bluuebunny/crossref_metadata_2025_split huggingface dataset:
Modeling cellular co-infection and reassortment of bluetongue virus in Culicoides midges
Authors: Cavany Sean M , Barbera Carly , Carpenter Molly , Rodgers Case , Sherman Tyler , Stenglein Mark , Mayo Christie , Perkins T Alex 
Published: September 2022

Abstract
When related segmented RNA viruses co-infect a single cell, viral reassortment can occur, potentially leading to new strains with pandemic potential. One virus capable of reassortment is bluetongue virus (BTV), which causes substantial health impacts in ruminants and is transmitted via Culicoides midges. Because midges can become co-infected by feeding on multiple different host species and remain infected for their entire life span, there is a high potential for reassortment to occur. Once a midge is co-infected, additional barriers must be crossed for a reassortant virus to emerge, such as cellular co-infection and dissemination of reassortant viruses to the salivary glands. We developed three mathematical models of within-midge BTV dynamics of increasing complexity, allowing us to explore the conditions leading to the emergence of reassortant viruses. In confronting the simplest model with published data, we estimate that the average life span of a bluetongue virion in the midge midgut is about 6 h, a key determinant of establishing a successful infection. Examination of the full model, which permits cellular co-infection and reassortment, shows that small differences in fitness of the two infecting strains can have a large impact on the frequency with which reassortant virions are observed. This is consistent with experimental co-infection studies with BTV strains with different relative fitnesses that did not produce reassortant progeny. Our models also highlight several gaps in existing data that would allow us to elucidate these dynamics in more detail, in particular the times it takes the virus to disseminate to different tissues, and measurements of viral load and reassortant frequency at different temperatures.
A juvenile skull from the early Palaeocene of China extends the appearance of crocodyloids in Asia back by 15–20 million years
Authors: Boerman Sophie A , Perrichon Gwendal , Yang Jian , Li Cheng-Sen , Martin Jeremy E , Speijer Robert P , Smith Thierry 
Published: September 2022

AbstractThe earliest Crocodylia from Asia have been represented so far only by alligatoroids and planocraniids. Although definitive crocodyloids are not known until the late Eocene, it has been hypothesized that Asiatosuchus-like basal crocodyloids originated in Asia before the late Palaeocene. In this paper, we describe a new fossil crocodyloid from the lower Palaeocene of Qianshan Basin, Anhui Province, China. The skull and lower jaw fragment exhibit several characteristics typical of juvenile crocodylians. They also display a combination of features not seen in any other taxon, warranting the erection of a new species and genus, Qianshanosuchus youngi gen. & sp. nov. Its affinities are tested in phylogenetic analyses based on two recent character matrices of Eusuchia. To assess the effect of juvenile characteristics on the outcome of the phylogenetic analyses, juvenile specimens of extant crocodylian taxa are analysed in the same way, showing that the effect of their ontogenetic stage on their placement in the tree is minimal. Our analyses point to a basal crocodyloid position for Q. youngi. With these findings, the presence of Crocodyloidea in Asia is extended to the early Palaeocene, 15–20 Myr earlier than formerly thought. Furthermore, our results corroborate previous hypotheses of a Palaeocene dispersal route of Asiatosuchus-like crocodyloids from Asia into Europe.
Movement Patterns of Transient and Prolonged Positioning Events in Nursing Home Residents: Results from the TEAM-UP Trial
Authors: Gadhoumi Kais , Sonenblum Sharon Eve , Kennerly Susan M. , Alderden Jenny , Sharkey Phoebe D. , Horn Susan D. , Yap Tracey L. 
Published: September 2022

ABSTRACT

OBJECTIVE
To characterize transient and prolonged body position patterns in a large sample of nursing home (NH) residents and describe the variability in movement patterns based on time of occurrence.

METHODS
This study is a descriptive, exploratory analysis of up to 28 days of longitudinal accelerometer data for 1,100 NH residents from the TEAM-UP (Turn Everyone and Move for Ulcer Prevention) clinical trial. Investigators analyzed rates of transient events (TEs; less than 60 seconds) and prolonged events (PEs; 60 seconds or longer) and their interrelationships by nursing shift.

RESULTS
Residents’ positions changed for at least 1 minute (PEs) nearly three times per hour. Shorter-duration movements (TEs) occurred almost eight times per hour. Residents’ PE rates were highest in shift 2 (3 pm to 11 pm), when the median duration and maximum lengths of PEs were lowest; the least active time of day was shift 3 (11 pm to 7 am). Three-quarters of all PEs lasted less than 15 minutes. The rate of TEs within PEs decreased significantly as the duration of PEs increased.

