Miracle-dz/UniFAR-FTUs huggingface dataset:
Totally extraperitoneal inguinal hernioplasty with titanium-coated lightweight polypropylene mesh

Background: This prospective study of a new titaniumcoated low-weight polypropylene (PP) mesh (16 g PP/ m 2 ) was designed to investigate the clinical efficacy and safety of totally extraperitoneal endoscopic hernioplasty (TEP). Methods: In this study, 400 patients (average age, 53.5 years; range, 19 – 80 years) witha total of 588 inguinal hernias underwent surgery with the TEP technique between September 2002 and October 2003. Of these patients, 12.4% had experienced recurrent hernias after open suture herniotomy. In 92% of the cases (368 patients with 540 hernias), a lightweight (16 g PP/m 2 ) titanium-coated polypropylene meshwas implanted without fixation, and in 8% (32 patients with48 hernias) an identical medium-weight (35 g PP/m 2 ) meshwas implanted. The first follow-up examination was scheduled for postoperative week 6. Results: In the lightweight mesh group, the mean group, operating time per patient was 61 min, corresponding to a calculated time per hernia of 41 min. Two intraoperative major complications occurred: an injury to the cecum and an injury to the bladder. In 12 cases (2%), bleeding from epigastric, testicular, or pubic bone vessels was observed. No injuries to pelvic vessels were seen. One patient was underwent an endoscopic revision to deal withan anticoagulation-related bleed. Th e mortality rate was 0%. In 12 patients, postoperative hematomas developed. One preperitoneal lipoma had to be extirpated. No infections of the mesh occurred.The median follow-up period for 371 patients (92.3%) was 7.2 weeks (range, 4–14 weeks). These 343 patients (with 504 hernias) had been provided with a lightweight titanium-coated polypropylene mesh(16 g PP/m 2 ) (followup rate, 93.2%). Of these patients, 3.5% reported persistent ingunial pain, 1.7% described a sensation of rigidity in the region of the groin, and 3.2% reported dysesthesia. The early recurrence rate was 0.2%. Conclusions: The TEP procedure can be performed safely and effectively withth e appreciably material-reduced and titanium-coated polypropylene meshwithout the need for fixation of the implant. The low early recurrence rate of 0.2% is evidence that the posterior wall of the inguinal canal is adequately augmented. The question whether the material reduction and the titanium coating of the mesh may bring about a reduction in postoperative chronic pain and the sensation of rigidity in the inguinal area via an improvement in biocompatibility must await the results of the scheduled follow-up examination 1 year after the surgical procedure.
Real-time long-term correlation tracking by single-shot multibox detection

Abstract. Long-term robust tracking remains a challenging problem in visual object tracking. Based on the popular tracking-by-detection framework, we propose an approach named real-time long-term correlation tracking by single-shot multibox detection (RLCT-SSD), in which tracking and detection work in parallel and cooperate together. Our algorithm consists of two parts: a tracking module is expected to track in real time and accurately, whereas a detection module is responsible for verifying the tracking results at intervals, and redetecting if necessary. The detector updates the tracking module when the tracking result is unreliable. We introduce a motion model on the basis of fast discriminative scale space tracker to design our tracking module. The detection module is based on the single-shot multibox detector algorithm. To further reduce the computational cost, we use the ShuffleNet as our base network of detection. The experimental results on OTB2013 and OTB2015 demonstrate that our RLCT-SSD performs favorably against most state-of-the-art trackers and achieves long-term accurate tracking running in real time.
Association between marijuana exposure and pulmonary function over 20 years.

