Miracle-dz/UniFAR-FTUs huggingface dataset:
Quo vadis Pantanal? Expected precipitation extremes and drought dynamics from changing sea surface temperature

Climate change poses a critical threat to the Pantanal, the largest wetland in the world. Models indicate an increase in the frequency of extreme precipitation events and extended periods of drought. These changes can amplify consequences for Pantanal’s ecological functioning, which has already experienced intensive human modification of its hydrological system and environmental health. The present study analyzed the spatial and temporal dynamics of rainfall and resulting extremes in the Brazilian area of the Upper Paraguay River Basin (UPRB) along with a co-evaluation of the global Sea Surface Temperature data (SST). The predicted results indicate that wet extreme precipitation events will become more frequent in the highlands, while severe and prolonged droughts triggered by warming SSTs in the Northern Hemisphere (North Atlantic and North Pacific oceans) will affect the Pantanal. The linear relations between precipitation with SST of very specific oceanic regions and even from specific oceanic indexes obtained in the present study significantly improve the forecasting capacity, mainly from a resulting reduction to two months of the lead-time between SST warming to concomitant precipitation impacts, and by explaining 80% of Pantanal´s precipitation variation from major oceanic indexes (e.g., ENSO, PDO, NAO, ATL3). Current SST trends will result in inter- and intra-annual flooding dynamic alterations, drastically affecting the Pantanal ecosystem functioning, with consequences for wildlife diversity and distribution. Regarding the foreseeable global climate and land use change scenarios, the results from the present study provide solid evidence that can be used at different decision-making levels (from local to global) for identifying the most appropriate management practices and effectively achieving sustainability of the anthropic activity occurring in the Pantanal.
Genomic Evidence for Complex Domestication History of the Cultivated Tomato in Latin America

Abstract The process of plant domestication is often protracted, involving underexplored intermediate stages with important implications for the evolutionary trajectories of domestication traits. Previously, tomato domestication history has been thought to involve two major transitions: one from wild Solanum pimpinellifolium L. to a semidomesticated intermediate, S. lycopersicum L. var. cerasiforme (SLC) in South America, and a second transition from SLC to fully domesticated S. lycopersicum L. var. lycopersicum in Mesoamerica. In this study, we employ population genomic methods to reconstruct tomato domestication history, focusing on the evolutionary changes occurring in the intermediate stages. Our results suggest that the origin of SLC may predate domestication, and that many traits considered typical of cultivated tomatoes arose in South American SLC, but were lost or diminished once these partially domesticated forms spread northward. These traits were then likely reselected in a convergent fashion in the common cultivated tomato, prior to its expansion around the world. Based on these findings, we reveal complexities in the intermediate stage of tomato domestication and provide insight on trajectories of genes and phenotypes involved in tomato domestication syndrome. Our results also allow us to identify underexplored germplasm that harbors useful alleles for crop improvement.
Food-Grade Emulsions and Emulsion Gels Prepared by Soy Protein-Pectin Complex Nanoparticles and Glycyrrhizic Acid Nanofibrils.

Glycyrrhizic acid (GA) and GA nanofibrils (GN) have been shown to be efficient natural emulsifiers for formation and stabilization of food emulsions. In this work, the emulsion properties of GN in the presence of soy protein isolate-pectin complex nanoparticles (SPNPs) were studied to understand the impact of the nanofibril-nanoparticle interactions on emulsion stabilization. In the presence of low GN concentrations (0.1-0.5 wt%), the synergy in reducing the interfacial tension was observed due to the SPNPs-GN complexation in bulk and at the interface by hydrogen bonding, endowing the prepared emulsions with overall smaller droplet size. However, obvious flocculation and clustering of oil droplets occurred in these emulsions (especially at 0.25 and 0.5 wt% GN), which are probably induced by a depletion mechanism. At high GN concentrations (1-2 wt%), due to the preferential adsorption, the GN mainly dominated the interface and the subsequent formation and properties of emulsions. Accordingly, the self-standing emulsion gels were obtained, showing small droplet size with d32 of about 1.0-1.5 μm, homogeneous appearance and microstructure, and encouraging rheological properties including high gel strength, shear sensitivity and good thixotropic recovery. This is mainly attributed to the formation of fibrillar hydrogel network in the continuous phase as well as around the droplet surfaces.
Cell envelope defects of different capsule‐null mutants in K1 hypervirulent Klebsiella pneumoniae can affect bacterial pathogenesis