CONCLUSIONS
The NH residents demonstrate complex patterns of movements of both short and prolonged duration while lying and sitting. Findings represent how NH residents naturally move in real-world conditions and provide a new set of metrics to study tissue offloading and its role in pressure injury prevention.
The optimal anticoagulation strategy for COVID-19, prophylactic or therapeutic?: a meta-analysis, trial sequential analysis, and meta-regression of more than 27,000 participants
Authors: Guo Mingyue , Han Qi , Xing Jiaxuan , Xu Feng , Wang Jiali , Li Chuanbao , Shan Zechen , Bian Yuan , Wang Hao , Xue Li , Yuan Qiuhuan , Pan Chang , De Yanshan , Wang Xingfang , Hao Panpan , Cao Shengchuan , Pang Jiaojiao , Chen Yuguo 
Published: September 2022

Abstract

Background
Anticoagulants are promising regimens for treating coronavirus disease 2019 (COVID-19). However, whether prophylactic or intermediate-to-therapeutic dosage is optimal remains under active discussion.

Methods
We comprehensively searched PubMed, Embase, Scopus, Web of Science, Cochrane Library, ClinicalTrials, and MedRxiv databases on April 26, 2022. Two independent researchers conducted literature selection and data extraction separately according to predetermined criteria. Notably, this is the first meta-analysis on COVID-19, taking serious consideration regarding the dosage overlap between the 2 comparison groups of prophylactic anticoagulation (PA) and intermediate-to-therapeutic anticoagulation (I-TA).

Results
We included 11 randomized controlled trials (RCTs) and 36 cohort studies with 27,051 COVID-19 patients. By analyzing all the RCTs, there was no significant difference in mortality between the PA and I-TA groups, which was further confirmed by trial sequential analysis (TSA) (odds ratio [OR]: 0.93; 95% confidence interval [CI]: 0.71–1.22; P = 0.61; TSA adjusted CI: 0.71–1.26). The rate of major bleeding was remarkably higher in the I-TA group than in the PA group, despite adjusting for TSA (OR: 1.73; 95% CI: 1.15–2.60; P = 0.009; TSA adjusted CI: 1.09–2.58). RCTs have supported the beneficial effect of I-TA in reducing thrombotic events. After including all studies, mortality in the I-TA group was significantly higher than in the PA group (OR: 1.38; 95% CI: 1.15–1.66; P = 0.0005). The rate of major bleeding was similar to the analysis from RCTs (OR: 2.24; 95% CI: 1.86–2.69; P < 0.00001). There was no distinct difference in the rate of thrombotic events between the 2 regimen groups. In addition, in both critical and noncritical subgroups, I-TA failed to reduce mortality but increased major bleeding rate compared with PA, as shown in meta-analysis of all studies, as well as RCTs only. Meta-regression of all studies suggested that there was no relationship between the treatment effect and the overall risk of mortality or major bleeding (P = 0.14, P = 0.09, respectively).

Conclusion
I-TA is not superior to PA for treating COVID-19 because it fails to lower the mortality rate but increases the major bleeding rate in both critical and noncritical patients.
Dexamethasone for the treatment of acute respiratory distress syndrome: A systematic review and meta-analysis
Authors: Feng Long-hua , Li Xiao-dan , Zhang Xiao-yu , Cheng Peng-jiang , Feng Zheng-yun 
Published: September 2022