CONTEXT Marijuana smoke contains many of the same constituents as tobacco smoke, but whether it has similar adverse effects on pulmonary function is unclear. OBJECTIVE To analyze associations between marijuana (both current and lifetime exposure) and pulmonary function. DESIGN, SETTING, AND PARTICIPANTS The Coronary Artery Risk Development in Young Adults (CARDIA) study, a longitudinal study collecting repeated measurements of pulmonary function and smoking over 20 years (March 26, 1985-August 19, 2006) in a cohort of 5115 men and women in 4 US cities. Mixed linear modeling was used to account for individual age-based trajectories of pulmonary function and other covariates including tobacco use, which was analyzed in parallel as a positive control. Lifetime exposure to marijuana joints was expressed in joint-years, with 1 joint-year of exposure equivalent to smoking 365 joints or filled pipe bowls. MAIN OUTCOME MEASURES Forced expiratory volume in the first second of expiration (FEV(1)) and forced vital capacity (FVC). RESULTS Marijuana exposure was nearly as common as tobacco exposure but was mostly light (median, 2-3 episodes per month). Tobacco exposure, both current and lifetime, was linearly associated with lower FEV(1) and FVC. In contrast, the association between marijuana exposure and pulmonary function was nonlinear (P < .001): at low levels of exposure, FEV(1) increased by 13 mL/joint-year (95% CI, 6.4 to 20; P < .001) and FVC by 20 mL/joint-year (95% CI, 12 to 27; P < .001), but at higher levels of exposure, these associations leveled or even reversed. The slope for FEV(1) was -2.2 mL/joint-year (95% CI, -4.6 to 0.3; P = .08) at more than 10 joint-years and -3.2 mL per marijuana smoking episode/mo (95% CI, -5.8 to -0.6; P = .02) at more than 20 episodes/mo. With very heavy marijuana use, the net association with FEV(1) was not significantly different from baseline, and the net association with FVC remained significantly greater than baseline (eg, at 20 joint-years, 76 mL [95% CI, 34 to 117]; P < .001). CONCLUSION Occasional and low cumulative marijuana use was not associated with adverse effects on pulmonary function.
Preseason preparation training and endothelial function in elite professional soccer players

Aim: To examine whether a high volume of soccer-specific training can lead to endothelial activation and/or dysfunction in professional soccer players due to exercise-induced oxidative stress. Methods: Twenty-three (15 nonsmokers and eight smokers) healthy, elite male professional soccer players (mean age: 25.2 ± 4.3 years, BMI: 23.1 ± 1.3 kg/m 2 , fat: 7.8% ± 2.6%) were selected for this study. All participants had a full clinical and laboratory evaluation. von Willebrand factor antigen (vWf Ag) plasma levels were measured on two different occasions: 1 day before the beginning of the preseason preparation period and after 7 weeks of strenuous exercise. Results: Mean vWf Ag plasma levels were significantly decreased from 95.1% ± 26% to 88.3% ± 27.2% at the end of the experimental period ( P = 0.018), suggesting a potential beneficial effect on the endothelium of these athletes. Further analysis showed that age greater than 29 years with an age range from 29 to 34 years can not impair this effect ( P  0.05). Conclusion: Strenuous exercise did not lead to endothelium activation or dysfunction in well-trained elite soccer players. On the contrary, it seemed to produce a beneficial effect on the endothelium of these
NF-kB c-Rel Dictates the Inflammatory Threshold by Acting as a Transcriptional Repressor

Unresolved inflammation is an underlying reason for several immune and inflammatory diseases as well as cancer. Both initiation and resolution of inflammatory response rely largely on the genes induced by NF-kB/Rel family of transcription factors. Previous studies have categorized NF-kB family proteins as transcriptional activators (homo or hetero dimers containing RelA, RelB or c-Rel) and transcriptional inhibitors (homodimers of p50 or p52). Here, we report the function of the subunit c-Rel with a transactivation domain, as a transcriptional repressor of selected proinflammatory genes. Genetic deletion of c-Rel enhances the expression of a subset of proinflammatory genes and also potentiates the expression of TNF-induced RelA-dependent mediators of inflammation. Interestingly, v-Rel, the viral homologue of c-Rel, also possesses this repressive function, indicating that the repressive function of c-Rel is evolutionarily conserved. We also found that c-Rel’s ability to repress transcription depends on it competency to bind consensus NF-kB-binding sites in the DNA. Our findings reveal a novel role of c-Rel as a transcriptional repressor in the maintenance of inflammatory homeostasis.
Draft Genome Sequence of Citrobacter freundii Strain A47, Resistant to the Mycotoxin Deoxynivalenol

ABSTRACT Here, we present the draft genome sequence of Citrobacter freundii strain A47 with a length of 4,878,242 bp, which contains 4,357 putative protein coding genes, including 270 unique genes. This work is expected to assist in obtaining novel gene(s) that code for deoxynivalenol (DON) de-epoxidation enzyme(s).
Edinburgh Research Explorer Impact of Zostavax Vaccination on T-Cell Accumulation and Cutaneous Gene Expression in the Skin of Older Humans After Varicella Zoster Virus Antigen-Specific Challenge

