bluuebunny/crossref_metadata_2025 huggingface dataset:
A read count-based method to detect multiplets and their cellular origins from snATAC-seq data
Authors: Thibodeau Asa , Eroglu Alper , Lawlor Nathan , Nehar-Belaid Djamel , Kursawe Romy , Marches Radu , Kuchel George A. , Banchereau Jacques , Stitzel Michael L. , Cicek A. Ercument , Ucar Duygu
Published: January 2021

Similar to other droplet-based single cell assays, single nucleus ATAC-seq (snATAC-seq) data harbor multiplets that confound downstream analyses. Detecting multiplets in snATAC-seq data is particularly challenging due to its sparsity and trinary nature (0 reads: closed chromatin, 1: open in one allele, 2: open in both alleles), yet offers a unique opportunity to infer multiplets when >2 uniquely aligned reads are observed at multiple loci. Here, we implemented the first read count-based multiplet detection method, ATAC-DoubletDetector, that detects multiplets independently of cell-type. Using PBMC and pancreatic islet datasets, ATAC-DoubletDetector captured simulated heterotypic multiplets (different cell-types) with ∼0.60 recall, showing ∼24% improvement over state of the art. ATAC-DoubletDetector detected homotypic multiplets with ∼0.61 recall, representing the first method to detect multiplets originating from the same cell type. Using our novel clustering-based algorithm, multiplets were annotated to their cellular origins with ∼85% accuracy. Application of ATAC-DoubletDetector will improve downstream analysis of snATAC-seq.
Why extinction estimates from extant phylogenies are so often zero
Authors: Louca Stilianos , Pennell Matthew W.
Published: January 2021

Time-calibrated phylogenies comprising only extant lineages are widely used to estimate historical speciation and extinction rates. Such extinction rate estimates have long been controversial as many phylogenetic studies report zero extinction in many taxa, a finding in conflict with the fossil record. To date, the causes of this widely observed discrepancy remain unresolved. Here we provide a novel and simple explanation for these “zero-inflated” extinction rate estimates, based on the recent discovery that there exist many alternative “congruent” diversification scenarios that cannot possibly be distinguished on the sole basis of extant timetrees. Consequently, estimation methods tend to converge to some scenario congruent to (i.e., statistically indistinguishable from) the true diversification scenario, but not necessarily to the true diversification scenario itself. This congruent scenario may in principle exhibit negative extinction rates, a biologically meaningless but mathematically feasible situation, in which case estimators will tend to hit and stick to the boundary estimate of zero extinction. To test this explanation, we estimated extinction rates using maximum likelihood for a set of simulated trees and for 121 empirical trees, while either allowing or preventing negative extinction rates. We find that the existence of congruence classes and imposed bounds on extinction rates can explain the zero-inflation of previous extinction rate estimates, even for large trees (1000 tips) and in the absence of any detectable model violations. Not only do our results likely resolve a long-standing mystery in phylogenetics, they demonstrate that model congruencies can have severe consequences in practice.
Fever, Diarrhea, and Severe Disease Correlate with High Persistent Antibody Levels against SARS-CoV-2
Authors: Amjadi Maya F. , O’Connell Sarah E. , Armbrust Tammy , Mergaert Aisha M. , Narpala Sandeep R. , Halfmann Peter J. , Bashar S. Janna , Glover Christopher R. , Heffron Anna S. , Taylor Alison , Flach Britta , O’Connor David H. , Kawaoka Yoshihiro , McDermott Adrian B. , Sethi Ajay K. , Shelef Miriam A.
Published: January 2021

Lasting immunity will be critical for overcoming the coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). However, factors that drive the development of high titers of anti-SARS-CoV-2 antibodies and how long those antibodies persist remain unclear. Our objective was to comprehensively evaluate anti-SARS-CoV-2 antibodies in a clinically diverse COVID-19 convalescent cohort at defined time points to determine if anti-SARS-CoV-2 antibodies persist and to identify clinical and demographic factors that correlate with high titers. Using a novel multiplex assay to quantify IgG against four SARS-CoV-2 antigens, a receptor binding domain-angiotensin converting enzyme 2 inhibition assay, and a SARS-CoV-2 neutralization assay, we found that 98% of COVID-19 convalescent subjects had anti-SARS-CoV-2 antibodies five weeks after symptom resolution (n=113). Further, antibody levels did not decline three months after symptom resolution (n=79). As expected, greater disease severity, older age, male sex, obesity, and higher Charlson Comorbidity Index score correlated with increased anti-SARS-CoV-2 antibody levels. We demonstrated for the first time that COVID-19 symptoms, namely fever, abdominal pain, diarrhea and low appetite, correlated consistently with higher anti-SARS-CoV-2 antibody levels. Our results provide new insights into the development and persistence of anti-SARS-CoV-2 antibodies.
Post operative acute kidney injury in abdominal Surgeries – A retrospective analysis of single center in western India
Authors: Vasavada Bhavin , Patel Hardik
Published: January 2021

AIM

The aim of our study was to evaluate the incidence and causative factors for acute kidney injury in abdominal surgeries.

Material and Methods

All the abdominal surgeries performed between April 2018 to December 2020, in our institution have been analyzed for acute kidney injury. Acute kidney injury defined according to acute kidney injury network classification. Categorical variables were evaluated by chi-square t-test or fisher’s t-test wherever appropriate and continuous variables by Mann Whitney U test for nonparametric data and student t-test for parametric test after skewness and kurtosis analysis. Statistical analysis was done using SPSS version 23. P< 0.05 was considered statistically significant.

