithospheric mantle at the Dead Sea Transform
Authors: Mohsen Ayman , Kind Rainer , Yuan Xiaohui 
Published: September 2020

SUMMARYThe Dead Sea Transform (DST) was formed in the mid-Cenozoic, about 18 Myr ago, as a result of the breakaway of the Arabian plate from the African plate. Higher resolution information about the sub-Moho structure is still sparse in this region. Here, we study seismic discontinuities in the mantle lithosphere in the region of the DST using a modified version of the P- and S-receiver function methods. We use open data from permanent and temporary seismic stations. The results are displayed in a number of depth profiles through the study area. The Moho is observed on both sides of the transform at nearly 40 km depth by S-to-p and in P-to-s converted signals. The lithosphere–asthenosphere boundary (LAB) on the eastern side of the DST is observed near 180–200 km depth, which is according to our knowledge the first LAB observation at that depth in this region. This observation could lead to the conclusion that the thickness of the Arabian lithosphere east of the DST is likely cratonic. In addition, we observe in the entire area a negative velocity gradient at 60–80 km depth, which was previously interpreted as LAB.
Staff recognition and its importance for surgical service delivery: a qualitative study in Freetown, Sierra Leone
Authors: Willott Chris , Boyd Nick , Wurie Haja , Smalle Isaac , Kamara T B , Davies Justine I , Leather Andrew J M 
Published: September 2020

Abstract
We examined the views of providers and users of the surgical system in Freetown, Sierra Leone on processes of care, job and service satisfaction and barriers to achieving quality and accessible care, focusing particularly on the main public tertiary hospital in Freetown and two secondary and six primary sites from which patients are referred to it. We conducted interviews with health care providers (N = 66), service users (n = 24) and people with a surgical condition who had chosen not to use the public surgical system (N = 13), plus two focus groups with health providers in primary care (N = 10 and N = 10). The overall purpose of the study was to understand perceptions on processes of and barriers to care from a variety of perspectives, to recommend interventions to improve access and quality of care as part of a larger study. Our research suggests that providers perceive their relationships with patients to be positive, while the majority of patients see the opposite: that many health workers are unapproachable and uncaring, particularly towards poorer patients who are unable or unwilling to pay staff extra in the form of informal payments for their care. Many health care providers note the importance of lack of recognition shown to them by their superiors and the health system in general. We suggest that this lack of recognition underlies poor morale, leading to poor care. Any intervention to improve the system should therefore consider staff–patient relations as a key element in its design and implementation, and ideally be led and supported by frontline healthcare workers.
Adoption of evidence-based global policies at the national level: intermittent preventive treatment for malaria in pregnancy and first trimester treatment in Kenya, Malawi, Mali and The Gambia
Authors: Webster Jayne , Hoyt Jenna , Diarra Samba , Manda-Taylor Lucinda , Okoth George , Achan Jane , Ghilardi Ludovica , D’Alessandro Umberto , Madanista Mwayi , Kariuki Simon , Kayentao Kassoum , Hill Jenny 
Published: September 2020

Abstract
In 2012, the World Health Organization (WHO) updated its policy on intermittent preventive treatment in pregnancy with sulphadoxine–pyrimethamine (IPTp-SP). A global recommendation to revise the WHO policy on the treatment of malaria in the first trimester is under review. We conducted a retrospective study of the national policy adoption process for revised IPTp-SP dosing in four sub-Saharan African countries. Alongside this retrospective study, we conducted a prospective policy adoption study of treatment of first trimester malaria with artemisinin combination therapies (ACTs). A document review informed development and interpretation of stakeholder interviews. An analytical framework was used to analyse data exploring stakeholder perceptions of the policies from 47 in-depth interviews with a purposively selected range of national level stakeholders. National policy adoption processes were categorized into four stages: (1) identify policy need; (2) review the evidence; (3) consult stakeholders and (4) endorse and draft policy. Actors at each stage were identified with the roles of evidence generation; technical advice; consultative and statutory endorsement. Adoption of the revised IPTp-SP policy was perceived to be based on strong evidence, support from WHO, consensus from stakeholders; and followed these stages. Poor tolerability of quinine was highlighted as a strong reason for a potential change in treatment policy. However, the evidence on safety of ACTs in the first trimester was considered weak. For some, trust in WHO was such that the anticipated announcement on the change in policy would allay these fears. For others, local evidence would first need to be generated to support a change in treatment policy. A national policy change from quinine to ACTs for the treatment of first trimester malaria will be less straightforward than experienced with increasing the IPTp dosing regimen despite following the same policy processes. Strong leadership will be needed for consultation and consensus building at national level.
Revealing antibiotic cross-resistance patterns in hospitalized patients through Bayesian network modelling
Authors: Cherny Stacey S , Nevo Daniel , Baraz Avi , Baruch Shoham , Lewin-Epstein Ohad , Stein Gideon Y , Obolski Uri 
Published: September 2020