Hypervirulent Klebsiella pneumoniae (hvKP) causes Klebsiella‐induced liver abscess. Capsule is important for the pathogenesis of Klebsiella in systemic infection, but its role in gut colonisation is not well understood. By generating ΔwcaJ, Δwza and Δwzy capsule‐null mutants in a prototypical K1 hypervirulent isolate, we show that inactivation of wza (capsule exportase) and wzy (capsule polymerase) confer cell envelope defects in addition to capsule loss, making them susceptible to bile salts and detergent stress. Bile salt resistance is restored when the initial glycosyltransferase wcaJ was inactivated together with wzy, indicating that build‐up of capsule intermediates contribute to cell envelope defects. Mouse gut colonisation competition assays show that the capsule and its regulator RmpA were not required for hvKP to persist in the gut, although initial colonisation was decreased in the mutants. Both ΔrmpA and ΔwcaJ mutants gradually outcompeted the wild type in the gut, whereas Δwza and Δwzy mutants were less fit than wild type. Together, our results advise caution in using the right capsule‐null mutant for determination of capsule's role in bacterial pathogenesis. With the use of ΔwcaJ mutant, we found that although the capsule is important for bacterial survival outside the gut environment, it imposes a fitness cost in the gut.
Surgical intervention for exercise‐induced laryngeal obstruction: A UK perspective

Exercise‐induced laryngeal obstruction (EILO) is a prevalent cause of exertional breathlessness and wheeze in young individuals. Typically diagnosed using the continuous laryngoscopy during exercise (CLE) test, treatment is largely based on breathing retraining promoting improved laryngeal function. In some cases, these techniques fail to alleviate symptoms, and surgical intervention with supraglottoplasty can be valuable in the supraglottic form of EILO. Globally, there is currently limited experience utilizing a surgical approach to EILO, and data regarding the optimum surgical technique and published outcomes and complication rates are thus limited.
Wear and osteolysis outcomes for highly cross-linked polyethylene in primary total hip arthroplasty compared with conventional polyethylene: a 15- to 18-year single-centre follow-up study

Background: Although highly positive results for wear reduction of highly cross-linked polyethylene (HXLPE) have been reported around the 10-year follow-up, the long-term result related to reoperation and wear-related survival is still an issue. Therefore, this study aimed to compare the follow-up results of a single manufacture’s polyethylene liner for >15 years in terms of survival and wear rate. Methods: This retrospective cohort study included 134 primary total hip arthroplasties (THAs) who were followed up for at least 15 years. The mean age at the time of surgery was 50.7 years (conventional polyethylene [CPE] group = 22; HXLPE group = 112). Linear and volumetric wear rates of polyethylene were measured, and the reoperation rate and radiographic osteolysis were evaluated and Kaplan-Meier survival analysis was performed in both groups. Implant-related complications were also examined. Results: HXLPE group showed a significantly lower wear rate in both linear and volumetric wear. None of the hip radiographs showed evidence of loosening or osteolysis in the HXLPE group. The survival rates at 15- to 18-year follow-up were 90.9% and 95.5% in the CPE and HXLPE groups when all-cause reoperation was the endpoint, and 90.9% and 100.0% when the wear-related reoperation was the endpoint, respectively. Implant-related complications were not different between the 2 groups. Conclusions: Wear reduction and osteolysis showed a great advantage in HXLPE after a 15-year follow-up. Although the CPE and HXLPE showed excellent survival, wear and osteolysis were more frequent in the CPE; therefore, the high risk of reoperation in the future should be considered.
Production, purification and evaluation of biodegradation potential of PHB depolymerase of Stenotrophomonas sp. RZS7