Results

We performed 402 gastrointestinal and hepatobiliary surgery from April 2018 to December 2020. After exclusion 372 patients were included in the study population. 20 patients (5.37%) were defined as having acute kidney injury according to acute kidney injury network classifications. On univariate analysis acute kidney injury was associated with open surgery (p= 0.003), Intraoperative hypotension (p<0.001), Colorectal surgeries (p<0.0001), Emergency surgery (p=0.028), CDC grade of surgery (p<0.001), increased used to blood products (p=0.001), higher ASA grade (p<0.0001), increased operative time(p<0.0001). On multivariate logistic regression analysis higher ASA grade (p<0.0001) and increased operative time (0.049) independently predicted acute kidney injury. Acute kidney injury was also significantly associated with 90 days mortality. (p= <0.0001).

Conclusion

Post-operative acute kidney injury was associated with significant mortality in abdominal surgery. Higher ASA grades and increased operative time predicted acute kidney injury.
Modelling Decay of Population Immunity With Proposed Second Dose Deferral Strategy
Authors: Graham Jurgens
Published: January 2021

A second dose deferred strategy has been proposed to increase initial population immunity as an alternative to the default two dose vaccine regimen with spacing of 21 or 28 days between vaccine doses for the mRNA vaccines from Pfizer and Moderna. This increased initial population immunity is only of value if one dose immunity does not decay so fast as to nullify the benefit. Because decay rates of one dose and two dose efficacy are currently unknown, a model to project population immunity between the two strategies was created. By evaluating the decay rate of one dose efficacy, two dose efficacy, and time until the second dose is given, the model shows that if there is an increased decay rate of one dose efficacy relative to the two dose decay rate, it is highly unlikely to nullify the benefit of increased population immunity seen in a second dose deferral strategy. Rather, all reasonable scenarios strongly favour a second dose deferral strategy with much higher projected population immunity in comparison to the default regimen.
Pain modulatory network is influenced by sex and age in a healthy state and during osteoarthritis progression in rats
Authors: Da Silva Joyce T. , Tricou Christina , Zhang Youping , Tofighbakhsh Amir , Seminowicz David A. , Ro Jin Y.
Published: January 2021

Old age and female sex are risk factors for the development of osteoarthritis (OA) and chronic pain. We investigated the effects of sex and age on pain modulatory networks in a healthy state and during OA progression. We used functional MRI to determine the effects of sex and age on periaqueductal gray functional connectivity (PAG FC) in a healthy state (pre‐OA) and during the early and late phases of monosodium iodoacetate‐induced OA in rats. We then examined how sex and age affect longitudinal changes in PAG FC in OA. In a healthy state, females exhibited more widespread PAG FC than males, and this effect was exaggerated with aging. Young males had moderate PAG FC changes during the early phase but recruited additional brain regions, including the rostral anterior cingulate cortex (ACC), during the late phase. Young females exhibited widespread PAG FC in the early phase, which includes connections to insula, caudal ACC, and nucleus accumbens (NAc). Older groups had strong PAG FC with fewer regions in the early phase, but they recruited additional brain regions, including NAc, in the late phase. Overall, our findings show that PAG FC is modulated by sex and age in a healthy state. A widespread PAG network in the early phase of OA pain may contribute to the transition from acute to chronic OA pain and the increased risk of developing chronic pain for females. Enhanced PAG FC with the reward system may represent a potential mechanism underlying chronic OA pain in elderly patients.
Variability in agricultural productivity and rural household consumption inequality: Evidence from Nigeria and Uganda
Authors: Amare Mulubrhan , Shiferaw Bekele , Takeshima Hiroyuki , Mavrotas George
Published: January 2021

This paper uses multiple rounds of panel data to assess the distributional implications of the variability in agricultural productivity in Nigeria and Uganda. It uses both a conventional decomposition and a regression‐based inequality decomposition approach to estimate the impact of climate‐induced variability in agricultural productivity. To mitigate the endogeneity associated with unobserved time‐invariant and time‐variant household fixed effects, we use rainfall shocks as a proxy for estimating the exogenous variability in agricultural productivity that affects consumption. Results suggest that a 10% increase in the variability of agricultural productivity tends to decrease household consumption by 3.7 and 5.2% on average for Nigeria and Uganda, respectively. Controlling for other factors, variability in agricultural productivity contributed to between 25% and 43% of consumption inequality between 2010 and 2015 for Nigeria; and 16% and 31% of consumption inequality between 2009 and 2011 for Uganda. We also show that variability in agricultural productivity increases changes in consumption inequality over time.
Productivity impact of drought tolerant maize varieties under rainfall stress in Malawi: A continuous treatment approach
Authors: Katengeza Samson P. , Holden Stein T.
Published: January 2021

Drought tolerant (DT) maize varieties have received massive support in sub‐Saharan Africa because of their potential to protect smallholder farmers against drought‐related maize yield losses. Using four waves of household farm panel data from six districts in Malawi, we examine the impact heterogeneity of this technology on maize productivity using a continuous treatment approach. We find strong evidence of positive correlation between maize yield and adoption of DT maize varieties. On average, an increase by one hectare in the area allocated to DT varieties increases maize yield by 547 Kg/ha representing a 44% increase from the average maize yield of 1,254 Kg/ha for our sample. Our findings give evidence that DT maize technology has potential to protect smallholder farmers against drought‐related production losses. Policies that promote increased allocation of maize area to DT maize hold potential to enhance food security. Smallholder farmers especially in drought‐prone areas should be encouraged to allocate at least one‐third of the maize plot to DT varieties while breeders continue with the efforts of breeding a DT variety that is not only drought tolerant but also adapted to all weather conditions. More importantly, the government should ensure provision of timely ex ante weather information to guide farmers on decision‐making with respect to maize varietal choices.
HIPEC: Turning up the heat on ovarian cancer
Authors: Farrell Rhonda , Burling Michael
Published: January 2021