Background. The live attenuated vaccine Zostavax was developed to prevent varicella zoster virus (VZV) reactivation that causes herpes zoster (shingles) in older humans. However, the impact of vaccination on the cutaneous response to VZV is not known. Methods. We investigated the response to intradermal VZV antigen challenge before and after Zostavax vaccination in participants >70 years of age by immunohistological and transcriptomic analyses of skin biopsy specimens collected from the challenge site. Results. Vaccination increased the proportion of VZV-specific CD4 + T cells in the blood and promoted the accumulation of both CD4 + and CD8 + T cells in the skin after VZV antigen challenge. However, Zostavax did not alter the proportion of resident memory T cells (CD4 + and CD8 + ) or CD4 + Foxp3 + regulatory T cells in unchallenged skin. After vaccination, there was increased cutaneous T-cell proliferation at the challenge site and also increased recruitment of T cells from the blood, as indicated by an elevated T-cell migratory gene signature. CD8 + T-cell–associated functional genes were also highly induced in the skin after vaccination. Conclusion. Zostavax vaccination does not alter the abundance of cutaneous resident memory T cells but instead increases the recruitment of VZV-specific T cells from the blood and enhances T-cell activation, particularly cells of the CD8 + subset, in the skin after VZV antigen challenge. the impact of vaccination on cutaneous immunity to VZV in older individuals. A cohort of volunteers aged >70 years was recruited, and their responses to VZV antigen challenge were assessed before and after vaccination. We show that, although vaccination increased the proportion of VZV-specific CD4 + T cells in the blood, the proportion of these cells within the skin (ie, skin-resident memory T cells [T RM ]) was not affected. Vaccination also enhanced the skin response to VZV antigen challenge and was associated with increased T-cell accumulation and proliferation at the site of antigen challenge. After vaccination, there was a marked upregulation of genes associated with migration and activation of T cells at the site of antigen challenge. Additionally, there was a pronounced expression of a CD8 + T-cell–related gene signature in the skin after VZV antigen challenge in vaccinated individuals. Taken together, these data suggest that the improved VZV-specific cutaneous immunity after Zostavax vaccination is due to the recruitment of VZV-specific T cells from the blood that are then activated and induced to proliferate in the skin.
Characteristics and Risk Factors for Mortality by COVID-19 Pandemic Waves in Fulton County, Georgia: A Cohort Study March 2020–February 2021

Background We examined differences in mortality among COVID-19 cases in the first, second and third waves of the COVID-19 pandemic. Methods A retrospective cohort study of COVID-19 cases in Fulton County, Georgia, USA, reported to a public health surveillance from March 2020 through February 2021. We estimated case fatality rates (CFR) by wave and used Cox proportional hazards random effects models in each wave, with random effects at individual and long-term-care-facility level, to determine risk factors associated with rates of mortality. Results Of 75,289 confirmed cases, 4,490 (6%) were diagnosed in wave one (CFR 31 deaths/100,000 person days [pd]), 24,293 (32%) in wave two (CFR 7 deaths/100,000 pd), and 46,506 (62%) in wave three (CFR 9 deaths/100,000 pd). Compared to females, males were more likely to die in each wave: Wave one (adjusted hazard ratio [aHR] 1.5, 95% confidence interval [CI] 1.2–1.8), wave two (aHR 1.5, 95% CI 1.2–1.8), and wave three (aHR 1.7, 95% CI 1.5–2.0). Compared to non-Hispanic Whites, non-Hispanic Blacks were more likely to die in each wave: Wave one (aHR 1.4, 95% CI 1.1–1.8), wave two (aHR 1.5, 95% CI 1.2–1.9), and wave three (aHR 1.7, 95% CI 1.4–2.0). Cases with any disability, chronic renal disease, and cardiovascular disease were more likely to die in each wave compared to those without these comorbidities. Conclusions Our study found gender and racial/ethnic disparities in COVID-19 mortality, and certain comorbidities associated with COVID-19 mortality. These factors have persisted throughout the COVID-19 pandemic waves, despite improvements in diagnosis and treatment.
Discovery of methylation loci and analyses of differential methylation from replicated high-throughput sequencing data

