Miracle-dz/UniFAR-FTUs huggingface dataset:
Variation in Diagnosis, Treatment, and Outcome of Esophageal Cancer in a Regionalized Care System in Ontario, Canada

Key Points Question Was there a uniform approach to diagnosis, staging, and treatment of patients with esophageal cancer after regionalization of thoracic surgery in Ontario, Canada? Findings In this cohort study of 10 364 patients, there was significant variation in use of staging tests as well as approach to treatment. Postoperative 30- and 90-day mortality was found to be reduced at high-volume centers. Meaning Despite regionalization of thoracic surgery, there remains significant variation between centers in the use of staging tests, treatments, and short-term mortality.
Hepatoprotective effects of Lactobacillus plantarum 299v supplemented via drinking water against aflatoxin-induced liver damage

ABSTRACT The aim of this study was to examine the impact of intake of a lactic acid bacterium, Lactobacillus plantarum 299v (Lp299v) on aflatoxin-induced hepatotoxicity in broilers. For this, broilers were intoxicated with dietary aflatoxins and simultaneously treated with live Lp299v in drinking water. One-day-old male broilers were divided into eight groups (n = 10/group) as follows. Aflatoxin groups fed basal diet contaminated with aflatoxins (200 or 2000 ppb). The probiotic groups received drinking water enriched with live (Lp299v) (108 CFU/ml). A group of birds was given a commercial mycotoxin binder (2.5 g/kg feed). Control groups received basal diet without probiotic or aflatoxin binder. The growth performance was calculated for the entire period (0–42 days), and blood and liver specimens were processed for histology and determination of liver damage markers. Results showed extensive damage including bile duct hyperplasia, hepatocellular ballooning, and necrosis in chickens fed aflatoxin alone. However, liver lesions were limited to lobular inflammation and pyknosis in broilers treated with aflatoxins along with Lp299v. The histology of the liver tissues from the birds on aflatoxin-free diet + probiotic appeared to be normal when compared to the respective controls. Histopathological indices in different experimental groups were corroborated with the liver damage markers namely, serum ALT, AST, LD, and γ-GT. It is concluded that the improvement in the growth performance and prevention of aflatoxin-related liver lesions could be mainly assigned to the probiotic therapy for the entire period of breeding, although the aflatoxin-binding ability of the Lp299v in inactivation of aflatoxins cannot be ruled out. RESEARCH HIGHLIGHTS Aflatoxin-related liver damage progression was inhibited by probiotics in broilers. Aflatoxin inactivation by probiotics can be assessed by liver histopathology. Growth performance in broilers was improved following the intake of probiotics.
Interocular Symmetry and Repeatability of Central Corneal Thickness and Corneal Endothelial Cell Morphology and Density in Healthy Eyes of Congolese

ABSTRACT Purpose To determine the limits of normal interocular symmetry and the repeatability of central corneal thickness (CCT) and endothelial cell morphology and density. Methods Two hundred and seventy-eight subjects (age: 10.9–80.7 years) with healthy eyes were studied. CCT as well as endothelial cell morphology and density were measured by non-contact specular microscopy. Three measurements were obtained per eye per participant. Upper and lower tolerance limits of normal interocular symmetry were defined as the 2.5th and 97.5th percentiles of the interocular differences in CCT, endothelial cell density (CECD), coefficient of variation (CoV), hexagonality, and cell size. Repeatability was determined using the intraclass coefficient correlation (ICC), the coefficient of variation (CV), and the test–retest variability standard deviation (TRTSD). Results The mean interocular differences were −1.05 ± 17.5 µm (p = .32) for CCT and 0.5 ± 90.8 cells/mm2 (p = .76) for CECD. The 2.5th and 97.5th percentiles of the interocular differences were −13.9 and 15.4 µm for CCT and −177.4 cells/mm2 to 182.0 cells/mm2 for CECD. Only interocular difference in CoV correlated weakly with age (r = −0.22, P < .001). ICCs were 0.93 (95% CI: 0.89–0.96, P < .001) for CCT and 0.95 (0.94–0.96, P < .001) for CECD. CV and TRTSD were 1.2% ± 5.3% and 4.4 ± 3.4 µm for CCT and 2.4% ± 3.9% and 17.7 ± 7.7 cells/mm2 for CECD, respectively. Conclusions CCT and CECD showed good repeatability and interocular symmetry in normal Congolese subjects. Absolute interocular differences in CCT and CECD exceeding 15.5 µm and 182 cells/mm2, respectively, should be considered suspicious and investigated. When comparing two intrasession measurements from the same eye, a difference of approximately 4.5 µm in CCT and 18 cells/mm2 or greater may be considered statistically significant.
Coinfection between SARS‐CoV‐2 and vector‐borne diseases in Luanda, Angola