There are numerous reports on poly-β-hydroxybutyrate (PHB) depolymerases produced by various microorganisms isolated from various habitats, however, reports on PHB depolymerase production by an isolate from plastic rich sites scares. Although PHB has attracted commercial significance, the inefficient production and recovery methods, inefficient purification of PHB depolymerase and lack of ample knowledge on PHB degradation by PHB depolymerase have hampered its large scale commercialization. Therefore, to ensure the biodegradability of biopolymers, it becomes imperative to study the purification of the biodegrading enzyme system. We report the production, purification, and characterization of extracellular PHB depolymerase from Stenotrophomonas sp. RZS7 isolated from a dumping yard rich in plastic waste. The isolate produced extracellular PHB depolymerase in the mineral salt medium (MSM) at 30°C during 4 days of incubation under shaking. The enzyme was purified by three methods namely ammonium salt precipitation, column chromatography, and solvent purification. Among these purification methods, the enzyme was best purified by column chromatography on the Octyl-Sepharose CL-4B column giving optimum yield (0.7993 Umg-1mL-1). The molecular weight of purified PHB depolymerase was 40 kDa. Studies on the assessment of biodegradation of PHB in liquid culture medium and under natural soil conditions confirmed PHB biodegradation potential of Stenotrophomonas sp. RZS7. The results obtained in Fourier-Transform Infrared (FTIR) analysis, High-Performance Liquid Chromatography (HPLC) study and Gas Chromatography Mass-Spectrometry (GC-MS) analysis confirmed the biodegradation of PHB in liquid medium by Stenotrophomonas sp. RZS7. Changes in surface morphology of PHB film in soil burial as observed in Field Emission Scanning Electron Microscopy (FESEM) analysis confirmed the biodegradation of PHB under natural soil environment. The isolate was capable of degrading PHB and it resulted in 87.74% biodegradation. A higher rate of degradation under the natural soil condition is the result of the activity of soil microbes that complemented the biodegradation of PHB by Stenotrophomonas sp. RZS7.
Ultrasound-guided radiofrequency ablation versus surgery for low risk papillary thyroid micro-carcinoma: results of over 5 years follow-up.

BACKGROUND Papillary thyroid micro-carcinoma (PTMC) typically carries an excellent prognosis regardless of the treatment option pursued. Radiofrequency ablation (RFA) for thyroid disease has been utilized for benign lesions and in patients who are poor surgical candidates for thyroid cancers with compression symptoms, but the efficacy and limitations of RFA as first line therapy for PTMC has not been described in adequate detail. The purpose of our study was to investigate RFA versus thyroidectomy in terms of efficacy, oncologic outcomes, quality of life, complications and costs over a five year period of follow-up. METHODS From January 2013 to November 2013, 174 consecutive patients with an isolated, solitary intrathyroidal PTMC were identified in a Chinese teaching hospital. Those with more aggressive or advanced PTMCs were not included. Ninety-four patients elected RFA and eighty patients elected surgery for treatment of these PTMC. Nodules were confirmed to be PTMC without an aggressive histological type by core needle biopsy in the RFA group and by final surgical pathology in the surgery group. The extent of surgery was decided based on patient preferences in consultation with the surgeons. Of all the patients, 58 (72.5%) underwent lobectomy, 22(27.5%) underwent total thyroidectomy, and 53(66.3%) underwent lymph node dissection. Pre- and post-treatment variables were compared between the two groups, including demographics, tumor characteristics, treatment, local tumor progression, lymph node metastasis, distant metastasis, local recurrence, complications and quality of life findings. RESULTS Patient specific variables were similar between groups, as were oncologic outcomes after five years of follow-up. When compared to RFA, surgery took longer, had a longer hospitalization time, and was costlier (all P<0.001). The surgery group had three complications with two (2.5%) permanent recurrent laryngeal nerve injuries and one (1.3%) case of permanent hypoparathyroidism, while none were reported in the RFA group (P=0.095). The surgery group had a lower post-treatment thyroid related quality of life. CONCLUSIONS For carefully selected low risk intrathyroidal PTMC, RFA was not oncologically inferior to open surgery, and was associated with a higher quality of life and lower overall costs.
Casposase structure and the mechanistic link between DNA transposition and spacer acquisition by CRISPR-Cas