Background:This meta-analysis aimed to evaluate the efficacy and safety of dexamethasone in the treatment of acute respiratory distress syndrome (ARDS).Methods:A systematic search of electronic databases was carried out from inception to May 1, 2022, including PUBMED, EMBASE, Cochrane Library, Wangfang, VIP, and CNKI. Other searches were also checked for dissertations/theses and the reference lists of the included studies. Two team members examined all citations and selected eligible articles. Randomized controlled trials (RCTs) reporting the efficacy and safety of dexamethasone for the treatment of ARDS were included, and the quality of eligible RCTs was assessed using the Cochrane Risk of Bias Tool. If necessary, we conducted data synthesis and meta-analysis. The primary outcome was all-cause mortality. Secondary outcomes were mechanical ventilation duration (day), ventilator-free status at 28 days; intensive care unit (ICU) free (day), ICU mortality, hospital mortality, sequential organ failure assessment (SOFA) as mean and range, SOFA as No. of patients, peak airway pressure (cmH2O), arterial oxygen pressure (mm Hg), days with PaO2> 10kPa, PaO2, and the occurrence rate of adverse events.Results:Four studies involving 702 patients were included in this analysis. This study showed that dexamethasone could significantly reduce all-cause mortality (odds ratio (OR) = 0.62, 95% confidence interval (CI) [0.44, 0.88], I2= 30%,P< .001), and decrease ventilator-free status at 28 days (MD = 3.65, 95% CI [1.49, 5.80], I2= 51%,P< .001). No significant differences in occurrence rates of adverse events were found between dexamethasone and routine or standard care.Conclusions:Evidence from the meta-analysis suggests that dexamethasone is an effective and relatively safe treatment for all-cause mortality and ventilator-free status at 28 days in patients with ARDS. Owning to the small number of eligible RCTs, the conclusions of present study are warranted in the future study.
Congenital aflatoxicosis, mal-detoxification genomics & ontogeny trigger immune-mediated Kotb disease biliary atresia variant: SANRA compliant review
Authors: Kotb Magd A. , Kotb Ahmed , Talaat Sahar , Shehata Sherif M. , El Dessouki Nabil , ElHaddad Ahmed A. , El Tagy Gamal , Esmat Haytham , Shehata Sameh , Hashim Mohamed , Kotb Hanan A. , Zekry Hanan , Abd Elkader Hesham M. , Kaddah Sherif , Abd El Baky Hend E. , Lotfi Nabil 
Published: September 2022

Biliary atresia (BA) is the most common indication for pediatric liver transplantation. We describe The BA variant: Kotb disease. Liver tissue in the Kotb disease BA is massively damaged by congenital aflatoxicosis resulting in inflammation, adhesions, fibrosis, bile duct proliferation, scarring, cholestasis, focal syncytial giant cell transformation, and typical immune response involving infiltration by CD4+, CD8+, CD68+, CD14+, neutrophil infiltration, neutrophil elastase spill, heavy loads of aflatoxin B1, accelerated cirrhosis, disruption of p53 and GSTPi, and have null glutathione S transferase M1 (GSTM1). All their mothers are heterozygous for GSTM1. This inability to detoxify aflatoxicosis results in progressive inflammatory adhesions and obliterative cholangiopathy early in life. The typical disruption of both p53 and GSTPi causes loss of fidelity of hepatic regeneration. Hence, regeneration in Kotb disease BA typically promotes accelerated cirrhosis. The immune response in Kotb disease BA is for damage control and initiation of regeneration, yet, this friendly fire incurs massive structural collateral damage. The Kotb disease BA is about actual ongoing hepatic entrapment of aflatoxins with lack of ability of safe disposal due to child detoxification-genomics disarray.
The Kotb disease BA is a product of the interaction of persistent congenital aflatoxicosis, genetic lack of GSTM1 detoxification, ontogenically impaired activity of other hepatic detoxification, massive neutrophil-elastase, immune-induced damage, and disturbed regeneration. Ante-natal and neonatal screening for aflatoxicosis, avoiding cord milking, and stringent control of aflatoxicosis content of human, poultry and live-stock feeds might prove effective for prevention, prompt diagnosis and management based on our recent understanding of its patho-genomics.
Cortisol secretory patterns in deep and moderate neuromuscular blockades in laparoscopic surgery under total intravenous anesthesia: A prospective, single-blinded, randomized controlled trial
Authors: Lee Jeongyoon , An Jihyun , Lee Dong Hwan , Lee Jihyang , Kim Eunju , Woo Kyeongyoon , Kim Kyeong Hyo 
Published: September 2022

Background:
Neuroendocrine stress response induces physiological changes depending on the type of surgery and anesthesia. Although the optimal depth of neuromuscular blockade for reducing this response remains unknown, deep neuromuscular blockade is known to improve the surgical environment. Therefore, we hypothesized that a patient’s stress response would be lower in surgical procedures under deep neuromuscular blockade than under moderate neuromuscular blockade.

Methods:
This prospective, randomized, single-blind study enrolled 72 patients who underwent laparoscopic gynecological surgery under general anesthesia and were assigned to group D (deep blockade: target train-of-four 0 and posttetanic count ≥ 1) or group M (moderate blockade: target train-of-four count 1–3). The primary endpoints were changing patterns in cortisol and adrenocorticotrophic hormone levels; the secondary endpoints were patient outcomes, such as hemodynamic variables, serum glucose level, postoperative pain in the postanesthesia care unit, and hospital stay.

