Miracle-dz/UniFAR-FTUs huggingface dataset:
Hepatitis B virus infection and the risk of cancer among the Chinese population

The relationship between hepatitis B virus (HBV) and nonhepatocellular cancers remains inconclusive. This large case‐control study aimed to assess the associations between HBV infection status and multiple cancers. Cases (n = 50 392) and controls (n = 11 361) were consecutively recruited from 2008 to 2016 at the First Affiliated Hospital of Nanjing Medical University. Multivariable adjusted odds ratios (aORs) and 95% confidence intervals (95% CIs) were estimated using logistic regression by adjusting age and gender. A meta‐analysis based on published studies was also performed to verify the associations. Of these, 12.1% of cases and 5.5% of controls were hepatitis B surface antigen (HBsAg) seropositive. We observed significant associations between HBsAg seropositivity and esophagus cancer (aOR [95% CI] = 1.32 [1.13‐1.54]), stomach cancer (1.46 [1.30‐1.65]), hepatocellular carcinoma (HCC; 39.11 [35.08‐43.59]), intrahepatic and extrahepatic bile duct carcinoma (ICC and ECC; 3.83 [2.58‐5.67] and 1.72 [1.28‐2.31]), pancreatic cancer (PaC; 1.37 [1.13‐1.65]), non‐Hodgkin lymphoma (NHL; 1.88 [1.61‐2.20]) and leukemia (11.48 [4.05‐32.56]). Additionally, compared to participants with HBsAg−/anti‐HBs−/anti‐HBc−, participants with HBsAg−/anti‐HBs−/anti‐HBc+, indicating past HBV‐infected, had an increased risk of esophagus cancer (aOR [95% CI] = 1.46 [1.24‐1.73]), stomach cancer (1.20 [1.04‐1.39]), HCC (4.80 [3.95‐5.84]) and leukemia (15.62 [2.05‐119.17]). Then the overall meta‐analysis also verified that HBsAg seropositivity was significantly associated with stomach cancer (OR [95% CI] = 1.23 [1.14‐1.33]), ICC (4.05 [2.78‐5.90]), ECC (1.73 [1.30‐2.30]), PaC (1.26 [1.09‐1.46]), NHL (1.95 [1.55‐2.44]) and leukemia (1.54 [1.26‐1.88]). In conclusion, both our case‐control study and meta‐analysis confirmed the significant association of HBsAg seropositivity with stomach cancer, ICC, ECC, PaC, NHL and leukemia. Of note, our findings also suggested that the risk of stomach cancer elevated for people whoever exposed to HBV.
Binding affinities of 438 HLA proteins to complete proteomes of seven pandemic viruses and distributions of strongest and weakest HLA peptide binders in populations worldwide

We report detailed peptide‐binding affinities between 438 HLA Class I and Class II proteins and complete proteomes of seven pandemic human viruses, including coronaviruses, influenza viruses and HIV‐1. We contrast these affinities with HLA allele frequencies across hundreds of human populations worldwide. Statistical modelling shows that peptide‐binding affinities classified into four distinct categories depend on the HLA locus but that the type of virus is only a weak predictor, except in the case of HIV‐1. Among the strong HLA binders (IC50 ≤ 50), we uncovered 16 alleles (the top ones being A*02:02, B*15:03 and DRB1*01:02) binding more than 1% of peptides derived from all viruses, 9 (top ones including HLA‐A*68:01, B*15:25, C*03:02 and DRB1*07:01) binding all viruses except HIV‐1, and 15 (top ones A*02:01 and C*14:02) only binding coronaviruses. The frequencies of strongest and weakest HLA peptide binders differ significantly among populations from different geographic regions. In particular, Indigenous peoples of America show both higher frequencies of strongest and lower frequencies of weakest HLA binders. As many HLA proteins are found to be strong binders of peptides derived from distinct viral families, and are hence promiscuous (or generalist), we discuss this result in relation to possible signatures of natural selection on HLA promiscuous alleles due to past pathogenic infections. Our findings are highly relevant for both evolutionary genetics and the development of vaccine therapies. However they should not lead to forget that individual resistance and vulnerability to diseases go beyond the sole HLA allelic affinity and depend on multiple, complex and often unknown biological, environmental and other variables.
Preparation and evaluation of caffeine bioadhesive emulgels for cosmetic applications based on formulation design using QbD tools

The aim of the present study was to evaluate the influence of the incorporation of caffeine as a model active ingredient on the quality attributes of a bioadhesive emulgel formulation previously optimized by Quality by Design (QbD) tools. Emulgels are emerging topical drug delivery systems for cosmetic or pharmaceutical uses, which combine the advantages of both emulsions and gels.
Incremental inputs improve the automated detection of implant loosening using machine-learning algorithms.

