Miracle-dz/UniFAR-FTUs huggingface dataset:
Factors associated with death in patients with tuberculosis in Brazil: Competing risks analysis

Objectives This study aimed to analyze the factors associated with likely TB deaths, likely TB-related deaths and deaths from other causes. Understanding the factors associated with mortality could help the strategy to End TB, especially the goal of reducing TB deaths by 95% between 2015 and 2035. Methods A retrospective, population-based cohort study of the causes of death was performed using a competing risk model in patients receiving treatment for TB. Patients had started TB treatment in Brazil 2008–2013 with any death certificates dated in the same period. We used three categories of deaths, according to ICD-10 codes: i) probable TB deaths; ii) TB-related deaths; iii) deaths from other causes. Results In this cohort, 39,997 individuals (14.1%) died, out of a total of 283,508 individuals. Of these, 8,936 were probable TB deaths (22.4%) and 3,365 TB-related deaths (8.4%), illustrating high mortality rates. 27,696 deaths (69.2%) were from other causes. From our analysis, factors strongly associated with probable TB deaths were male gender (sHR = 1.33, 95% CI: 1.26–1.40), age over 60 years (sHR = 9.29, 95% CI: 8.15–10.60), illiterate schooling (sHR = 2.33, 95% CI: 2.09–2.59), black (sHR = 1.33, 95% CI: 1.26–1.40) and brown (sHR = 13, 95% CI: 1.07–1.19) color/race, from the Southern region (sHR = 1.19, 95% CI: 1.10–1.28), clinical mixed forms (sHR = 1.91, 95% CI: 1.73–2.11) and alcoholism (sHR = 1.90, 95% CI: 1.81–2.00). Also, HIV positive serology was strongly associated with probable TB deaths (sHR = 62.78; 95% CI: 55.01–71.63). Conclusions In conclusion, specific strategies for active surveillance and early case detection can reduce mortality among patients with tuberculosis, leading to more timely detection and treatment.
Identification of fungal populations during the storage period of Tibetan tea.

The fungal populations in the storage period of Tibetan tea were identified to study the relationship between tea quality and microbe species populations.The results showed that there were 5 main species populations of Aspergillus(Aspergillus niger),Penicillium(Penicillium glabrum,Penicillium roqueforti,Baen penicillium),and Rhizopus(Rhizopus) in the storage period of Tibetan tea.These microbes could affect quality formation of Tibetan tea during the storage period directly or indirectly.
Twelve tips for facilitating and implementing clinical debriefing programmes

Abstract Contemporary clinical practice places a high demand on healthcare workforces due to complexity and rapid evolution of guidelines. We need embedded workplace practices such as clinical debriefing (CD) to support everyday learning and patient care. Debriefing, defined as a ‘guided reflective learning conversation’, is most often undertaken in small groups following simulation-based experiences. However, emerging evidence suggests that debriefing may also enhance learning in clinical environments where facilitators need to simultaneously balance psychological safety, learning goals and emotional well-being. This twelve tips article summarises international experience collated at the recent Association for Medical Education in Europe (AMEE) debriefing symposium. These tips encompass the benefits of CD, as well as suggested approach to facilitation. Successful CD programmes are frequently team focussed, interdisciplinary, implemented in stages and use a clear structure.
The mononuclear phagocyte system contributes to fibrosis in post-transplant obliterans bronchiolitis

