Miracle-dz/UniFAR-FTUs huggingface dataset:
Evaluation of risk factors associated with the development of MDR- and XDR-TB in a tertiary care hospital: a retrospective cohort study

Background Drug resistant tuberculosis (DR-TB) infringes substantial burden in terms of longer treatment duration, morbidity and mortality. Timely identification of patients at risks of DR-TB will aid individualized treatment. Current study was aimed to ascertain several factors associated with DR-TB among patients attending a tertiary care hospital. Methods This retrospective study was conducted among patients with confirmed diagnosis of DR-TB and drug susceptible TB (DS-TB) seeking medical care from a tertiary care hospital during 2014–2019. The types of DR-TB included were rifampicin resistant tuberculosis (RR-TB), Multidrug resistant tuberculosis (MDR-TB) and extensively drug resistant tuberculosis (XDR-TB). Appropriate statistical methods were implied to evaluate the factors associated with DR-TB. Results Out of 580 patients, DS-TB was diagnosed in 198 (34.1%) patients while DR-TB was present in 382 patients. Of resistance cases, RR-TB, MDR-TB and XDR-TB were diagnosed in 176 (30.3%), 195 (33.6%) and 11 (1.9%) patients, respectively. Significant differences (P < 0.05) in demographics and clinico-laboratory characteristics were observed between patients with DS-TB and DR-TB. Logistic regression analysis revealed age ≤38 years (OR: 2.5), single marital status (OR: 11.1), tobacco use (OR: 2.9), previous treatment (OR: 19.2), treatment failure (OR: 9.2) and cavity on chest X-ray (OR: 30.1) as independent risk factors for MDR-TB. However, XDR-TB was independently associated with age group of ≤38 years (OR: 13.6), students (OR: 13.0), previous treatment (OR: 12.5), cavity on chest X-ray (OR: 59.6). The independent risk factors associated with RR-TB are age ≤38 years (OR: 2.8), females (OR: 5.7), unemployed (OR: 41.5), treatment failure (OR: 4.9), previous treatment (OR: 38.2) and cavity on chest X-ray (OR: 4.3). ROC curve analysis accentuate the excellent predictive accuracy of all logistic regression models as shown by AUC (0.968, P < 0.001) for MDR-TB, AUC (0.941, P < 0.001) for XDR-TB and AUC (0.962, P < 0.001) for RR-TB. Conclusions Current study demonstrates a sizeable extent of resistant cases among pulmonary TB patients. This study presaged significant risk of DR-TB among females, young adults, unemployed, smokers, patients with previous treatment failure and cavitation on chest X-ray. Timely identification of high risk patients will give pronounced advantages regarding appropriate choices of prevention, treatment and disease control.
Cancer of the anal canal, a reality in the Colombian coffee region. Clinical-epidemiological review 2000–2019

Introduction Anal cancer is a rare pathology which has increased over the last few decades, and, therefore, gained importance for the quality of life of affected individuals. Thus, a review has been conducted in the Colombian coffee region (Departments of Caldas, Quindío y Risaralda) describing its behaviour and clinical-epidemiological profile. Materials and methods Descriptive review of 437 patients of Western SAS Oncologists between January 2000 and December 2019 with a diagnosis of anal cancer. Results 62% of cases presented in women with a median age of 62 years, 30% in the sixth decade; centred at 65% in three main cities designated as capitals (Manizales, Pereira and Armenia); 62% as localised disease, with 40% stage II-A and 6% as initial metastasis; 29% presented positive ganglia, particularly N1a; squamous cell or epidermoid histology in 90%; 16% poorly differentiated; 5% related to Human Immunodeficiency Virus infection; localisation in the medial area of the anal canal in 63% of cases; 83% completed treatment, and 92% of them received chemotherapy/radiation therapy with 87% based on the Nigro protocol; finally, 11% presented with relapse in the liver in 10% of cases and 55% local. Conclusion Four hundred and thirty-seven patients evaluated over 20 years with follow up at median 34.13 months (standard deviation 41.75) with median survival at later ages decreasing to 62% in patients older than 80 years, and differences in survival in localised disease at 78% in comparison to 46% in advanced metastasis. Finally, the overall 5-year survival rate is 69% with a median survival of 191 months in the study.
UGT1A1 Polymorphism for Irinotecan Dose Escalation in Patients with BRAF-Mutated Metastatic Colorectal Cancer Treated with First-Line Bevacizumab and FOLFIRI