Key to CRISPR-Cas adaptive immunity is maintaining an ongoing record of invading nucleic acids, a process carried out by the Cas1-Cas2 complex that integrates short segments of foreign genetic material (spacers) into the CRISPR locus. It is hypothesized that Cas1 evolved from casposases, a novel class of transposases. We show here that the Methanosarcina mazei casposase can integrate varied forms of the casposon end in vitro, and recapitulates several properties of CRISPR-Cas integrases including site-specificity. The X-ray structure of the casposase bound to DNA representing the product of integration reveals a tetramer with target DNA bound snugly between two dimers in which single-stranded casposon end binding resembles that of spacer 3'-overhangs. The differences between transposase and CRISPR-Cas integrase are largely architectural, and it appears that evolutionary change involved changes in protein-protein interactions to favor Cas2 binding over tetramerization; this in turn led to preferred integration of single spacers over two transposon ends.
From organ to cell: Multi-level telomere length assessment in patients with idiopathic pulmonary fibrosis

Rationale A subset of patients with idiopathic pulmonary fibrosis (IPF) contains short leukocyte telomeres or telomere related mutations. We previously showed that alveolar type 2 cells have short telomeres in fibrotic lesions. Our objectives were to better understand how telomere shortening associates with fibrosis in IPF lung and identify a subset of patients with telomere-related disease. Methods Average telomere length was determined in multiple organs, basal and apical lung, and diagnostic and end-stage fibrotic lung biopsies. Alveolar type 2 cells telomere length was determined in different areas of IPF lungs. Results In IPF but not in controls, telomere length in lung was shorter than in other organs, providing rationale to focus on telomere length in lung. Telomere length did not correlate with age and no difference in telomere length was found between diagnostic and explant lung or between basal and apical lung, irrespective of the presence of a radiological apicobasal gradient or fibrosis. Fifteen out of 28 IPF patients had average lung telomere length in the range of patients with a telomerase (TERT) mutation, and formed the IPFshort group. Only in this IPFshort and TERT group telomeres of alveolar type 2 cells were extremely short in fibrotic areas. Additionally, whole exome sequencing of IPF patients revealed two genetic variations in RTEL1 and one in PARN in the IPFshort group. Conclusions Average lung tissue telomere shortening does not associated with fibrotic patterns in IPF, however, approximately half of IPF patients show excessive lung telomere shortening that is associated with pulmonary fibrosis driven by telomere attrition.
Blind killing of both male and female Drosophila embryos by a natural variant of the endosymbiotic bacterium Spiroplasma poulsonii

Spiroplasma poulsonii is a vertically transmitted endosymbiont of Drosophila melanogaster that causes male‐killing, that is the death of infected male embryos during embryogenesis. Here, we report a natural variant of S. poulsonii that is efficiently vertically transmitted yet does not selectively kill males, but kills rather a subset of all embryos regardless of their sex, a phenotype we call ‘blind‐killing’. We show that the natural plasmid of S. poulsonii has an altered structure: Spaid, the gene coding for the male‐killing toxin, is deleted in the blind‐killing strain, confirming its function as a male‐killing factor. Then we further investigate several hypotheses that could explain the sex‐independent toxicity of this new strain on host embryos. As the second non‐male‐killing variant isolated from a male‐killing original population, this new strain raises questions on how male‐killing is maintained or lost in fly populations. As a natural knock‐out of Spaid, which is unachievable yet by genetic engineering approaches, this variant also represents a valuable tool for further investigations on the male‐killing mechanism.
High levels of genetically-intact HIV in HLA-DR+ memory T-cells indicates their value for reservoir studies.