Co‐epidemics happening simultaneously can generate a burden on healthcare systems. The co‐occurrence of SARS‐CoV‐2 with vector‐borne diseases (VBD), such as malaria and dengue in resource‐limited settings represents an additional challenge to the healthcare systems. Herein, we assessed the coinfection rate between SARS‐CoV‐2 and VBD to highlight the need to carry out an accurate diagnosis and promote timely measures for these infections in Luanda, the capital city of Angola. This was a cross‐sectional study conducted with 105 subjects tested for the SARS‐CoV‐2 and VBD with a rapid detection test in April 2021. The participants tested positive for SARS‐CoV‐2 (3.80%), malaria (13.3%), and dengue (27.6%). Low odds related to testing positivity to SARS‐CoV‐2 or VBD were observed in participants above or equal to 40 years (odds ratio [OR]: 0.60, p = 0.536), while higher odds were observed in male (OR: 1.44, p = 0.392) and urbanized areas (OR: 3.78, p = 0.223). The overall co‐infection rate between SARS‐CoV‐2 and VBD was 11.4%. Our findings showed a coinfection between SARS‐CoV‐2 with malaria and dengue, which could indicate the need to integrate the screening for VBD in the SARS‐CoV‐2 testing algorithm and the adjustment of treatment protocols. Further studies are warranted to better elucidate the relationship between COVID‐19 and VBD in Angola.
Evaluation of the food environment of public hospitals in a Brazilian metropolis

Abstract Objective: To characterise the food environment of public hospitals in a Brazilian metropolis. Design: A cross-sectional study involving the audit of mini-kitchens, non-commercial food services, commercial food services and vending machines within hospitals and interviews with workers and managers. Environmental dimensions assessed included: availability, accessibility, affordability, convenience, nutrition information, promotion and advertising, infrastructure for food and ambience, in addition to decisions-level aspects. Setting: Rio de Janeiro, Brazil. Participants: 24 public hospitals in the municipal health network. Results: Of the hospitals assessed, 92·0 % had a non-commercial food service, 87·5 % had mini-kitchens (facilities to consume food taken from home), 37·5 % had commercial food services and 25·0 % had vending machines. Mini-kitchens were available in most but not all hospitals, a key facility given that few commercial or non-commercial food services were open 24 h a day. The food availability in the hospitals surveyed did not promote healthy eating. A wide variety of ultra-processed foods and drinks was found and advertising promoting their consumption, even in non-commercial food services with menus planned by nutritionists. Water filters/fountains were present in around 50 % of mini-kitchens and non-commercial food services but were unavailable in commercial food services. According to workers interviewed, the temperature of the environment was the worst-rated aspect of mini-kitchens, non-commercial food services and commercial food services. Nutrition service managers reported little involvement in producing biddings and proposals for hiring outside companies to run non-commercial food services or commercial food services. Conclusion: The food environment of the hospitals studied did not promote healthy eating habits.
Genomic Stability and Genetic Defense Systems in Dolosigranulum pigrum, a Candidate Beneficial Bacterium from the Human Microbiome