Bronchiolitis obliterans syndrome (BOS) is a fibrotic disease that is heavily responsible for the high mortality rates after lung transplantation. Myofibroblasts are primary effectors of this fibrotic process, but their origin is still debated. The purpose of this work was to identify the precursors of mesenchymal cells responsible for post-transplant airway fibro-obliteration. Lineage-tracing tools were used to track or deplete potential sources of myofibroblasts in the heterotopic tracheal transplantation model. Allografts were analysed by histology, confocal microscopy, flow cytometry or single-cell transcriptomic analysis. BOS explants were evaluated by histology and confocal microscopy. Myofibroblasts in the allografts were recipient-derived. When recipient mice were treated with tacrolimus, we observed rare epithelial-to-mesenchymal transition phenomena and an overall increase in donor-derived myofibroblasts (p=0.0467), but the proportion of these cells remained low (7%). Haematopoietic cells, and specifically the mononuclear phagocyte system, gave rise to the majority of myofibroblasts found in occluded airways. Ablation of Cx3cR1+ cells decreased fibro-obliteration (p=0.0151) and myofibroblast accumulation (p=0.0020). Single-cell RNA sequencing revealed similarities between myeloid-derived cells from allografts and both murine and human samples of lung fibrosis. Finally, myofibroblasts expressing the macrophage marker CD68 were increased in BOS explants when compared to controls (14.4% versus 8.5%, p=0.0249). Recipient-derived myeloid progenitors represent a clinically relevant source of mesenchymal cells infiltrating the airways after allogeneic transplantation. Therapies targeting the mononuclear phagocyte system could improve long-term outcomes after lung transplantation. Bronchiolitis obliterans syndrome remains a major cause of mortality after lung transplantation. The mononuclear phagocyte system actively contributes to fibrotic occlusion of rejected airways, thereby representing a promising novel therapeutic target. https://bit.ly/3hQh8UL
Notes on the Larvae of the Chalcidoidea

During recent years students of the biology of the parasitic Hymenoptera have made several attempts to classify the larvae of these insects in groups based on certain striking features of the external anatomy. Thus Richardson ('13) in his paper on Spalangia, and Wheeler ('23) in her account of the braconid parasites of aphids, distinguish respectively 9 and 10 types of hymenopterous larvrA¦ distributed among the several parasitic families. Up to the present, however, so far as the writers are aware, no efforts have been made to define such larval types within the individual superfamilies of the parasitic Hymenoptera, although in almost every group a considerable number of larvrae have been described.
Stock Discrimination of Capelin (Mallotus villosus) in the Northwest Atlantic

Although capelin is an important commercial and forage species of the Newfoundland region, firm evidence for the designation of separate stocks does not exist. In a previous analysis of meristic characters of capelin, the authors assumed that meristic data were multivariate normal, an assumption that is not usually met. Consequently, the data were reanalyzed by using non-parametric methodology to assess differences in meristic characters, and the results of the analyses were examined to determine the relative importance of individual characters in the separation of stocks. Groups of capelin samples from five areas were tested by using 11 meristic characters in two age-groups. Capelin from western Newfoundland and Southeast Shoal of the Grand Bank continued to be clearly identified as separate stocks. The delineations of capelin from the other three areas were less clear, although independent paired comparisons with age combined differentiated the Labrador-Northeast Newfoundland and the northern Grand Bank-Avalon stocks, and separate analysis of age 3 and 4 capelin indicated that these two stocks were different from the St. Pierre Bank stock.
Protracted hyperthermia and delayed rhabdomyolysis in ecstasy toxicity

Abstract Rationale: Despite toxicity and unpredictable adverse effects, ecstasy use has increased in the United States. Onset of hyperpyrexia, rhabdomyolysis, disseminated intravascular coagulation (DIC), among other symptoms, occurs within hours of ingestion. Moreover, patients who experience hyperpyrexia, altered mental status, DIC, and multiorgan failure, rarely survive. This case presents a chronic ecstasy user whose symptoms would have predicted mortality. The report demonstrates a patient who experiences protracted hyperthermia, with delayed rhabdomyolysis and DIC. In addition, his peak creatine kinase (CK) of 409,440 U/L was far greater than the expected 30,000 to 100,000 U/L, being the second largest CK recorded in a survivor. Patient concerns: This case report presents a 20-year-old man who presented to the emergency department after experiencing a severe reaction to ecstasy. He was a chronic user who took his baseline dosage while performing at a music event. He experienced hyperpyrexia immediately (106.5°F) while becoming stiff and unresponsive. Before emergency medical service arrival, his friends placed cold compresses on the patient and rested him in an ice filled bathtub. Diagnoses: Per history from patient's friends and toxicology results, the patient was diagnosed with ecstasy overdose, which evolved to include protracted hyperthermia and delayed rhabdomyolysis. Interventions: Due to a Glasgow coma scale score of 5, he was intubated and sedated with a propofol maintenance. Hyperpyrexia resolved (temperature dropped to 99.1°F) after start of propofol maintenance. He was extubated after 24 hours, upon which he experienced hyperthermia (101.4°F at 48 hours), delayed rhabdomyolysis, and DIC (onset at 37 hours). He remained in hyperthermia for 120 hours until carvedilol permanently returned his temperature to baseline. His plasma CK reached a peak of 409,440 U/L at 35 hours. Outcomes: After primary management with intravenous fluids, the patient returned to baseline health without any consequences and was discharged after 8 days. A follow-up of 3 months postdischarge revealed no complications or disability. Lessons: Clinically, the case highlights how physicians should be aware of the unusual time course adverse effects of ecstasy can have. Lastly, as intensity and duration of hyperpyrexia are predictors of mortality, our case indicates maintenance of sedation with propofol and use of oral carvedilol; both are efficacious for temperature reduction in ecstasy toxicity.
Mitochondrial Genome Evolution of Placozoans: Gene Rearrangements and Repeat Expansions