AIMS The aim of this study was to evaluate the ability of a machine-learning algorithm to diagnose prosthetic loosening from preoperative radiographs and to investigate the inputs that might improve its performance. METHODS A group of 697 patients underwent a first-time revision of a total hip (THA) or total knee arthroplasty (TKA) at our institution between 2012 and 2018. Preoperative anteroposterior (AP) and lateral radiographs, and historical and comorbidity information were collected from their electronic records. Each patient was defined as having loose or fixed components based on the operation notes. We trained a series of convolutional neural network (CNN) models to predict a diagnosis of loosening at the time of surgery from the preoperative radiographs. We then added historical data about the patients to the best performing model to create a final model and tested it on an independent dataset. RESULTS The convolutional neural network we built performed well when detecting loosening from radiographs alone. The first model built de novo with only the radiological image as input had an accuracy of 70%. The final model, which was built by fine-tuning a publicly available model named DenseNet, combining the AP and lateral radiographs, and incorporating information from the patient's history, had an accuracy, sensitivity, and specificity of 88.3%, 70.2%, and 95.6% on the independent test dataset. It performed better for cases of revision THA with an accuracy of 90.1%, than for cases of revision TKA with an accuracy of 85.8%. CONCLUSION This study showed that machine learning can detect prosthetic loosening from radiographs. Its accuracy is enhanced when using highly trained public algorithms, and when adding clinical data to the algorithm. While this algorithm may not be sufficient in its present state of development as a standalone metric of loosening, it is currently a useful augment for clinical decision making. Cite this article: Bone Joint J 2020;102-B(6 Supple A):101-106.
Postoperative T1 tilt is a risk factor for postoperative distal adding-on in Lenke type 1 adolescent idiopathic scoliosis

Abstract Retrospective comparable study. Postoperative loss of correction, which is referred to as the distal adding-on phenomenon, sometimes occurs during the postoperative course in Lenke type 1 adolescent idiopathic scoliosis (AIS). Selection of the lowest instrumented vertebra (LIV) has been reported to be one of the significant factors for preventing distal adding-on. However, proximal parameters, such as the Cobb angle of the proximal thoracic (PT) curve, radiographic shoulder height, and T1 tilt, were rarely described in previous reports. This study aimed to identify the risk factors for postoperative distal adding-on, including proximal radiographic parameters, in Lenke type 1 AIS. Preoperative and postoperative radiographs of 34 consecutive patients with Lenke type 1 curve who underwent selective thoracic fusion were analyzed. The patients were divided into an adding-on group and a no-adding-on group according to the presence of adding-on at a 2-year follow-up. The 2 groups were compared with regard to age at surgery, Lenke lumbar modifier, Risser grade, instrumentation type, and radiographic parameters. Distal adding-on was noted in 10 patients (29%). The adding-on group had significant variables including preoperative larger PT Cobb angle (P = .002), larger main thoracic (MT) flexibility (P = .006), smaller thoracolumbar (TL) Cobb angle (P = .012), larger LIV shift (P < .001), larger T1 tilt (P = .001), postoperative larger PT Cobb angle (P = .012), smaller MT Cobb angle (P = .016), smaller TL Cobb angle (P < .001), larger PT–MT mismatch (P < .001), larger LIV shift (P = .026), and larger T1 tilt (P = .006) when compared with the findings in the no-adding-on group. Postoperative T1 tilt was significantly correlated with PT–MT mismatch. Our findings suggest that not only the LIV but also proximal parameters, including T1 tilt and PT–MT mismatch, are associated with postoperative distal adding-on in Lenke type 1 AIS. Strategies to reduce postoperative T1 tilt and PT–MT mismatch are required to prevent distal adding-on.
Deep learning-based BCI for gait decoding from EEG with LSTM recurrent neural network