Results:
The baseline characteristics were comparable between the 67 patients included in the 2 groups (34 in group M and 33 in group D). Cortisol and adrenocorticotrophic hormone levels increased perioperatively in both groups but without significant intergroup differences. Serum glucose level increased perioperatively and decreased postoperatively, but without a significant intergroup difference. Postoperative pain, fentanyl requirement in the postanesthesia care unit, and hospital stay were also comparable.

Conclusions:
Compared with moderate neuromuscular blockade, deep neuromuscular blockade improved the surgical environment without significant intergroup differences in the hormonal stress response.
The safety and efficacy of melatonin in the treatment of COVID-19: A systematic review and meta-analysis
Authors: Wang Xin-Chen , Wu Guang-Liang , Cai Ye-Feng , Zhang Shi-Jie 
Published: September 2022

Background:
As an infectious disease caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the common signs of coronavirus disease 2019 (COVID-19) are respiratory symptoms, fever, cough, shortness of breath, and dyspnea, with multiple organ injuries in severe cases. Therefore, finding drugs to prevent and treat COVID-19 is urgently needed and expected by the public. Several studies suggested beneficial effects of melatonin for the relevant prevention and treatment. To explore the effect and safety of melatonin in the treatment and provide theoretical support and reference for seeking the most suitable drug for COVID-19, the meta-analysis was carried out accordingly.

Methods:
It included randomized clinical trials of patients with COVID-19 treated with melatonin. Total effective rate was the primary outcome, while C-reactive protein (CRP), arterial oxygen saturation (SaO2), white blood cell count (WBC) were the secondary measures. Random-effect and fixed-effect models were used to evaluate the effect size of some indicators in this meta-analysis.

Results:
Six eligible studies with 338 participants were included. One hundred seventy subjects were treated with melatonin adjuvant therapy and 168 subjects were assigned to the control group, with total excellent effective rate in subjects treated with melatonin [odds ratio = 3.05, 95 % confidence interval (CI) = 1.47, 6.31, P = .003]. Homogeneity was analyzed by fixed effect model (I
2 = 0%). There was no significant difference in CRP between the melatonin group and the control group (weighted mean difference [WMD] = –0.36, 95% CI = –3.65, 2.92, P = .83). Significant difference was not existed in SaO2 between the melatonin treatment group and the control group (WMD = 1, 95% CI = –1.21, 3.22, P = .37). In terms of WBC, there was no significant difference between the 2 groups (WMD = –1.07, 95% CI = –2.44, 0.30, P = .13).

Conclusions:
The meta-analysis showed that melatonin had the beneficial effects for COVID-19 prevention and treatment as an adjunctive agent in combination with basic treatment for the treatment.
18F-FDG PET/CT Findings of Myeloid Sarcoma Involving the Left Ventricle and Kidney in a Pediatric Patient
Authors: Zhang Mingyu , Yang Xu , Si Yukun , Kan Ying , Yang Jigang 
Published: September 2022

Abstract
A 1-year-old girl presented with vomiting for 1 week. Abdominal ultrasound revealed a mass with increased blood flow in the left lower abdomen. A malignancy was suspected. 18F-FDG PET/CT showed multiple lesions in the left ventricular wall, the kidney, and the left lower abdomen. Biopsy of the left abdominal mass confirmed the diagnosis of myeloid sarcoma associated with acute myeloid leukemia. After 4 cycles of chemotherapy, follow-up PET/CT was performed for evaluating the therapy response, which showed complete resolution.
What Are Patients Told About Innovative Surgical Procedures? A Qualitative Synthesis of 7 Case Studies in the United Kingdom
Authors: Elliott Daisy , Ochieng Cynthia A. , Zahra Jesmond , McNair Angus G.K. , Main Barry G. , Skilton Anni , Blencowe Natalie S. , Cousins Sian , Paramasivan Sangeetha , Hoffmann Christin , Donovan Jenny L. , Blazeby Jane M. 
Published: September 2022

Objectives:
To investigate how information about innovative surgical procedures is communicated to patients.

Background:
Despite the national and international guidance that patients should be informed whether a procedure is innovative and has uncertain outcomes, little is known about current practice.