Clinical trials of heated intraperitoneal chemotherapy (HIPEC ) for the treatment of advanced ovarian cancer are showing promising survival outcomes. HIPEC has the potential to eliminate ovarian cancer cells from peritoneal surfaces more effectively than systemic chemotherapy through enhanced pharmacokinetic and hyperthermia effects. However, many questions remain to be answered, particularly regarding the true place of HIPEC in the current era of new and effective targeted treatments. Concerns around the potential for increased morbidity, adverse effects on quality of life, and increased resource use following HIPEC use, can only be properly evaluated with ongoing high‐quality clinical trials.
Malignant hyperthermia 2020
Authors: Hopkins P. M. , Girard T. , Dalay S. , Jenkins B. , Thacker A. , Patteril M. , McGrady E.
Published: January 2021

Malignant hyperthermia is defined in the International Classification of Diseases as a progressive life‐threatening hyperthermic reaction occurring during general anaesthesia. Malignant hyperthermia has an underlying genetic basis, and genetically susceptible individuals are at risk of developing malignant hyperthermia if they are exposed to any of the potent inhalational anaesthetics or suxamethonium. It can also be described as a malignant hypermetabolic syndrome. There are no specific clinical features of malignant hyperthermia and the condition may prove fatal unless it is recognised in its early stages and treatment is promptly and aggressively implemented. The Association of Anaesthetists has previously produced crisis management guidelines intended to be displayed in all anaesthetic rooms as an aide memoire should a malignant hyperthermia reaction occur. The last iteration was produced in 2011 and since then there have been some developments requiring an update. In these guidelines we will provide background information that has been used in updating the crisis management recommendations but will also provide more detailed guidance on the clinical diagnosis of malignant hyperthermia. The scope of these guidelines is extended to include practical guidance for anaesthetists dealing with a case of suspected malignant hyperthermia once the acute reaction has been reversed. This includes information on care and monitoring during and after the event; appropriate equipment and resuscitative measures within the operating theatre and ICU; the importance of communication and teamwork; guidance on counselling of the patient and their family; and how to make a referral of the patient for confirmation of the diagnosis. We also review which patients presenting for surgery may be at increased risk of developing malignant hyperthermia under anaesthesia and what precautions should be taken during the peri‐operative management of the patients.
Effectiveness of acceptance and commitment therapy for mental illness in cancer patients: A systematic review and meta‐analysis of randomised controlled trials
Authors: Li Zhihong , Li Yanfei , Guo Liping , Li Meixuan , Yang Kehu
Published: January 2021

Background

Disease awareness is an important aspect of psychological adjustment in cancer patients; however, there is limited evidence that acceptance and commitment therapy (ACT) is recommended for the treatment of mental illness in cancer patients.

Purpose

To assess the effectiveness of ACT for cancer patients with mental illness.

Methods

Ten databases were searched for publications up to July 25, 2020, using combinations of search terms related to mental health, cancer, and randomised controlled trials (RCTs). Two researchers independently screened the literature, extracted data, and assessed the quality of the study.

Results

Seventeen RCTs (877 cancer patients) were mainly of low quality, compared with control group, ACT was associated with improved outcomes after treatment completion and at 1‐3 months and at 3‐6 months of follow‐up for depression (Standardised mean difference [SMD] = −0.93, 95% CI, −1.36 to −0.51, P < .001), anxiety (SMD = −1.22, 95% CI, −2.16 to −0.29, P = .01), quality of life (SMD = 0.85, 95% CI, 0.17 to 1.11, P = .01), psychological distress (SMD = −0.80, 95% CI, −1.24 to 0.35, P < .001), and stress (SMD = −0.54, 95% CI, −1.02 to −0.07, P = .03). After 6 months of follow‐up, depression, anxiety, quality of life, and stress were still significant. ACT was associated with psychological flexibility and was not associated with a reduction in fear at treatment completion. However, psychological flexibility (1‐3 months) decreased and fear (1‐6 months) decreased, and the longer‐term effect was still significant.

Conclusion

ACT can be an important component of future cancer care, as it may alleviate depression, anxiety, stress, and fear, and improve quality of life. However, further research is required to determine long‐term treatment effects. High‐quality RCTs are needed to more reliably estimate treatment effects.
Coffee and type 2 diabetes risk: Is the association mediated by adiponectin, leptin, c‐reactive protein or Interleukin‐6? A systematic review and meta‐analysis
Authors: Osama Hasnaa , Abdelrahman Mona A. , Madney Yasmin M. , Harb Hadeer S. , Saeed Haitham , Abdelrahim Mohamed E. A.
Published: January 2021

Aim

Coffee and diabetes risk association has been demonstrated in numerous studies; however, the exact mechanism has not been clarified yet. The present meta‐analysis was conducted to cover the current knowledge regarding the effect of coffee on Type 2 Diabetes (T2D), in addition to the evaluation of adiponectin, leptin, C‐reactive protein (CRP) and Interleukin‐6 (IL‐6) levels among coffee consumers as relatively possible mediators of this effect.

Method

A comprehensive search of the literature was carried out using search engines up to March 2020. The effect sizes were investigated using the standardised mean difference (SMD) and odds ratios (OR) or relative risk (RR) with its 95% confidence interval (CI). A total of 69 cross‐sectional and cohort studies were included and divided as follows: 31 articles for T2D risk, 15 studies for adiponectin, 6 studies for leptin, 12 studies for CRP and 5 studies for IL‐6.