OBJECTIVE The contribution of HLA-DR+ memory CD4+ T-cells to the HIV reservoir during prolonged antiretroviral therapy is unclear as these cells are commonly excluded when assessing for replication-competent HIV. To address this issue, we examined the distribution of genetically intact HIV DNA within HLA-DR- and HLA-DR+ memory CD4 T-cells and the RNA transcriptional profile of these cells during ART. DESIGN/METHODS Full-length DNA sequencing was used to examine the HIV DNA landscape within HLA-DR+ and HLA-DR- memory CD4+ T-cells. RNA quantification and sequencing was used to interrogate the relationship between HLA-DR status and HIV RNA transcription. RESULTS HLA-DR+ CD4+ T-cells contained a high frequency of genetically-intact HIV genomes, contributing over half of the genetically-intact viral sequences to the reservoir. Expansions of genetically identical sequences were identified in all T-cell subsets, indicating that cellular proliferation maintains genetically-intact and defective viral DNA during therapy. Intracellular HIV RNA levels in HLA-DR+ and HLA-DR- T-cells were not statistically different by either LTR qPCR quantification or single-genome RNA sequencing of the p6-RT region. CONCLUSIONS The high proportion of intact viral DNA sequences in the proliferative HLA-DR+ subset suggests they are critical in maintaining HIV infection during effective therapy. As such, these cells should be included in any immune intervention targeting HIV during effective therapy.
Prevalence of Molecular Subtypes of Breast Cancer: A Single Institutional Experience of 2062 Patients.

Objective The aim of the study was to analyze the prevalence of molecular subtypes of all breast cancer patients treated at tertiary cancer centre in West India in 12 years. Materials and Methods A retrospective observational study carried out in Tertiary Cancer Care Centre in Western India. Electronic medical records of all breast cancer patients were retrieved from the hospital database between March 2007 to March 2019. Patient's characteristic, histological features and molecular subtypes were collected and analyzed. Results A total of 2062 women fulfilled the criteria for this study and were analyzed. The median age of study population was 51 years (range 22-100 years). Among these, 1357 (65.8%) were of ≤55 years and 705 (34.2%) were over 55 years. The overall incidence of Hormonal Receptor-positive patients (either estrogen-receptor (ER) or progesterone-receptor (PR) or both) was 1162 (56.4%). The Mean tumor size was 3.8cm (range 0-18cm). The most common histology was IDC (96%). Axillary nodes were positive in 62.5%. Luminal type A was positive in 762 (37%) patients while Luminal type B was present in 157 (7.6%) patients. Basal-like subtype was observed in 537 (26%) patients while HER2 rich subtype was seen in 229 (11.1%). The incidence of Luminal A subtype increased with age. The highest observed among patients (72%) aged 70 years or more. Incidence of Basal like subtype was highest in patients less than 30 years (52%). Conclusion Luminal-like disease is the most common molecular subtype in India. Identification of Basal like breast cancer, a highly aggressive, biologically and clinically distinct subtype different than its non-basal variant, is important for treatment planning and target therapy.
Japanese Kawasaki Disease Scoring Systems: Are they Applicable to the Iranian Population?

BACKGROUND Kawasaki disease (KD) is the most frequent cause of coronary artery aneurysm (CAA) in children. This study tried to evaluate the accuracy of different KD scores developed for prediction of CAA, in an Iranian population. METHODS This is a cross-sectional retrospective investigation on pediatric patients with a diagnosis of KD. Clinical manifestations, laboratory, and echocardiographic data were recorded. Five Kawasaki scores, including Kobayashi, Egami, Sano, Nakano, and Harada, were assessed and analyzed in relation to CAA and intravenous immunoglobulin (IVIG) resistance. RESULTS During five years, we recruited 121 cases of KD under 13 years of age. The rates of CAA and IVIG resistance were 16.5%, and 13.2% respectively. The IVIG resistance group was significantly younger than responder patients. All five scores had low sensitivity in predicting CAA or IVIG resistant cases; the highest sensitivity pertained to the Harada score with 50% sensitivity and 59% specificity (the area under the curve: 0.545, with a 95% confidence interval: 0.423 to 0.667) in predicting CAA, which is lower than the usual acceptable criteria for a screening test. The specificity of all other scores were more than 85% in predicting CAA or IVIG resistance. Gender, fever before therapy and laboratory data showed no significant difference between the groups. CONCLUSION The Kobayashi, Egami, Sano, Nakano and Harada scores have limited usefulness in the Iranian population to predict high risk patients for coronary artery involvement or IVIG resistance; in our study, age under one year was a risk factor for IVIG resistance.