Dolosigranulum pigrum is a candidate beneficial bacterium with potential for future therapeutic use. This is based on its positive associations with characteristics of health in multiple studies of human nasal microbiota across the span of human life. ABSTRACT Dolosigranulum pigrum is positively associated with indicators of health in multiple epidemiological studies of human nasal microbiota. Knowledge of the basic biology of D. pigrum is a prerequisite for evaluating its potential for future therapeutic use; however, such data are very limited. To gain insight into D. pigrum’s chromosomal structure, pangenome, and genomic stability, we compared the genomes of 28 D. pigrum strains that were collected across 20 years. Phylogenomic analysis showed closely related strains circulating over this period and closure of 19 genomes revealed highly conserved chromosomal synteny. Gene clusters involved in the mobilome and in defense against mobile genetic elements (MGEs) were enriched in the accessory genome versus the core genome. A systematic analysis for MGEs identified the first candidate D. pigrum prophage and insertion sequence. A systematic analysis for genetic elements that limit the spread of MGEs, including restriction modification (RM), CRISPR-Cas, and deity-named defense systems, revealed strain-level diversity in host defense systems that localized to specific genomic sites, including one RM system hot spot. Analysis of CRISPR spacers pointed to a wealth of MGEs against which D. pigrum defends itself. These results reveal a role for horizontal gene transfer and mobile genetic elements in strain diversification while highlighting that in D. pigrum this occurs within the context of a highly stable chromosomal organization protected by a variety of defense mechanisms. IMPORTANCE Dolosigranulum pigrum is a candidate beneficial bacterium with potential for future therapeutic use. This is based on its positive associations with characteristics of health in multiple studies of human nasal microbiota across the span of human life. For example, high levels of D. pigrum nasal colonization in adults predicts the absence of Staphylococcus aureus nasal colonization. Also, D. pigrum nasal colonization in young children is associated with healthy control groups in studies of middle ear infections. Our analysis of 28 genomes revealed a remarkable stability of D. pigrum strains colonizing people in the United States across a 20-year span. We subsequently identified factors that can influence this stability, including genomic stability, phage predators, the role of MGEs in strain-level variation, and defenses against MGEs. Finally, these D. pigrum strains also lacked predicted virulence factors. Overall, these findings add additional support to the potential for D. pigrum as a therapeutic bacterium.
Potential Use of Senolytics for Pharmacological Targeting of Precancerous Lesions

Senescence is a cell state that contributes to several homeostatic and pathologic processes. In addition to being induced in somatic cells in response to replicative exhaustion (replicative senescence) as part of organismal aging, senescence can also be triggered prematurely by oncogene hyperactivation or tumor suppressor dysfunction [oncogene-induced senescence (OIS)]. Consequently, senescent cells comprise a major component of precancerous lesions of skin, oral mucosa, nasopharynx, prostate, gut, and lung. Unfortunately, invasive (or minimally invasive) interventions are currently the only available approach employed to eradicate premalignant lesions that carry the potential for cancer progression. Senolytics are a newly emerging drug class capable of selectively eliminating senescent cells. Although senolytics have been successfully demonstrated to mitigate a myriad of aging-related pathologies and to cull senescent cancer cells, there is a paucity of evidence for the potential use of senolytics as a novel approach to eliminate oncogene-induced senescent cells. This Emerging Concepts commentary will 1) summarize evidence in established models of OIS including B-Raf–induced nevi, transgenic lung cancer, and pancreatic adenocarcinoma models, as well as evidence from clinical precancerous lesions; 2) suggest that OIS is targetable; and 3) propose the utilization of senolytic agents as a revolutionary means to interfere with the ability of senescent premalignant cells to progress to cancer in vitro and in vivo. If proven to be effective, senolytics will represent an emerging tool to pharmacologically treat precancerous lesions. SIGNIFICANCE STATEMENT The treatment of premalignant lesions is largely based on the utilization of invasive (or minimally invasive) measures. Oncogene-induced senescence (OIS) is one form of senescence that occurs in response to oncogene overexpression in somatic cells and is present in precancerous lesions. Although the contribution of OIS to disease progression is undetermined, recent evidence suggests that senescent cells are permissive for malignant transformation. Accordingly, the pharmacological targeting of oncogene-induced senescent cells could potentially provide a novel, less invasive, means for the treatment of premalignant disease.
A chromosome-scale genome assembly and karyotype of the ctenophore Hormiphora californensis