Results

Overall, coffee consumption was inversely associated with T2D risk with an estimated pooled RR of 0.73 (95% confidence interval [0.68, 0.80] for the highest vs lowest coffee consumption categories. The combined SMD between the different coffee intake categories, showed that coffee consumption was associated with higher adiponectin levels (P = .002), and lower level of leptin (P = .04) and CRP (P = .2), with apparently no change in IL‐6 levels (P = .91).

Conclusion

The present meta‐analysis showed strong epidemiological evidence that coffee consumption is inversely associated with the risk of T2D. Also, adiponectin, leptin concentrations appeared to be potential mediators of the coffee effect on diabetes, while IL‐6 levels did not.
Central nervous system inflammatory demyelinating diseases and neuroimmunology in Singapore—Epidemiology and evolution of an emerging subspecialty
Authors: Tan Kevin , Yeo Tianrong , Yong Kok Pin , Thomas Terrence , Wang Furene , Tye Janis , Quek Amy May Lin
Published: January 2021

The clinico‐pathologic entity of central nervous system inflammatory demyelinating diseases (CNS IDD) such as multiple sclerosis (MS) and neuromyelitis optica spectrum disorders (NMOSD) was recognized in Singapore as early as the 1960s but were previously under‐diagnosed and under‐researched. Access to neuroimmunology expertise, advanced neuroimaging and novel neural antibody biomarkers that distinguish aquaporin‐4 antibody‐positive NMOSD (AQP4 NMOSD) and myelin oligodendrocyte glycoprotein antibody disease (MOGAD) from MS have revolutionized the clinical management of patients with CNS IDD in Singapore. Based on pooled cross‐sectional data from government‐funded hospitals in 2020, we identified 468 CNS IDD patients (265 MS, 152 AQP4 NMOSD, and 51 MOGAD) in Singapore. Based on a population size of approximately 4 million, the crude prevalence estimates of MS are 6.6 per 100 000, AQP4 NMOSD 3.8 per 100 000, and MOGAD 1.3 per 100 000. There are marked differences in MS and AQP4 NMOSD prevalence between ethnic groups; MS prevalence is highest in Eurasian (mixed Caucasian‐Asian ancestry) (23.9 per 100 000), followed by Indian (17.5 per 100 000), Malay (9.2 per 100 000), and Chinese (4 per 100 000); AQP4 NMOSD prevalence is highest in Chinese (4.5 per 100 000), followed by Eurasian (3.9 per 100 000), Malay (1.5 per 100 000), and Indian (1.1 per 100 000). The past decade has seen remarkable growth in neuroimmunology in Singapore. We aim to foster the development of interdisciplinary care, clinical, translational, and health services research that impact local healthcare policies and research priorities, and patient support groups to better navigate through this rapidly evolving landscape.
Humeral Head Replacement in the Treatment of Comminuted Proximal Humeral Fracture
Authors: Zhang Xinghuo , Zhang Yakui , Guo Tao , Liu Liang , Cheng Wenhao
Published: January 2021

Objective

To investigate the outcomes of humeral head replacement in the treatment of patients with comminuted proximal humeral fracture.

Methods

Between February 2013 and September 2016, 56 patients underwent humeral head replacement in our hospital. Of them, 18 cases were diagnosed as comminuted proximal humeral fracture before the operation. The mean age of the patients was 69.5 years old (ranging from 61 to 79 years old). Of them, there were six males and 12 females. All the patients in this group had fresh fractures. They were all treated by artificial humeral head replacements. After the prosthesis was fixed by bone cement reliably, the greater or lesser trochanter and prosthesis handle were sutured and fixed firmly. The interval time from injury to operation ranged from 1 to 5 days. The Constant Functional Score, operation time, blood loss, nerve injury, joint dislocation rate, and infection rate were recorded at the final follow‐up. The clinical data of these patients were retrospectively studied. All of the data were recorded in average form.

Results

In this study, the mean duration of follow‐up was 4 years, ranging from 3 to 6 years. The operation time ranged from 75 to 120 min, with the average of 82 min. The blood loss ranged from 100 to 400 mL, with the average of 210 mL. The mean score of Constant Functional Score was 83.5 ± 3.1. Of them, 14 cases achieved excellent and good (scores of more than 80), and four cases achieved moderate and poor (scores of less than 80). No patient suffered from joint dislocation, unstable joint, or infection after the operation. There were two patients with axillary nerve injury before the operation. However, the function could be recovered within 3–6 weeks after the surgery.

Conclusion

The artificial humeral head replacement could be applied for the treatment of patients with comminuted proximal humeral fracture. During the surgery process, the stable structure of shoulder joint could be completely restructured, and the rehabilitation plan should be adjusted reasonably and timely after the operation.
Risk factors for progression from low level BK dnaemia to unfavorable outcomes after BK management via immunosuppressive reduction
Authors: Kharel Abish , Djamali Arjang , Jorgenson Margaret R. , Alzoubi Beyann , Swanson Kurtis J. , Garg Neetika , Aziz Fahad , Mohamed Maha A. , Mandelbrot Didier A. , Parajuli Sandesh
Published: January 2021

Backgrounds

Effective management of BK viremia (BKPyV‐DNAemia) in kidney transplant recipients (KTRs) involves regular monitoring and adjustment of immunosuppression. With this strategy, the majority of patients will clear BK or have ongoing, but non‐significant, low‐level BKPyV‐DNAemia. However, despite adjustments, some will develop more severe sequelae of BK including BKPyV‐DNAemia >5 log10copies/mL and BK nephropathy, and others may develop de novo DSA (dnDSA) or acute rejection (AR).