Methods:
This qualitative study followed 7 “case studies” of surgical innovation in hospitals across the United Kingdom. Preoperative interviews were conducted with clinician innovators (n=9), preoperative real-time consultations between clinicians and patients were audio-recorded (n=37). Patients were interviewed postoperatively (n=30). Data were synthesized using thematic analytical methods.

Results:
Interviews with clinicians demonstrated strong intentions to inform patients about the innovative nature of the procedure in a neutral manner, although tensions between fully informing patients and not distressing them were raised. In the consultations, only a minority of clinicians actually made explicit statements about, (1) the procedure being innovative, (2) their limited clinical experience with it, (3) the paucity of evidence, and (4) uncertainty/unknown outcomes. Discussions about risks were generalized and often did not relate to the innovative component. Instead, all clinicians optimistically presented potential benefits and many disclosed their own positive beliefs. Postoperative patient interviews revealed that many believed that the procedure was more established than it was and were unaware of the unknown risks.

Conclusions:
There were contradictions between clinicians’ intentions to inform patients about the uncertain outcomes of innovative and their actual discussions with patients. There is a need for communication interventions and training to support clinicians to provide transparent data and shared decision-making for innovative procedures.
The Global and Regional Prevalence of Abdominal Aortic Aneurysms: A Systematic Review and Modeling Analysis
Authors: Song Peige , He Yazhou , Adeloye Davies , Zhu Yuefeng , Ye Xinxin , Yi Qian , Rahimi Kazem , Rudan Igor ,   on behalf of the Global Health Epidemiology Research Group (GHERG)
Published: September 2022

Objective:
To estimate the global and regional prevalence and cases of abdominal aortic aneurysms (AAAs) in 2019 and to evaluate major associated factors.

Background:
Understanding the global prevalence of AAA is essential for optimizing health services and reducing mortality from reputed AAA.

Methods:
PubMed, MEDLINE, and Embase were searched for articles published until October 11, 2021. Population-based studies that reported AAA prevalence in the general population, defined AAA as an aortic diameter of 30 mm or greater with ultrasonography or computed tomography. A multilevel mixed-effects meta-regression approach was used to establish the relation between age and AAA prevalence for high-demographic sociodemographic index and low-and middle-sociodemographic index countries. Odds ratios of AAA associated factors were pooled using a random-effects method.

Results:
We retained 54 articles across 19 countries. The global prevalence of AAA among persons aged 30 to 79 years was 0.92% (95% CI, 0.65–1.30), translating to a total of 35.12 million (95% CI, 24.94–49.80) AAA cases in 2019. Smoking, male sex, family history of AAA, advanced age, hypertension, hypercholesterolemia, obesity, cardiovascular disease, cerebrovascular disease, claudication, peripheral artery disease, pulmonary disease, and renal disease were associated with AAA. In 2019, the Western Pacific region had the highest AAA prevalence at 1.31% (95% CI, 0.94–1.85), whereas the African region had the lowest prevalence at 0.33% (95% CI, 0.23–0.48).

Conclusions:
A substantial proportion of people are affected by AAA. There is a need to optimize epidemiological studies to promptly respond to at-risk and identified cases to improve outcomes.
Fully efficient, two-stage analysis of multi-environment trials with directional dominance and multi-trait genomic selection
Authors: Endelman Jeffrey B. 
Published: September 2022

ABSTRACTPlant breeders interested in genomic selection often face challenges to fully utilizing the multi-trait, multi-environment datasets they rely on for selection. R package StageWise was developed to go beyond the capabilities of most specialized software for genomic prediction, without requiring the programming skills needed for more general-purpose software for mixed models. As the name suggests, one of the core features is a fully efficient, two-stage analysis for multiple environments, in which the full variance-covariance matrix of the Stage 1 genotype means is used in Stage 2. Another feature is directional dominance, including for polyploids, to account for inbreeding depression in outbred crops. StageWise enables selection with multi-trait indices, including restricted indices with one or more traits constrained to have zero response. For a potato dataset with 943 genotypes evaluated over 6 years, including the Stage 1 errors in Stage 2 reduced the Akaike Information Criterion (AIC) by 29, 67, and 104 for maturity, yield, and fry color, respectively. The proportion of variation explained by heterosis was largest for yield but still only 0.03, likely because of limited variation for the genomic inbreeding coefficient. Due to the large additive genetic correlation (0.57) between yield and maturity, naïve selection on an index combining yield and fry color led to an undesirable response for later maturity. The restricted index coefficients to maximize genetic merit without delaying maturity were identified. The software and three vignettes are available at https://github.com/jendelman/StageWise.