Abstract Here, we present a karyotype, a chromosome-scale genome assembly, and a genome annotation from the ctenophore Hormiphora californensis (Ctenophora: Cydippida: Pleurobrachiidae). The assembly spans 110 Mb in 44 scaffolds and 99.47% of the bases are contained in 13 scaffolds. Chromosome micrographs and Hi-C heatmaps support a karyotype of 13 diploid chromosomes. Hi-C data reveal three large heterozygous inversions on chromosome 1, and one heterozygous inversion shares the same gene order found in the genome of the ctenophore Pleurobrachia bachei. We find evidence that H. californensis and P. bachei share thirteen homologous chromosomes, and the same karyotype of 1n = 13. The manually curated PacBio Iso-Seq-based genome annotation reveals complex gene structures, including nested genes and trans-spliced leader sequences. This chromosome-scale assembly is a useful resource for ctenophore biology and will aid future studies of metazoan evolution and phylogenetics.
Low seropositivity and suboptimal neutralisation rates in patients fully vaccinated against COVID‐19 with B‐cell malignancies

Patients with haematological malignancies are at increased risk of severe disease and death from COVID-19 and are less likely to mount humoral immune responses to COVID-19 vaccination, with the B cell malignancies a particularly high-risk group. Our COV-VACC study is evaluating the immune response to COVID-19 vaccination in patients with B cell malignancies. Eligible patients were either receiving active treatment or had received treatment within the last 24 months. Patients were vaccinated with either the BNT162b2 (Pfizer-BioNTech) (n=41) or ChAdOx1 nCoV-19 (Oxford-AstraZeneca) (n=14) vaccines. The median age of participants was 60 years (range: 27-82) and 50% were receiving systemic anti-cancer therapy (SACT) at the time of vaccination. This interim analysis from the first 55 participants describes anti-S seropositivity rates, neutralising antibody activity and association with peripheral lymphocyte subsets. After the first vaccine dose, 36% overall had detectable anti-S antibodies rising to 42% after the second dose. Sera from seropositive patients was assessed for neutralisation activity in vitro. Of the seropositive patients after first dose (n=17), only 41% were able to neutralise SARS-CoV-2 pseudotyped virus with a 50% inhibitory dilution factor (ID50) of >1:50. After two doses (n=21) 57% of the seropositive patients had detectable neutralisation activity (median ID50 of 1:469, range 1:70 - 1:3056). Total blood lymphocyte, CD19, CD4 and CD56 counts were significantly associated with seropositivity. Patients vaccinated more than 6 months after completing therapy were significantly more likely to develop antibodies than those within 6 months of treatment or on active treatment; OR: 5.93 (1.29 - 27.28). Our data has important implications for patients with B cell malignancies as we demonstrate a disconnect between anti-S seropositivity and virus neutralisation in vitro following vaccination against COVID-19. Urgent consideration should be given to revaccinating patients with B-cell malignancies after completion of anti-cancer treatment as large numbers currently remain at high risk of infection with the increasing transmission of SARS-CoV-2 in many countries.
Deep learning methods for automatic segmentation of lower leg muscles and bones from MRI scans of children with and without cerebral palsy

Cerebral palsy is a neurological condition that is known to affect muscle growth. Detailed investigations of muscle growth require segmentation of muscles from MRI scans, which is typically done manually. In this study, we evaluated the performance of 2D, 3D, and hybrid deep learning models for automatic segmentation of 11 lower leg muscles and two bones from MRI scans of children with and without cerebral palsy. All six models were trained and evaluated on manually segmented T1‐weighted MRI scans of the lower legs of 20 children, six of whom had cerebral palsy. The segmentation results were assessed using the median Dice similarity coefficient (DSC), average symmetric surface distance (ASSD), and volume error (VError) of all 13 labels of every scan. The best performance was achieved by H‐DenseUNet, a hybrid model (DSC 0.90, ASSD 0.5 mm, and VError 2.6 cm3). The performance was equivalent to the inter‐rater performance of manual segmentation (DSC 0.89, ASSD 0.6 mm, and VError 3.3 cm3). Models trained with the Dice loss function outperformed models trained with the cross‐entropy loss function. Near‐optimal performance could be attained using only 11 scans for training. Segmentation performance was similar for scans of typically developing children (DSC 0.90, ASSD 0.5 mm, and VError 2.8 cm3) and children with cerebral palsy (DSC 0.85, ASSD 0.6 mm, and VError 2.4 cm3). These findings demonstrate the feasibility of fully automatic segmentation of individual muscles and bones from MRI scans of children with and without cerebral palsy.
Canada's System of Liability Coverage in the Event of Medical Harm: Is It Time for No-Fault Reform?