Methods

This was a single‐center study of KTRs transplanted at the University of Wisconsin‐Madison between 01/01/2015 and 12/31/2017. In this study, we sought to elucidate characteristics associated with the progression of BKPyV‐DNAemia to unfavorable outcomes after decreasing immunosuppressive medications for the management of BK viremia as described in consensus guidelines.

Results

A total of 224 KTRs fulfilled our selection criteria; 118 (53%) resolved or had persistent low DNAemia, 64 (28%) had severe BK/nephropathy, and 42 (19%) developed dnDSA or AR. In multivariable analysis, female gender (HR: 2.05; 95% CI: 1.08‐3.90;P = .02); previous rejection (HR: 2.90; 95% CI: 1.04‐8.12;P = .04), and early infection (HR: 0.81; 95% CI: 0.72‐0.90;P < .001) were associated with the development of severe BK/nephropathy. Conversely, non‐depleting induction at transplant (HR: 2.06; 95% CI: 1.03‐4.11;P = .03), HLA mismatches >3 (HR: 2.27; HR: 1.01‐5.06;P = .04), and delayed graft function (HR: 4.14; 95% CI: 1.12‐15.28;P = .03) were associated with development of dnDSA and/or rejection.

Conclusion

Our study suggests that almost half of KTRs with BKPyV‐DNAemia managed by our immunosuppressant adjustment protocol progress unfavorably. Identification of these risk factors could assist the frontline clinician in creating an individualized immunosuppressive modification plan potentially mitigating negative outcomes.
Aerobic Capacity According to Playing Role and Position in Elite Female Basketball Players Using Laboratory and Field Tests
Authors: Scanlan Aaron T. , Stojanović Emilija , Milanović Zoran , Teramoto Masaru , Jeličić Mario , Dalbo Vincent J.
Published: January 2021

Purpose: To compare the aerobic capacity of elite female basketball players between playing roles and positions determined using maximal laboratory and field tests. Methods: Elite female basketball players from the National Croatian League were grouped according to playing role (starter: n = 8; bench: n = 12) and position (backcourt: n = 11; frontcourt: n = 9). All 20 players completed 2 maximal exercise tests in a crossover fashion 7 days apart. First, the players underwent a laboratory-based continuous running treadmill test with metabolic measurement to determine their peak oxygen uptake (VO2peak). The players then completed a maximal field-based 30-15 Intermittent Fitness Test (30-15 IFT) to estimate VO2peak. The VO2peak was compared using multiple linear regression analysis with bootstrap standard errors and playing role and position as predictors. Results: During both tests, starters attained a significantly higher VO2peak than bench players (continuous running treadmill: 47.4 [5.2] vs 44.7 [3.5] mL·kg−1·min−1, P = .05, moderate; 30-15 IFT: 44.9 [2.1] vs 41.9 [1.7] mL·kg−1·min−1, P < .001, large), and backcourt players attained a significantly higher VO2peak than frontcourt players (continuous running treadmill: 48.1 [3.8] vs 43.0 [3.3] mL·kg−1·min−1, P < .001, large; 30-15 IFT: 44.2 [2.2] vs 41.8 [2.0] mL·kg−1·min−1, P < .001, moderate). Conclusions: Starters (vs bench players) and guards (vs forwards and centers) possess a higher VO2peak irrespective of using laboratory or field tests. These data highlight the role- and position-specific importance of aerobic fitness to inform testing, training, and recovery practices in elite female basketball.
Draft Genome Sequences of 284 Xanthomonas citri pv. citri Strains Causing Asiatic Citrus Canker
Authors: Richard Damien , Rieux Adrien , Lefeuvre Pierre , Hamza Azali , Lobin Kanta Kumar , Naiken Mark , Stravens Randy , Boyer Claudine , Boyer Karine , Javegny Stéphanie , Pruvost Olivier
Published: January 2021

High-quality Illumina assemblies were produced from 284
Xanthomonas citri
pv. citri pathotype A strains mostly originating from the Southwest Indian Ocean region, a subset of which was also sequenced using MinION technology. Some strains hosted chromosomally encoded transcription activator-like effector (TALE) genes, an atypical feature for this bacterium.
Draft Genome Sequences of Three Strains of Pseudomonas syringae pv. eriobotryae, a Pathogen Causing Canker Disease in Loquat, Isolated in Japan
Authors: Tashiro Hiroaki , Nagano Yukio , Jiromaru Ayaka , Sakaguchi Ryunosuke , Hiehata Naofumi , Fukuda Shinji
Published: January 2021

The phytopathogenic bacterium
Pseudomonas syringae
pv. eriobotryae causes canker disease in loquat. Isolates from Japan are classified into three groups based on pathogenicity and pigment production. In this study, we report the draft genome sequences of three strains, one belonging to each of the three groups.
Two SARS-CoV-2 Genome Sequences of Isolates from Rural U.S. Patients Harboring the D614G Mutation, Obtained Using Nanopore Sequencing
Authors: Jenjaroenpun Piroon , Wanchai Visanu , Ono-Moore Kikumi D. , Laudadio Jennifer , James Laura P. , Adams Sean H. , Prior Fred , Nookaew Intawat , Ussery David W. , Wongsurawat Thidathip
Published: January 2021