Abstract Placozoans, nonbilaterian animals with the simplest known metazoan bauplan, are currently classified into 20 haplotypes belonging to three genera, Polyplacotoma, Trichoplax, and Hoilungia. The latter two comprise two and five clades, respectively. In Trichoplax and Hoilungia, previous studies on six haplotypes belonging to four different clades have shown that their mtDNAs are circular chromosomes of 32–43 kb in size, which encode 12 protein-coding genes, 24 tRNAs, and two rRNAs. These mitochondrial genomes (mitogenomes) also show unique features rarely seen in other metazoans, including open reading frames (ORFs) of unknown function, and group I and II introns. Here, we report seven new mitogenomes, covering the five previously described haplotypes H2, H17, H19, H9, and H11, as well as two new haplotypes, H23 (clade III) and H24 (clade VII). The overall gene content is shared between all placozoan mitochondrial genomes, but genome sizes, gene orders, and several exon–intron boundaries vary among clades. Phylogenomic analyses strongly support a tree topology different from previous 16S rRNA analyses, with clade VI as the sister group to all other Hoilungia clades. We found small inverted repeats in all 13 mitochondrial genomes of the Trichoplax and Hoilungia genera and evaluated their distribution patterns among haplotypes. Because Polyplacotoma mediterranea (H0), the sister to the remaining haplotypes, has a small mitochondrial genome with few small inverted repeats and ORFs, we hypothesized that the proliferation of inverted repeats and ORFs substantially contributed to the observed increase in the size and GC content of the Trichoplax and Hoilungia mitochondrial genomes.
β3- adrenergic receptor gene polymorphism analysis and application

Objective:To investigate the effect of β3- adrenergic receptor gene polymorphism on obesity and insulin resistance. Methods:With PCR-RFLP and PCR-dideoxy-chain-termination method of DNA sequencing, we investigated the influence of the β3- adrenergic receptor gene polymorphism on obesity, insulin resistance and lipid profile in native Chinese. Results: β3-AR 190 T→C mutation was detected among 48 diabetic patients and 32 volunteers. Conclusion:This genetic variation is likely to be involved in early onset of Type 2 diabetes. But it's not the major factor affecting on obesity and dyslipidemia.
Cellular senescence: friend or foe to respiratory viral infections?

Cellular senescence permanently arrests the replication of various cell types and contributes to age-associated diseases. In particular, cellular senescence may enhance chronic lung diseases including COPD and idiopathic pulmonary fibrosis. However, the role cellular senescence plays in the pathophysiology of acute inflammatory diseases, especially viral infections, is less well understood. There is evidence that cellular senescence prevents viral replication by increasing antiviral cytokines, but other evidence shows that senescence may enhance viral replication by downregulating antiviral signalling. Furthermore, cellular senescence leads to the secretion of inflammatory mediators, which may either promote host defence or exacerbate immune pathology during viral infections. In this Perspective article, we summarise how senescence contributes to physiology and disease, the role of senescence in chronic lung diseases, and how senescence impacts acute respiratory viral infections. Finally, we develop a potential framework for how senescence may contribute, both positively and negatively, to the pathophysiology of viral respiratory infections, including severe acute respiratory syndrome due to the coronavirus SARS-CoV-2. Senescence associates with fibrotic lung diseases. Emerging therapies to reduce senescence may treat chronic lung diseases, but the impact of senescence during acute respiratory viral infections is unclear and requires future investigation. https://bit.ly/2SAPpx6
Physiological and productive response of lactating dairy cows to the alpine transhumance at the end of the summer grazing*