Motivation: Cytosine methylation is widespread in most eukaryotic genomes and is known to play a substantial role in various regulatory pathways. Unmethylated cytosines may be converted to uracil through the addition of sodium bisulphite, allowing genome-wide quantification of cytosine methylation via high-throughput sequencing. The data thus acquired allows the discovery of methylation ‘loci’, contiguous regions of methylation consistently methylated across biological replicates. The mapping of these loci allows for associations with other genomic factors to be identified, and for analyses of differential methylation to take place. Results: The segmentSeq R package has been extended to identify methylation loci from high-throughput sequencing data from multiple conditions. A statistical model is then developed that accounts for biological replication and variable rates of non-conversion of cytosines in each sample to compute posterior likelihoods of methylation at each locus within an empirical Bayesian framework. The same model is used as a basis for analysis of differential methylation between multiple experimental conditions with the baySeq R package. These analyses are demonstrated on a set of data derived from Dicer-like mutants in Arabidopsis to reveal complex interactions between the different Dicer-like mutants and their methylation pathways. Availability: The segmentSeq and baySeq packages are available on the Bioconductor (http://www.bioconductor.org). Contact: tjh48@cam.ac. uk
Assessment of Physico-chemical and Microbiological qualities of Abattoir Wastewater in Sokoto, Nigeria.

: Wastewater samples were collected from three different points in Sokoto (Nigeria) abattoir and the physico-chemical and the microbiological qualities were determined. The pH of the wastewater was near neutral in the range of 7.22-7.47. The physico-chemical parameters were biochemical oxygen demand (BOD) (31.4mg/l), dissolved oxygen (DO) (85.0mg/l), and chemical oxygen demand (COD) (3.20mg/l). The microorganisms identified, mostly pathogenic, included Escherichia coli, Salmonella typhi, Neisseria lactamica, Klebsiella pneumoniae, Serratia marcescens, Branhamella catarrhalis, and Shigella sp, Aspergillus clavatus, Aspergillus flavus, Aspergillus niger, Curvularia sp , Trichophyton rubrum, and Penicillium echinulatum . The potential public health implications associated with discharging untreated abattoir wastewater into the environment and thus, the need for adequate treatment to ensure decontamination as well as providing wastewater treatment facility in the abattoir are discussed.
Antimicrobial susceptibility of Escherichia coli isolated from diabetic patients in Mogadishu, Somalia

Background Urinary tract infections (UTIs) are a major concern for diabetic patients due to the impact of diabetes on the urinary tract and immune system. Escherichia coli is the most common pathogen causing UTIs in diabetic patients and is known for its resistance. This study aimed to assess the antimicrobial susceptibility of Escherichia coli strains isolated from diabetic patients in Mogadishu, Somalia. Methods This descriptive cross-sectional study was conducted at Ummah Hospital in Mogadishu, Somalia, from November 2021 to April 2022. Clean catch mid-stream urine specimens were collected from each participant and uropathogens were identified using standard techniques. The samples were cultured on CLED agar and antibiotic susceptibility patterns were determined using the Kirby-Bauer disk diffusion method. Data analysis was performed using SPSS version 20. Results The overall prevalence of uropathogens among diabetic patients was 236/350 (67.5%) with Escherichia coli being the most common organism. According to multivariate logistic regression, the results showed that Female diabetic patients had a significantly higher likelihood of developing UTIs compared to males (AOR = 2.5, 95% CI: 1.357–4.522, p = 0.003). The duration of diabetes, history of previous UTIs, and previous antibiotic use were also significantly associated with UTIs. All isolates were found to be resistant to Cefotaxime (100%). In addition, high resistance rates were observed with ofloxacin (91%), ciprofloxacin (77.8%), amikacin (60.9%), ceftriaxone (58.3%), and cefepime (51.8%). The most sensitive antibiotics were colistin and imipenem (99.6 and 88.6%, respectively), followed by gentamycin (70%). Conclusion This study found a high prevalence of uropathogens and increased multi-drug resistance. Continuous surveillance is needed to monitor uropathogen prevalence and resistance rates, guiding treatment recommendations, rational prescription programs, and policy decisions.
The Open Access Israeli Journal of Aquaculture – Bamidgeh