Many Canadians believe that physicians have malpractice insurance via the Canadian Medical Protective Association (CMPA). However, the CMPA is not an insurance company; it is a defence fund for physicians and has no obligation to compensate all claimants. CMPA expenses have increased nearly tenfold in 30 years and although public budgets support the majority of CMPA fees, less than 0.3% of injured patients receive compensation. A reform of the system is vital. Several developed countries have adopted a “no-fault” system to provide more equity and transparency and to ensure that the majority of funds go directly to injured patients rather than toward the payment of legal and administrative fees.
Jump performance and mechanics after a regular training bout in elite volleyball players.

BACKGROUND Volleyball is a complex intermittent sport characterized by short explosive technical movements, many of which involve vertical jumping. The assessment of mechanical jumping variables in relation to both injury prevention and performance enhancement through the use of wearable technologies is becoming a new training tool among professional volleyball players. METHODS The present study aimed to assess the vertical jumping mechanics before and after a controlled load (volume and intensity) of a routine volleyball training session among male professional players. Twelve male elite professional volleyball players (23.7 ± 4.9 years, 198.1 ± 6.2 cm, 92.2 ± 10.3 kg) of national and international level belonging to the same Brazilian first league team were recruited. Biomechanical analysis of vertical unilateral countermovement jump (CMJ) and bilateral CMJ tests were performed before and after a routine training session of these players at their usual training court. An inertial orientation sensor placed at the third lumbar vertebra was employed for biomechanical data collection. RESULTS In relation to the unilateral CMJ, a 10% decrease (p = 0.02) in the vertical ground reaction force after training compared to pre-training values was observed. However, no significant differences were observed in the remaining outcomes. Regarding the bilateral CMJ, no significant differences were observed in all assessed outcomes. CONCLUSIONS Our findings showed no evidence of fatigue after a controlled regular in season volleyball training session in professional players. In addition, this volleyball training session induced a significant reduction in the vertical ground reaction force during unilateral CMJ in volleyball players.
Coffee consumption and gastric cancer: a pooled analysis from the Stomach cancer Pooling Project consortium

Objective This study aimed to evaluate and quantify the relationship between coffee and gastric cancer using a uniquely large dataset from an international consortium of observational studies on gastric cancer, including data from 18 studies, for a total of 8198 cases and 21 419 controls. Methods A two-stage approach was used to obtain the pooled odds ratios (ORs) and the corresponding 95% confidence intervals (CIs) for coffee drinkers versus never or rare drinkers. A one-stage logistic mixed-effects model with a random intercept for each study was used to estimate the dose–response relationship. Estimates were adjusted for sex, age and the main recognized risk factors for gastric cancer. Results Compared to never or rare coffee drinkers, the estimated pooled OR for coffee drinkers was 1.03 (95% CI, 0.94–1.13). When the amount of coffee intake was considered, the pooled ORs were 0.91 (95% CI, 0.81–1.03) for drinkers of 1–2 cups per day, 0.95 (95% CI, 0.82–1.10) for 3–4 cups, and 0.95 (95% CI, 0.79–1.15) for five or more cups. An OR of 1.20 (95% CI, 0.91–1.58) was found for heavy coffee drinkers (seven or more cups of caffeinated coffee per day). A positive association emerged for high coffee intake (five or more cups per day) for gastric cardia cancer only. Conclusions These findings better quantify the previously available evidence of the absence of a relevant association between coffee consumption and gastric cancer.