Objective. Mobile Brain/Body Imaging (MoBI) frameworks allowed the research community to find evidence of cortical involvement at walking initiation and during locomotion. However, the decoding of gait patterns from brain signals remains an open challenge. The aim of this work is to propose and validate a deep learning model to decode gait phases from Electroenchephalography (EEG). Approach. A Long-Short Term Memory (LSTM) deep neural network has been trained to deal with time-dependent information within brain signals during locomotion. The EEG signals have been preprocessed by means of Artifacts Subspace Reconstruction (ASR) and Reliable Independent Component Analysis (RELICA) to ensure that classification performance was not affected by movement-related artifacts. Main results. The network was evaluated on the dataset of 11 healthy subjects walking on a treadmill. The proposed decoding approach shows a robust reconstruction (AUC > 90%) of gait patterns (i.e. swing and stance states) of both legs together, or of each leg independently. Significance. Our results support for the first time the use of a memory-based deep learning classifier to decode walking activity from non-invasive brain recordings. We suggest that this classifier, exploited in real time, can be a more effective input for devices restoring locomotion in impaired people.
Effects of gut microbiome and environment on the development of eczema in Chinese infants

Abstract Background: Eczema is a relapsing and persistent inflammatory skin disease affecting about one-fifth of children worldwide. As in other developed countries, the prevalence of this chronic disease in Hong Kong is approximately 30%. Moreover, the number of local cases reported has been on a rising trend since 1995. Eczema frequently starts in early infancy. A total of 45% of all cases begin within the first six months of life, 60% during the first year and 85% before the age of 5. The pathophysiology of eczema is multi-factorial and is a complex inter-relationship between skin barrier, genetic predisposition, immunologic development, microbiome, environment, nutrition, and pharmacological and psychological factors. Objective: To characterize the longitudinal changes of gut microbial profile in early childhood and to examine the association between gut microbiome diversity, environmental factors and the development of eczema in early childhood. Method: We will conduct a longitudinal cohort study that follows 1250 Hong Kong Chinese infants for 2 years and assess the gut microbiome and other potential environmental factors in the aetiology of eczema. Parents will be asked to provide demographic data, their infant birth data, allergy condition, diet, environmental conditions as well as the data on maternal stress. Stool specimen will be collected for gut microbiome diversity analysis. We will examine newborn infants at enrollment, at 4 months, 1 year and 2 years after birth. Expected results: This study will evaluate the association between gut microbiome, environmental factors and the development of eczema in Chinese infants. Findings from this study may be used to develop a predictive path model to guide effective health promotion, disease prevention and management.
The Homogenization of Ethnic Differences in Singapore English? A Consonantal Production Study

Past research on Singapore English (SgE) has shown that there are specific segmental and prosodic patterns that are unique to the three major ethnic groups, Chinese, Malay, and Indian in Singapore. These features have been highlighted as the “stereotypical” ethnic markers of SgE speakers, assuming substrate influence from the speakers’ “ethnic” languages (Mandarin, Malay, and Tamil). However, recent research suggests that Singaporeans are becoming increasingly English dominant and has challenged the position of the ethnic languages as true “mother tongues” of Singaporeans. Hence, this study seeks to question if such “stereotypical” ethnic features exist, and if so, the extent to which a less dominant ethnic language would affect the phonology of speakers’ English. This study looks specifically at the production of consonants /f/, /θ/, /t/, /v/, and /w/ as salient segmental features in SgE. Participants’ phonetic behavior of /θ/, which was produced similarly across the three ethnic groups, disputed substrate influence. Tamil speakers were the most disparate, particularly with the /v/-/w/ contrast production. However, these deviations were often sporadic phonetic changes, which scarcely reflect robust speech patterns in the community. As a result, consonantal production in SgE is found to be largely independent of substrate influence and relatively uniform across the three ethnicities. The homogeneity observed in this study sheds light on bilinguals’ acquisition of sounds, and it also provides phonological evidence toward the understanding of the evolutionary process of postcolonial Englishes.
Heat stress reduces growth rate of red deer calf: Climate warming implications