Abstract The study aimed at verifying if the prolonged walking and fasting of the driving down transhumance from an alpine pasture to the farm of origin at the end of the summer grazing may impair health and productive response of lactating cows belonging to two specialised dairy breeds. The study considered a herd of 380 dairy cows and heifers of Italian Holstein and Italian Brown breeds that faced a driving down transhumance with a vertical drop of about 1050 m. The animals walked for about 40 km completing the journey in 23 h, including three resting periods. Ten Holstein and nine Brown lactating cows were selected and monitored before and after the driving down transhumance taking individual blood samples and recording milk yield. The prolonged physical exercise and the limited water and energy intake during the driving down transhumance impaired cows’ metabolic profile resembling a status of ketosis. A significant drop in milk yield was observed in all the monitored animals regardless of the breed. The production loss was more severe (49.4%) in cows with high milk yield and less days in milk. These animals required also a prolonged time to recover from the milk drop due to the driving down transhumance and, based on these findings, they should be excluded from this practise.
Mutational landscape of K-Ras substitutions at 12th position-a systematic molecular dynamics approach

Abstract K-Ras is a small GTPase and acts as a molecular switch by recruiting GEFs and GAPs, and alternates between the inert GDP-bound and the dynamic GTP-bound forms. The amino acid at position 12 of K-Ras is a hot spot for oncogenic mutations (G12A, G12C, G12D, G12R, G12S, and G12V), disturbing the active fold of the protein, leading to cancer development. This study aimed to investigate the potential conformational changes induced by these oncogenic mutations at the 12th position, impairing GAP-mediated GTP hydrolysis. Comprehensive computational tools (iStable, FoldX, SNPeffect, DynaMut, and CUPSAT) were used to evaluate the effect of these six mutations on the stability of wild type K-Ras protein. The docking of GTP with K-Ras was carried out using AutoDock4.2, followed by molecular dynamics simulations. Furthermore, on comparison of binding energies between the wild type K-Ras and the six mutants, we have demonstrated that the G12A and G12V mutants exhibited the strongest binding efficiency compared to the other four mutants. Trajectory analyses of these mutations revealed that G12A encountered the least deviation, fluctuation, intermolecular H-bonds, and compactness compared to the wildtype, which was supported by the lower Gibbs free energy value. Our study investigates the molecular dynamics simulations of the mutant K-Ras forms at the 12th position, which expects to provide insights about the molecular mechanisms involved in cancer development, and may serve as a platform for targeted therapies against cancer. Communicated by Ramaswamy H. Sarma
Cervical Intraepithelial Neoplasia- Predictive molecular growth factors in natural history

There is considerable controversy regarding the possible over-treatment of patients with mild Cervical Intraepithelial Neoplasia (CIN), with lesions being often excised or ablated. Thus, identifying the markers of potentially malignant lesions would be of a great prognostic value. In the current study, we hypothesized that using colposcopic, cytological and histological findings together with assessing the expression of molecular growth factors can predict CIN outcome. The study group consisted of 285 women between 19 and 81 years of age (median age, 37,8 years). The follow up were 60 months and considered 138 women: 50 women with Subclinical Papillomavirus Infection (SPI), 50 women with CIN1 and 38 women with CIN2. All patients underwent cytology, colposcopy, and sampling for subsequent testing for HPV. In cases in which colposcopy suggested the presence of suspicious lesions, biopsy specimens were taken. HPV DNA was genotyped for HPV types 16, 18, 31, 33, and 45 by multiplex PCR. Transcripts of HR HPV types 16, 18, 31, 33, and 45 were detected by the NucliSens EasyQ HPV assay. The VEGF expression was analyzed with immunohistochemistry, RNA extraction, cDNA synthesis and RT-PCR analysis and Western blot. We found that so called lymphangiogenetic switch (over expression of VEGF C and VEGFR-2) appears already in CIN 2, which is a rare observation, Persistent HPV HR infection is not only a trigger but also a maintenance factor in the cervical carcinogenesis. CIN2/3 and cervical cancer is in high percentage associated with the presence of HR DNA HPV as well as E6/E7 DNA mRNA. In CIN2/3 and cervical cancer VEGF and its receptor expression correlate with the stage of cervical carcinogenesis. Progression of cervical intraepithelial neoplasia occurs when co expression of all: HR DNA HPV, E6/E7 HR HPV mRNA and VEGF is present.
Polypharmacy, potentially inappropriate prescribing and medication complexity in Turkish older patients in the community pharmacy setting