The functional diversity (FD) of the microbial communities found in pond waters was examined with the BIOLOG method for five different aquaculture groups: (1) monoculture of crab Portunus trituberculatus, (C); (2) polyculture of crab and white shrimp Litopenaeus vannamei, (CS); (3) polyculture of crab and short-necked clam Ruditapes philippinarum, (CB); (4) polyculture of crab, white shrimp, and short-necked clam (CSB); (5) polyculture of white shrimp and short-necked clam (SB). The results showed that the average well color development (AWCD) value which represents microbial metabolic activity was highest in the CSB group (P < 0.05). The McIntosh index, Shannon index, and Shannon evenness index, in the CSB group were significantly higher compared to the others (P < 0.05). These data indicated that both the microbial metabolic activity and functional diversity of the water microbial community in the CSB group were significantly higher than in the other communities (P < 0.05). The principal component analysis (PCA) results indicated that the carbon sources and the metabolic activity of the water microbial communities in the CSB group were different from the others. The redundancy analysis (RDA) results revealed that the FD of the microbial communities in all five groups was closely related to environmental factors. The critical environmental variables influencing the functional diversity of the water microbial communities were TOC, NO2 -N and NH4 -N in July, and TP, NH4 -N and PO4 P in September. This study may provide a novel strategy for optimizing polyculture structure in swimming crab ponds. The IJA appears exclusively as a peer-reviewed on-line open-access journal at http://www.siamb. org.il/. To read papers free of charge, please register online at registration form. Sale of IJA papers is strictly forbidden.
Development of molecular markers for determining continental origin of wood from white oaks (Quercus L. sect. Quercus)

25 To detect and avoid illegal logging of valuable tree species, identification methods for the 26 origin of timber are necessary. We used next-generation sequencing to identify chloroplast 27 genome regions that differentiate the origin of white oaks from the three continents; Asia, 28 Europe, and North America. By using the chloroplast genome of Asian Q. mongolica as a 29 reference, we identified 861 variant sites (672 single nucleotide polymorphisms (SNPs); 189 30 insertion/deletion (indel) polymorphism) from representative species of three continents (Q. 31 mongolica from Asia; Q. petraea and Q. robur from Europe; Q. alba from North America), 32 and we identified additional chloroplast polymorphisms in pools of 20 individuals each from 33 Q. mongolica (789 variant sites) and Q. robur (346 variant sites). Genome sequences were 34 screened for insertion/deletion (indel) polymorphisms to develop markers that identify 35 continental origin of oak species, and that can be easily evaluated using a variety of 36 detection methods. We identified five indel and one SNP that reliably identify continent-of37 origin, based on evaluations of up to 1078 individuals representing 13 white oak species and 38 three continents. Due to the size of length polymorphisms revealed, this marker set can be 39 visualized using capillary electrophoresis or high resolution gel (acrylamide or agarose) 40 electrophoresis. With these markers, we provide the wood trading market with an instrument 41 to comply with the U.S. and European laws that require timber companies to avoid the trade 42 of illegally harvested timber. 43 44
Generating open world descriptions of video using common sense knowledge in a pattern theory framework

The task of interpretation of activities as captured in video extends beyond just the recognition of observed actions and objects. It involves open world reasoning and constructing deep semantic connections that go beyond what is directly observed in the video and annotated in the training data. Prior knowledge plays a big role. Grenander’s canonical pattern theory representation oﬀers an elegant mechanism to capture these semantic connections between what is observed directly in the image and past knowledge in large-scale common sense knowledge bases, such as ConceptNet. We represent interpretations using a connected structure of basic detected (grounded) concepts, such as objects and actions, that are bound by semantics with other background concepts not directly observed, i.e., contextualization cues. Concepts are basic generators and the bonds are deﬁned by the semantic relationships between concepts. Local and global regularity constraints govern these bonds and the overall connection structure. We use an inference engine based on energy minimization using an eﬃcient Markov Chain Monte Carlo that uses the ConceptNet in its move proposals to ﬁnd these structures that describe the image content. Using four diﬀerent publicly available large datasets, Charades, Microsoft Visual Description Corpus (MSVD), Breakfast Actions, and CMU Kitchen, we