Two coding-complete sequences of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) were obtained from samples from two patients in Arkansas, in the southeastern corner of the United States. The viral genome was obtained using the ARTIC Network protocol and Oxford Nanopore Technologies sequencing.
Complete Genome Sequence of Clostridium botulinum CJ0611A1, a Type A(B) Isolate Associated with an International Outbreak of Botulism from Commercial Carrot Juice
Authors: Harris Richard , Dussault Forest , Flint Annika , Austin John W. , Weedmark Kelly
Published: January 2021

We report the complete genome (3.9-Mb chromosome, 5.9-kb plasmid) of
Clostridium botulinum
CJ0611A1, a type A(B) strain isolated from carrot juice distributed in Canada and linked to an international 2006 foodborne botulism outbreak. This strain encodes a full-length
bont/A1
gene and a truncated
bont/B
gene.
Complete Genome Sequence of a Serotype 7 Listeria monocytogenes Strain, FSL R9-0915
Authors: Peters Tracey Lee , Hudson Lauren K. , Bryan Daniel W. , Song Yaxiong , den Bakker Henk C. , Kucerova Zuzana , Denes Thomas G.
Published: January 2021

Listeria monocytogenes
serotype 7 lacks glycosidic constituents in wall teichoic acids. Here, we present the complete genome sequence of
L. monocytogenes
serotype 7 strain FSL R9-0915 and an analysis of genes known to affect
L. monocytogenes
antigenicity. This strain was used as a control strain in
Listeria
phage host-range analyses.
Complete Genome Sequence of Sphingobium barthaii KK22, a High-Molecular-Weight Polycyclic Aromatic Hydrocarbon-Degrading Soil Bacterium
Authors: Mori Jiro F. , Kanaly Robert A.
Published: January 2021

Sphingobium barthaii
KK22
T
is a high-molecular-weight polycyclic aromatic hydrocarbon-degrading soil bacterium that has been investigated in biotransformation, microbial ecology, and DNA damage studies. The complete genome sequence of
S. barthaii
revealed four closed circular sequences, including two chromosomes, a megaplasmid, and a smaller plasmid, by hybrid assembly using short- and long-read sequencing technologies.
Draft Genome Sequence of Pseudomonas saudiphocaensis Strain AGROB56, Isolated from a Dairy Farm in New Zealand
Authors: Gupta Tanushree B. , Risson Alexis N. , Jauregui Ruy , Maclean Paul , Brightwell Gale
Published: January 2021

Here, we report the draft genome sequence of a new
Pseudomonas saudiphocaensis
strain, AGROB56, with lipolytic potential, isolated from a sheep dairy farm in New Zealand. The genome is 3.61 Mbp, with a GC content of 61.1%, and the genome sequence was found closely related to
Pseudomonas saudiphocaensis
20 BN
T
Bacterial Diversity Profiling around the Orca Seamount in the Bransfield Strait, Antarctica, Based on 16S rRNA Gene Amplicon Sequences
Authors: Serrano Wilbert , Olaechea Raul M. , Cerpa Luis , Herrera Jose , Indacochea Aldo
Published: January 2021

Hydrothermal vent activity is often associated with submarine volcanism. Here, we investigated the presence of microorganisms related to hydrothermal activity in the Orca seamount. Data profiling of the 16S rRNA gene amplicon sequences revealed a diversity pattern dominated mainly by the phyla
Proteobacteria
,
Acidobacteria
,
Planctomycetes
, and
Bacteroidetes
.
Genome Sequences of Two GH Clade SARS-CoV-2 Strains Isolated from Patients with COVID-19 in South Korea
Authors: Kim Minwoo , Lee Youn-Jung , Yoon Jae Sun , Ahn Jin Young , Kim Jung Ho , Choi Jun Yong , Oh Jong-Won
Published: January 2021

We report the genome sequences of two GH clade severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) strains isolated from nasopharyngeal swabs from patients with coronavirus disease 2019 (COVID-19) in South Korea. These strains had two mutations in the untranslated regions and seven nonsynonymous substitutions in open reading frames, compared with Wuhan/Hu-1/2019, showing 99.96% sequence identity.
Supplemental Material: Transport and accumulation of plastic litter in submarine canyons—The role of gravity flows
Authors: Zhong Guangfa , Peng Xiaotong
Published: January 2021

Study background and methods, and Figure S1 and Table S1.
Supplemental Material: Extreme Quaternary plate boundary exhumation and strike slip localized along the southern Fairweather fault, Alaska, USA
Authors: Lease Richard , al. et
Published: January 2021

Methods and data.
Contact interaction analysis of pion GTMDs
Authors: Zhang Jin-Li , Cui Zhu-Fang , Ping Jia-Lun , Roberts Craig D.
Published: January 2021

A contact interaction is used to calculate an array of pion twist-two, -three and -four generalised transverse light-front momentum dependent parton distribution functions (GTMDs). Despite the interaction’s simplicity, many of the results are physically relevant, amongst them a statement that GTMD size and shape are largely prescribed by the scale of emergent hadronic mass. Moreover, proceeding from GTMDs to generalised parton distributions, it is found that the pion’s mass distribution form factor is harder than its electromagnetic form factor, which is harder than the gravitational pressure distribution form factor; the pressure in the neighbourhood of the pion’s core is commensurate with that at the centre of a neutron star; the shear pressure is maximal when confinement forces become dominant within the pion; and the spatial distribution of transversely polarised quarks within the pion is asymmetric. Regarding transverse momentum dependent distribution functions, their magnitude and domain of material support decrease with increasing twist. The simplest Wigner distribution associated with the pion’s twist-two dressed-quark GTMD is sharply peaked on the kinematic domain associated with valence-quark dominance; has a domain of negative support; and broadens as the transverse position variable increases in magnitude.
Cross-modulation between microwave beams interpreted as a stochastic process
Authors: Cacciari I. , Mugnai D. , Ranfagni A. , Petrucci A.
Published: January 2021