Climate models agree in predicting scenarios of global warming. In endothermic species heat stress takes place when they are upper their thermal neutral zone. Any physiological or behavioural mechanism to mitigate heat stress is at the cost of diverting energy from other physiological functions, with negative repercussions for individual fitness. Tolerance to heat stress differs between species, age classes and sexes, those with the highest metabolic rates being the most sensitive to stressing thermal environments. This is especially important during the first months of life, when most growth takes place. Red deer (Cervus elaphus) is supposedly well adapted to a wide range of thermal environments, based on its worldwide distribution range, but little is known about the direct effect that heat stress may have on calf growth. We assessed the effect that heat stress, measured by heat stress indices and physical environment variables (air temperature, relative air humidity, wind speed and solar radiation), have on calf and mother body weights from calf´s birth to weaning. We used 9265 longitudinal weekly body weight records of calf and mother across 19 years in captive Iberian red deer. We hypothesised that (i) heat stress in hot environments has a negative effect on calf growth, especially in males, as they are more energetically demanding to produce than females; and that (ii) the body weight of the mother through lactation should be negatively affected by heat stress. Our results supported hypothesis (i) but not so clearly hypothesis (ii). By weaning (day 143) calves growing under low heat stress environment grew up to 1.2 kg heavier than those growing in high heat stress environment, and males were more affected by heat stress than females. The results have implications in animal welfare, geographical clines in body size and adaptation to climate change.
The Epidemiology of Burn Injuries in Saudi Arabia: A Systematic Review.

INTRODUCTION Burns are potentially catastrophic injuries that disproportionately affect non-Western countries. We summarize results on the epidemiology of burn injuries in Saudi Arabia of all eligible papers through 2019, specifically evaluating the age and gender of patients, the location and mechanism of injury, burn size and severity and outcomes. METHODS Between July 5th and July 10th, 2019, a comprehensive literature review was performed on MEDLINE, EMBASE, Google scholar, and the Cochrane library. For this search, "Saudi Arabia", coupled with the search terms "burn", "thermal burn", "flame burn", "chemical burn", "electrical burn", and "contact burn" to identify all abstracts potentially relating to the topic of interest. RESULTS 11 studies, encompassing 3308 patients, met eligibility criteria. Younger children (variably defined as ≤10-12), accounted for 52% of all burns. Males outnumbered females by an overall ratio of 1.42:1. 83% of burns occurred at homes. Scald injuries accounted for 62.4% of injuries, followed by flame-induced burns (28.7%), electrical burns (3.3%), and chemical burns (2.8%). Pertaining to burn extent and severity, 80-100% of the burns were limited to <40% total body surface area, while roughly 60% were second degree burns. Most patients remain in the hospital for 1-4 weeks. Overall mortality across studies including patients of all ages was 6.9%, while just 0.76% in the two studies restricted to pediatric patients. CONCLUSIONS Scald injuries involving young children comprise the lion's share of burn injuries in Saudi Arabia. Increased public awareness is necessary to reduce the incidence and severity of these potentially catastrophic injuries.
Maternal Cash Transfers Led To Increases In Facility Deliveries And Improved Quality Of Delivery Care In Nigeria.

Ninety-nine percent of global maternal deaths occur in low- and middle-income countries. The high mortality rates are often attributed to a large portion of births occurring outside of formal health care facilities. This has prompted the creation of programs to promote the use of formal delivery care. However, poor-quality care in health facilities in low- and middle-income countries is well documented. It is not clear that shifting births into health facilities in these settings necessarily leads to better-quality care. We present results from a randomized controlled trial in Nigeria that evaluated a conditional cash transfer intervention that paid pregnant women to deliver in a health facility. We found that the intervention led to a 41 percent increase in facility deliveries. We also found improvements in the quality of delivery care (as a result of more births taking place in formal health care settings) and in overall satisfaction with care. We found no evidence of a reduction in preventable complications that led to maternal deaths, though we found some improvements in self-reported health. Our results indicate that promoting facility deliveries can improve the quality of care received, even in settings where formal care quality is poor. However, modest quality improvements might not be sufficient to substantially improve health outcomes.
Mathematical Models of Species Interactions in Time and Space