Background Patients with metastatic colorectal cancer (mCRC) and BRAF V600E mutation have a poor prognosis, with a median progression-free survival (PFS) of only 5–7 months after initial therapy. The current standard first-line chemotherapy for these patients includes FOLFOX or FOLFIRI plus bevacizumab. In this study, we explored the effects and oncological outcomes of UGT1A1 polymorphism for irinotecan escalation in patients with BRAF-mutated mCRC. Patients and Methods. This retrospective study included 17 patients with BRAF-mutated mCRC between April 2016 and December 2019. UGT1A1 genotyping was performed on all patients prior to initiating bevacizumab plus FOLFIRI chemotherapy. The primary endpoint was PFS, and the secondary endpoints were toxicity, response rate, disease control rate, and overall survival (OS). Results Fifteen and two patients had UGT1A1 1∗/1∗ and 1∗/28∗, respectively. Eight underwent irinotecan dose escalation with tolerable adverse effects (AEs), and nine maintained an irinotecan dose of 180 mg/m2 or required deescalation to 150 mg/m2 due to intolerable AEs. After a median follow-up period of 15.7 (range, 3–54) months, the median PFS and OS were 9.4 and 15.7 months, respectively. Grade 3/4 AEs were observed in three (6%) patients. The disease control and partial response rates were 64.7% and 11.8%, respectively, indicating that most patients (14, 82.3%) could maintain this as a first-line line therapy with stable disease or proceed to second-line therapy if disease progression occurred, thereby maintaining acceptable performance status. Conclusions The oncological outcomes of patients with BRAF-mutated mCRC treated using FOLFIRI plus bevacizumab with irinotecan dose escalation as a first-line therapy are acceptable with tolerable AEs; this may be a feasible treatment option in such patients. Pretherapeutic UGT1A1 genotyping-guided dose adjustment can achieve favorable outcomes.
A Rare Case of Eosinophilic Gastroenteritis and Ampullitis Leading to Benign Papillary Stenosis

Eosinophilic gastroenteritis is characterized by eosinophilic infiltration of the gastrointestinal wall. There have been limited studies of eosinophilic infiltration involving the ampulla. We present a 70-year-old woman with a history of asthma, eosinophilic esophagitis, and eosinophilic sinusitis, who underwent work up for postprandial abdominal pain and abnormal liver function tests. The patient had various imaging studies done, including computed tomography (CT) scan, magnetic resonance imaging (MRI), and magnetic resonance cholangiopancreatography (MRCP). Dilated extrahepatic bile duct with distal tapering towards the ampulla was noted on MRCP and afterwards on endoscopic ultrasound (EUS). Endoscopic retrograde cholangiopancreatography (ERCP) revealed an inflamed major ampulla with benign papillary stenosis. The patient was treated with sphincterotomy, sphincteroplasty/dilation of distal common bile duct, and placement of an 11.5 Fr × 7 cm plastic stent into the bile duct. Additionally, she was started on prednisone, which was gradually tapered down. The patient demonstrated significant improvement with systemic steroid therapy. Liver function tests (LFTs) completely normalized after ERCP. Ampullitis leading to papillary stenosis secondary to eosinophilic infiltration of the major papilla is a rare manifestation of eosinophilic gastrointestinal disorders (EGIDs). Early diagnosis would lead to appropriate medical and endoscopic management.
Assessing the COVID‐19 Impact on Air Quality: A Machine Learning Approach

The worldwide research initiatives on Corona Virus disease 2019 lockdown effect on air quality agree on pollution reduction, but the most reliable method to pollution reduction quantification is still in debate. In this paper, machine learning models based on a Gradient Boosting Machine algorithm are built to assess the outbreak impact on air quality in Quito, Ecuador. First, the precision of the prediction was evaluated by cross‐validation on the four years prelockdown, showing a high accuracy to estimate the real pollution levels. Then, the changes in pollution are quantified. During the full lockdown, air pollution decreased by −53 ± 2%, −45 ± 11%, −30 ± 13%, and −15 ± 9% for NO2, SO2, CO, and PM2.5, respectively. The traffic‐busy districts were the most impacted areas of the city. After the transition to the partial relaxation, the concentrations have nearly returned to the levels as before the pandemic. The quantification of pollution drop is supported by an assessment of the prediction confidence.
Professional roles and relationships during the COVID-19 pandemic: a qualitative study among US clinicians