ABSTRACT Objective This study aimed to evaluate polypharmacy, potentially inappropriate prescribing (PIP) and medication complexity in Turkish older patients in the community pharmacy setting and to determine the factors associated with PIP. Methods This descriptive cross-sectional study was conducted in the community pharmacy setting in Istanbul. Older patients (≥65 years old) who chronically used at least one medication and visited the community pharmacy for any reason in the past 4 months were invited in this study. PIP was determined by using the Ghent Older People’s Prescriptions Community Pharmacy Screening (GheOP3S)-tool. The Turkish version of the Medication Regimen Complexity Index (MRCI) was used to determine medication complexity. Results Polypharmacy (defined as the concurrent use of five or more medications) was found in 69.0% of 158 patients. A total of 398 PIPs were detected and 83.5% (n = 132) of older patients had at least one PIP. The median (IQR) MRCI score was 12.5 (7.0–19.6). The factors associated with having ≥2 PIP were advanced age (≥75 years old) (OR = 2.87, 95% CI 1.41–5.81; p < 0.05), higher number of chronic diseases (when ≥3, OR = 8.51, 95% CI 3.66–19.76; p < 0.05), receiving polypharmacy (OR = 8.92, 95% CI 4.09–19.46; p < 0.05), and higher MRCI scores (when MRCI ≥12.5, OR = 4.40, 95% CI 2.22–8.71; p < 0.05). Conclusion More than half of the Turkish older patients had polypharmacy and the rate of PIP was high. A higher number of PIP was associated with advanced age, higher number of chronic diseases, polypharmacy, and more complex medication regimens.
Defining features of diabetes resilience in emerging adults with type 1 diabetes

Emerging adulthood presents unique challenges for type 1 diabetes (T1D) management. Barriers to achieving optimal diabetes outcomes have been studied but less is known about how emerging adults overcome these challenges. Characterizing emerging adults' protective factors may help guide T1D care during this developmental period. We anticipated identifying social, cognitive, and behavioral protective factors and were open to additional themes.
Tracking the response of industrial fishing fleets to large marine protected areas in the Pacific Ocean

Large marine protected areas (MPAs) of unprecedented size have recently been established across the global oceans, yet their ability to meet conservation objectives is debated. Key areas of debate include uncertainty over nations’ abilities to enforce fishing bans across vast, remote regions and the intensity of human impacts before and after MPA implementation. We used a recently developed vessel tracking data set (produced using Automatic Identification System detections) to quantify the response of industrial fishing fleets to 5 of the largest MPAs established in the Pacific Ocean since 2013. After their implementation, all 5 MPAs successfully kept industrial fishing effort exceptionally low. Detected fishing effort was already low in 4 of the 5 large MPAs prior to MPA implementation, particularly relative to nearby regions that did not receive formal protection. Our results suggest that these large MPAs may present major conservation opportunities in relatively intact ecosystems with low immediate impact to industrial fisheries, but the large MPAs we considered often did not significantly reduce fishing effort because baseline fishing was typically low. It is yet to be determined how large MPAs may shape global ocean conservation in the future if the footprint of human influence continues to expand. Continued improvement in understanding of how large MPAs interact with industrial fisheries is a crucial step toward defining their role in global ocean management.
Quality Evaluation of the Muscle of Cultured Plaice Fed with Three Different Diets

Muscle quality of plaice Paralichthys olivaceus fed with fresh food, dry pellet and moist pellet was evaluated with respect to proximate composition, fatty acids composition, lipid class and free amino acids composition, compared with wild plaice muscle.In the muscle of plaice fed with pellets monoenes ratio was high and in wild plaice muscle the ratios of polyenes and saturates were high in comparison with the plaice fed with fresh food.As for lipids class, cultured plaice contained triglyceride and phospholipid more than 90% and wild plaice contained 87% of phospholipid and mono-and diglyceride in total lipid. Taurine was contained in the highest amount in cultured and wild plaice muscle. In the muscle of plaice fed with fresh food lysine was high, and in the muscle of plaice fed with dry pellet, anserine was high, which resulted from the diet.