Three widely used species interaction models, the Nicholson-Bailey and Hassell-Varley host-parasite models and the Lotka-Volterra predator-prey model, are extended into space as well as time. One type of equilibrium having the same number of individuals at all locations is shown to exist analytically for the "symmetric dispersal" case. Another kind of equilibrium having different numbers of individuals at different locations in two-dimensional space is demonstrated by simulation. Stability analysis suggests that space-time models having symmetric dispersal are no more stable near equilibrium than the simple time models upon which they are based. In many situations the space-time models are less stable than the simple time models. This result can be reconciled with the experimental literature if one assumes a "stochastic persistence" effect which predicts that expected extinction time will increase with the number of independent subpopulations.
SARS-CoV-2 Infection in Health Care Workers: Cross-sectional Analysis of an Otolaryngology Unit

The restart of routine in- and outpatient activity in the COVID-19 postepidemic peak needs to be carefully planned in light of specific patterns of viral diffusion. We evaluated SARS-CoV-2 serology in the entire personnel of a COVID-19-free otolaryngology department in a highly affected area. The aim was to determine the prevalence of SARS-CoV-2 positivity among staff to clarify the impact of different risk factors for infection. The entire staff of the otolaryngology unit was tested for SARS-CoV-2 serology. Symptomatic staff members were tested with nasal/pharyngeal swabs. All answered a survey focused on the number of in- and extrahospital positive contacts and type of activities in the unit. Five (9%) were positive for SARS-CoV-2 infection. The only variable associated with a higher risk of infection was the number of extrahospital contacts without personal protective equipment (P = .008). Our study shows that in non-COVID-19 departments, the use of adequate personal protective equipment leads to low rates of infection among health care workers. The prevalent risk of infection was related to extrahospital contact.
The Origin of the Legumes is a Complex Paleopolyploid Phylogenomic Tangle Closely Associated with the Cretaceous–Paleogene (K–Pg) Mass Extinction Event

Abstract The consequences of the Cretaceous–Paleogene (K–Pg) boundary (KPB) mass extinction for the evolution of plant diversity remain poorly understood, even though evolutionary turnover of plant lineages at the KPB is central to understanding assembly of the Cenozoic biota. The apparent concentration of whole genome duplication (WGD) events around the KPB may have played a role in survival and subsequent diversification of plant lineages. To gain new insights into the origins of Cenozoic biodiversity, we examine the origin and early evolution of the globally diverse legume family (Leguminosae or Fabaceae). Legumes are ecologically (co-)dominant across many vegetation types, and the fossil record suggests that they rose to such prominence after the KPB in parallel with several well-studied animal clades including Placentalia and Neoaves. Furthermore, multiple WGD events are hypothesized to have occurred early in legume evolution. Using a recently inferred phylogenomic framework, we investigate the placement of WGDs during early legume evolution using gene tree reconciliation methods, gene count data and phylogenetic supernetwork reconstruction. Using 20 fossil calibrations we estimate a revised timeline of legume evolution based on 36 nuclear genes selected as informative and evolving in an approximately clock-like fashion. To establish the timing of WGDs we also date duplication nodes in gene trees. Results suggest either a pan-legume WGD event on the stem lineage of the family, or an allopolyploid event involving (some of) the earliest lineages within the crown group, with additional nested WGDs subtending subfamilies Papilionoideae and Detarioideae. Gene tree reconciliation methods that do not account for allopolyploidy may be misleading in inferring an earlier WGD event at the time of divergence of the two parental lineages of the polyploid, suggesting that the allopolyploid scenario is more likely. We show that the crown age of the legumes dates to the Maastrichtian or early Paleocene and that, apart from the Detarioideae WGD, paleopolyploidy occurred close to the KPB. We conclude that the early evolution of the legumes followed a complex history, in which multiple auto- and/or allopolyploidy events coincided with rapid diversification and in association with the mass extinction event at the KPB, ultimately underpinning the evolutionary success of the Leguminosae in the Cenozoic. [Allopolyploidy; Cretaceous–Paleogene (K–Pg) boundary; Fabaceae, Leguminosae; paleopolyploidy; phylogenomics; whole genome duplication events]