Objective The COVID-19 pandemic has transformed healthcare delivery in the USA, but there has been little empirical work describing the impact of these changes on clinicians. We conducted a study to address the following question: how has the pandemic impacted US clinicians’ professional roles and relationships? Design Inductive thematic analysis of semi-structured interviews. Setting Clinical settings across the USA in April and May of 2020. Participants Clinicians with leadership and/or clinical roles during the COVID-19 pandemic. Measures Emergent themes related to professional roles and relationships. Results Sixty-one clinicians participated in semi-structured interviews. Study participants were practising in 15 states across the USA, and the majority were White physicians from large academic centres. Three overlapping and inter-related themes emerged from qualitative analysis of interview transcripts: (1) disruption: boundaries between work and home life became blurred and professional identity and usual clinical roles were upended; (2) constructive adaptation: some clinicians were able to find new meaning in their work and described a spirit of collaboration, shared goals, open communication and mutual respect among colleagues; and (3) discord and estrangement: other clinicians felt alienated from their clinical roles and experienced demoralising work environments marked by division, value conflicts and mistrust. Conclusions Clinicians encountered marked disruption of their professional roles, identities and relationships during the pandemic to which they and their colleagues responded in a range of different ways. Some described a spirit of collaboration and camaraderie, while others felt alienated by their new roles and experienced work environments marked by division, value conflicts and mistrust. Our findings highlight the importance of effective teamwork and efforts to support clinician well-being during the COVID-19 pandemic.
Global Significant Changes in Formaldehyde (HCHO) Columns Observed From Space at the Early Stage of the COVID‐19 Pandemic

Satellite HCHO data are widely used as a reliable proxy of non‐methane volatile organic compounds (NMVOCs) to constrain underlying emissions and chemistry. Here, we examine global significant changes in HCHO columns at the early stage of the COVID‐19 pandemic (January–April 2020) compared with the same period in 2019 with observations from the TROPOspheric Monitoring Instrument (TROPOMI). HCHO columns decline (11.0%) in the Northern China Plain (NCP) because of a combination of meteorological impacts, lower HCHO yields as NOx emission plunges (by 36.0%), and reduced NMVOC emissions (by 15.0%) resulting from the lockdown. HCHO columns change near Beijing (+8.4%) due mainly to elevated hydroxyl radical as NOx emission decreases in a NOx‐saturated regime. HCHO columns change in Australia (+17.5%), Northeastern Myanmar of Southeast Asia (+14.9%), Central Africa (+7.8%), and Central America (+18.9%), consistent with fire activities. Our work also points to other changes related to temperature and meteorological variations.
Highly concentrated water-in-oil emulsions: Influence of electrolyte on their properties and stability

Abstract Concentrated water-in-oil emulsions of over 95% internal phase by volume were prepared using a variety of low HLB emulsifiers. These emulsions coarsened with time to produce a fraction of large droplets that grow at the expense of smaller droplets. This resulted in a decrease in yield stress and eventually to visible phase separation of water. There was a significant effect of emulsifier type, and the optimum HLB appears to be ∼5 for mineral oil. None of the emulsions prepared with distilled water as the internal phase could withstand a single freeze/thaw cycle. In contrast to the gradual coarsening process at room temperature, freeze/thaw instability was sudden and involved an inversion process that took place in the frozen state. The properties of these concentrated emulsions changed dramatically when electrolyte was introduced into the aqueous phase at concentrations as low as 0.02 M . The rate of coarsening decreased, and coalescence of water droplets during the freeze/thaw process was inhibited. The emulsions retained their yield stress over prolonged storage and a lower droplet size was often produced under the same conditions of emulsification. These effects seemed to be general and were observed with a variety of emulsifiers and electrolytes. The electrolytes appeared to enhance the stability of these water-in-oil emulsions by increasing the resistance of the water droplets to coalescence. It is proposed that this was achieved by a higher adsorption density of emulsifier at room temperature storage , and in the frozen state by the fractionation of a concentrated electrolyte solution that wetted the ice crystals and prevented their fusion. Analysis of emulsion rheology and processing suggested that this enhanced coalescence stability was adequate to account for the changes in yield stress and droplet sizes observed.
Regulatory role of long non-coding RNA UCA1 in signaling pathways and its clinical applications