Further and more detailed experimental work demonstrates an anomalous transfer of modulation between two microwave beams in the near-field and confirms the results already obtained. The behavior of the measured signal versus the attenuation of each beam intensity suggests a model based on the existence of hybrid terms containing the product of both the relative field amplitudes. In addition, the undulating shape of the signal suggests the presence of stochastic processes.
Hyperparameter-free Regularization by Sampling from an Infinite Space of Neural Networks
Authors: Whitehead Thomas M.
Published: January 2021

Stochastic activation functions, where the output of an activation function is a hyper-parameter-free random function of the inputs, generalize the concept of dropout to sampling from an infinitely large space of related networks. Stochastic activation functions provide intrinsic regularization and sparsification of artificial neural networks, along with cheap and accurate estimates of the uncertainty in the predictions from a network. Examples are presented against standard benchmarking datasets.
The Organic Isotopologue Frontier
Authors: Gilbert Alexis
Published: January 2021

Organic molecules are key components of the Earth-life system. Their stable isotope composition provides information on various problems such as past climate, energy resources, or the synthesis of prebiotically relevant molecules on Earth and elsewhere. Organic molecules are made of isotopologues, molecules differing in the number and/or position of isotope substitution. Recent years have witnessed a boom in technological development dedicated to isotopologue measurement, leading to an unprecedented degree of information regarding organic (bio)synthesis. While applications in Earth and planetary sciences has been limited so far to simple hydrocarbons, typically methane, isotopologue proxies are expected to rapidly emerge in biogeochemistry, providing new types of environmental and biological tracers. This review describes principles and measurement techniques, as well as present and potential biogeochemical applications. ▪  Stable isotopes of organic molecules are widely used in biogeo-chemistry. ▪  Isotope analysis at the intramolecular level is expected to provide new information on the origin of molecules. ▪  Recent technological developments unlocked the potential of intramolecular isotope analysis, providing new proxies in biogeochemistry and new opportunities to clarify questions related to Earth and planetary sciences.
Metastatic Papillary Thyroid Carcinoma in a Paediatric Patient
Authors: Mothata Nthabiseng Ellen , Morulana Takalani Gidion , Tshifularo Nyaweleni , Nemutaduni Phumudzo Bridgett , Nyakale Nozipho Elizabeth , Khaba Moshawa Calvin
Published: January 2021

Papillary thyroid carcinoma is the most common endocrine cancer in the paediatric population. Although the disease is diagnosed at a later stage, the prognosis is favourable. When these patients present with lymph nodal and/or pulmonary metastases, they may be initially confused for infectious diseases such as tuberculosis. Therefore, thorough clinical assessment including radiology and microbiological and histopathological assessment is important for early and correct diagnosis. We report an 11-year-old female patient who presented with cervical lymphadenopathy and the histopathological assessment confirmed metastatic papillary thyroid carcinoma. Subsequent radiological investigation revealed further metastasis to the lung. This manuscript highlights the difficulties that might be encountered in the initial management of paediatric PTC which present atypically.
Genotype-Phenotype Correlation in Patients with Congenital Adrenal Hyperplasia due to 21-Hydroxylase Deficiency in Cuba
Authors: Espinosa Reyes Tania Mayvel , Collazo Mesa Teresa , Lantigua Cruz Paulina Arasely , Agramonte Machado Adriana , Domínguez Alonso Emma , Falhammar Henrik
Published: January 2021

Background. There are several studies that show a good genotype-phenotype correlation in congenital adrenal hyperplasia (CAH) due to 21-hydroxylase deficiency (21OHD). However, there is well-documented evidence of inconsistency in some cases. Objectives. To determine if there is a correlation between the identified mutations and the clinical manifestations of 21OHD in the Cuban population. Methods. A cross-sectional descriptive study of all patients referred for a molecular diagnosis of 21OHD in Cuba from January 2000 to December 2018. The clinical manifestations of each patient were identified and classified according to the phenotype. The CYP21A2 gene was analyzed for the presence of 5 point mutations involved in the pathogenesis of 21OHD (intron 2, deletion of 8bp, I172N, P30L, and Q318X); correlation was sought between the phenotypic characteristics and the frequencies of point mutations in the patients using the Spearman test. Results. A total of 55 patients underwent direct analysis of the CYP21A2 gene in order to determine the presence of the 5 point mutations. Point mutations were identified in 31 patients, which corresponded to 56%. A statistically significant genotype-phenotype correlation was found. Conclusions. The correlation between the detected molecular defect and the clinical expression of 21OHD was reasonable in the Cuban population, which could allow phenotypic predictions to be made from the genotype.
MMP-9 Concentration in Peritoneal Fluid Is a Valuable Biomarker Associated with Endotoxemia in Equine Colic
Authors: Barton Ann Kristin , Richter Ina-Gabriele , Ahrens Tanja , Merle Roswitha , Alalwani Abdollah , Lilge Svenja , Purschke Katrin , Barnewitz Dirk , Gehlen Heidrun
Published: January 2021