Abstract

Objectives
Microbial resistance exhibits dependency patterns between different antibiotics, termed cross-resistance and collateral sensitivity. These patterns differ between experimental and clinical settings. It is unclear whether the differences result from biological reasons or from confounding, biasing results found in clinical settings. We set out to elucidate the underlying dependency patterns between resistance to different antibiotics from clinical data, while accounting for patient characteristics and previous antibiotic usage.

Methods
Additive Bayesian network modelling was employed to simultaneously estimate relationships between variables in a dataset of bacterial cultures derived from hospitalized patients and tested for resistance to multiple antibiotics. Data contained resistance results, patient demographics and previous antibiotic usage, for five bacterial species: Escherichia coli (n = 1054), Klebsiella pneumoniae (n = 664), Pseudomonas aeruginosa (n = 571), CoNS (n = 495) and Proteus mirabilis (n = 415).

Results
All links between resistance to the various antibiotics were positive. Multiple direct links between resistance of antibiotics from different classes were observed across bacterial species. For example, resistance to gentamicin in E. coli was directly linked with resistance to ciprofloxacin (OR = 8.39, 95% credible interval 5.58–13.30) and sulfamethoxazole/trimethoprim (OR = 2.95, 95% credible interval 1.97–4.51). In addition, resistance to various antibiotics was directly linked with previous antibiotic usage.

Conclusions
Robust relationships among resistance to antibiotics belonging to different classes, as well as resistance being linked to having taken antibiotics of a different class, exist even when taking into account multiple covariate dependencies. These relationships could help inform choices of antibiotic treatment in clinical settings.
Large pseudoaneurysm arising from the deep femoral artery after hip fracture fixation
Authors: Bowden Sylvie , Jaberi Arash , Roche-Nagle Graham 
Published: September 2020

Abstract
Hip fracture is a common condition of increasing global concern. Vascular injury as a complication after hip fracture repair is rare. A 90-year-old woman developed swelling and pain to her proximal thigh 1 month after uneventful hip fracture fixation. Ultrasound revealed a large pseudoaneurysm of the deep femoral artery, which was successfully treated with transcatheter embolization. Pseudoaneurysms have numerous etiologies. In this case, vascular injury is suspected to be a consequence of proximal migration of the lesser trochanteric fragment. Unfortunately, pseudoaneurysms are often not appreciated due to the nonspecific nature of the presenting symptoms. Diagnosis should be confirmed radiologically and management depends on the location and size of the pseudoaneurysm, as well as patient comorbidities. Pseudoaneurysm after hip fracture fixation is a rare but serious complication. Diagnosis is challenging due to nonspecific symptoms. A high index of suspicion is imperative to prevent life-threatening rupture.
Recent Work in African Philosophy: Its Relevance beyond the Continent
Authors: Metz Thaddeus 
Published: September 2020

AbstractIn this article I critically discuss some recent English language books in African philosophy. Specifically, I expound and evaluate key claims from books published by sub-Saharan thinkers since 2017 that address epistemology, metaphysics, and value theory and that do so in ways of interest to an audience of at least Anglo-American-Australasian analytic philosophers. My aim is not to establish a definitive conclusion about these claims, but rather to facilitate cross-cultural engagement by highlighting their relevance, at least to many western philosophers, and by presenting challenges to these claims that such philosophers would be likely to mount.