The purpose of the study was to compare the results of sepsis scoring (clinical examination and clinical pathology) to the concentrations of matrix-metalloproteinases (MMPs) -2, -8, and -9; tissue-inhibitor of metalloproteinases (TIMPs) -1 and -2; and inflammatory chemokines interleukin (IL) 1β and tumor-necrosis-factor-alpha (TNF-α) in plasma and peritoneal fluid of equine colic patients. A modified sepsis scoring including general condition, heart and respiratory rate, rectal temperature, mucous membranes, white blood cell count (WBC), and ionized calcium was applied in 47 horses presented with clinical signs of colic. Using this scoring system, horses were classified as negative (n=32, ≤6/19 points), questionable (n=9, 7-9/19 points), or positive (n=6, ≥10/19 points) for sepsis. MMPs, TIMPs, IL-1β, and TNF-α concentrations were evaluated in plasma and peritoneal fluid using species-specific sandwich ELISA kits. In a linear discriminant analysis, all parameters of sepsis scoring apart from calcium separated well between sepsis severity groups (P<0.05). MMP-9 was the only biomarker of high diagnostic value, while all others remained insignificant. A significant influence of overall sepsis scoring on MMP-9 was found for peritoneal fluid (P=0.005) with a regression coefficient of 0.092, while no association was found for plasma (P=0.085). Using a MMP-9 concentration of >113 ng/ml in the peritoneal fluid was found to be the ideal cutoff to identify positive sepsis scoring (≥10/19 points; sensitivity of 83.3% and specificity of 82.9%). In conclusion, MMP-9 was found to be a biomarker of high diagnostic value for sepsis and endotoxemia in equine colic. The evaluation of peritoneal fluid seems preferable in comparison to plasma. As abdominocentesis is commonly performed in the diagnostic work-up of equine colic, a pen-side assay would be useful and easy-to-perform diagnostic support in the decision for therapeutic intervention.
ATR Inhibition as an Attractive Therapeutic Resource against Cancer
Authors: Italiano Antoine
Published: January 2021

In this issue of Cancer Discovery, Yap and colleagues demonstrate in a phase I trial enrolling 22 patients diagnosed with advanced solid tumors that BAY 1895344, a new potent and specific ATR inhibitor, is safe and able to induce durable responses in ATM-deficient tumors. This compelling clinical activity paves the way for innovative combination regimens that rely on exploitation of DNA damage response defects in cancer.

See related article by Yap et al., p. 80.
Barrett’s Esophageal Adenocarcinoma Involving a White Globe Appearance within the Long-Segment Barrett’s Esophagus
Authors: Kubota Yo , Tanabe Satoshi , Harada Yohei , Nakatani Seigo , Furue Yasuaki , Wada Takuya , Watanabe Akinori , Ishido Kenji , Katada Chikatoshi , Koizumi Wasaburo
Published: January 2021

The diagnosis of Barrett’s esophageal adenocarcinoma (BEA) in patients with Barrett’s esophagus (BE) using endoscopy can be difficult and there are few specific endoscopic findings for BEA. However, white globe appearance (WGA) has been reported to be a specific endoscopic finding for early gastric cancer. We encountered a 51-year-old male patient with BEA exhibiting WGA. Esophagogastroduodenoscopy identified a red, depressed lesion of 10 mm within the long-segment BE (LSBE), while magnifying endoscopy with narrow-band imaging identified WGA. Endoscopic submucosal dissection (ESD) was performed based on our suspicion of BEA. Based on the ESD findings, we diagnosed adenocarcinoma accompanying LSBE histopathologically. WGA was identified, and intraglandular necrotic debris was discovered histologically at the same site. Therefore, WGA may be helpful in the diagnosis of BEA.
Sicherheit von Dupilumab bei schwerer atopischer Dermatitis und Covid-19-Infektion: zwei Fallberichte
Authors: Ferrucci Silvia , Romagnuolo Maurizio , Angileri L. , Berti Emilio , Tavecchio Simona
Published: January 2021

Dupilumab ist ein vollständig humaner monoklonaler Antikörper, der gegen die Alfa-Untereinheit des Interleukin (IL)-4-Rezeptors gerichtet ist und die Signalübertragung von IL-4 und IL-13, wichtiger Schlüsselzytokine vom Typ 2 in der Pathophysiologie der atopischen Dermatitis (AD), blockiert. Er verfügt über eine gute Wirksamkeit mit schnellem Ansprechen bei guter Sicherheit und wenigen Nebenwirkungen. Deleuran et al. wiesen in einer Arbeit die Langzeitsicherheit und -Wirksamkeit von Dupilumab nach. Ihren Angaben zufolge traten bei etwa 2 % der Patienten virale Infektionen der oberen Atemwege, Husten und Grippe auf.
Prevalence of hypertension: predictive analytics review
Authors: Nor Nur Arifah Mohd , Mohamed Azlinah , Mutalib Sofianita
Published: January 2021

Hypertension is one of the non-communicable disease (NCD) that is classify as a global health risk with many critical health cases. Malaysia raise the same concern of the increasing NCD health problem. This paper aims to study the techniques used in predictive analytics namely healthcare and identify the factors of prevalence on hypertension. This review would give a better understanding of proper techniques and suggest the technique commonly used in predictive analytics especially for medical data and at the same time provide significant factors of prevalence hypertension. A total of 27 papers reviewed, several techniques on predictive analytics in healthcare are neural network, decision tree, naïve bayes, regression and support vector machine. The rise of economic growth and correlated socio-demographic have cause rise in hypertension problem over past years. The factors of hypertension depicted in this review namely gender, age, locality, family history, physically inactive and unhealthy life style not conform to any boundaries thus far. Thus, the choice on the technique and hypertension factors for predictive analytics is significant to come out with the significant predictive model. The predictive model on prevalence of hypertension may predict the severity of adult having hypertension in future work.