Long non-coding RNA metastasis-associated urothelial carcinoma associated 1 (UCA1) plays a pivotal role in various human diseases. Its gene expression is regulated by several factors, including transcription factors, chromatin remodeling and epigenetic modification. UCA1 is involved in the regulation of the PI3K/AKT, Wnt/β-catenin, MAPK, NF-κB and JAK/STAT signaling pathways, affecting a series of cellular biological functions, such as cell proliferation, apoptosis, migration, invasion and tumor drug resistance. Furthermore, UCA1 is used as a novel potential biomarker for disease diagnosis and prognosis, as well as a target for clinical gene therapy. The present review systematically summarizes and elucidates the mechanisms of upstream transcriptional regulation of UCA1, the regulatory role of UCA1 in multiple signaling pathways in the occurrence and development of several diseases, and its potential applications in clinical treatment.
Acoustically Enriched Environment during the Critical Period of Postnatal Development Positively Modulates Gap Detection and Frequency Discrimination Abilities in Adult Rats

Throughout life, sensory systems adapt to the sensory environment to provide optimal responses to relevant tasks. In the case of a developing system, sensory inputs induce changes that are permanent and detectable up to adulthood. Previously, we have shown that rearing rat pups in a complex acoustic environment (spectrally and temporally modulated sound) from postnatal day 14 (P14) to P28 permanently improves the response characteristics of neurons in the inferior colliculus and auditory cortex, influencing tonotopical arrangement, response thresholds and strength, and frequency selectivity, along with stochasticity and the reproducibility of neuronal spiking patterns. In this study, we used a set of behavioral tests based on a recording of the acoustic startle response (ASR) and its prepulse inhibition (PPI), with the aim to extend the evidence of the persistent beneficial effects of the developmental acoustical enrichment. The enriched animals were generally not more sensitive to startling sounds, and also, their PPI of ASR, induced by noise or pure tone pulses, was comparable to the controls. They did, however, exhibit a more pronounced PPI when the prepulse stimulus was represented either by a change in the frequency of a background tone or by a silent gap in background noise. The differences in the PPI of ASR between the enriched and control animals were significant at lower (55 dB SPL), but not at higher (65-75 dB SPL), intensities of background sound. Thus, rearing pups in the acoustically enriched environment led to an improvement of the frequency resolution and gap detection ability under more difficult testing conditions, i.e., with a worsened stimulus clarity. We confirmed, using behavioral tests, that an acoustically enriched environment during the critical period of development influences the frequency and temporal processing in the auditory system, and these changes persist until adulthood.
Valleriite, a Natural Two-Dimensional Composite: X-ray Absorption, Photoelectron, and Mössbauer Spectroscopy, and Magnetic Characterization

Valleriite is of interest as a mineral source of basic and precious metals and as an unusual material composed of two-dimensional (2D) Fe–Cu sulfide and magnesium hydroxide layers, whose characteristics are still very poorly understood. Here, the mineral samples of two types with about 50% of valleriites from Noril’sk ore provenance, Russia, were examined using Cu K- and Fe K-edge X-ray absorption fine structure (XAFS) spectroscopy, X-ray photoelectron spectroscopy (XPS), 57Fe Mössbauer spectroscopy, and magnetic measurements. The Cu K X-ray absorption near-edge structures (XANES) spectra resemble those of chalcopyrite, however, with a higher electron density at Cu+ centers and essentially differ from those of bornite Cu5FeS4; the Fe K-edge was less informative because of accompanying oxidized Fe-containing phases. The post-edge XANES and extended XAFS (EXAFS) analysis reveal differences in the bond lengths, e.g., additional metal–metal distances in valleriites as compared with chalcopyrite. The XPS spectra confirmed the Cu+ and Fe3+ state in the sulfide sheets and suggest that they are in electron equilibrium with (Mg, Al) hydroxide layers. Mössbauer spectra measured at room temperature comprise central doublets of paramagnetic Fe3+, which decreased at 78 K and almost disappeared at 4.2 K, producing a series of hyperfine Zeeman sextets due to internal magnetic fields arising in valleriites. Magnetic measurements do not reveal antiferromagnetic transitions known for bornite. The specific structure and properties of valleriite are discussed in particular as a platform for composites of the 2D transition metal sulfide and hydroxide (mono)layers stacked by the electrical charges, promising for a variety of applications.
Superlattice Formation in Fatty Acid Monolayers on a Divalent Ion Subphase: Role of Chain Length, Temperature, and Subphase Concentration

We report the study of behenic acid Langmuir monolayers spread over chloride salts solutions of cadmium, lead, magnesium, or manganese. These monolayers were investigated by means of surface pressure−area isotherms and grazing incidence X-ray diffraction (GIXD). The effect of the concentration of cations in the subphase on the structure of the monolayers was probed at room temperature and for three different subphase pHs (5.5, 7.5, 10.5). A threshold in subphase concentration is detected for the formation of a superlattice structure corresponding to an inorganic organized layer in addition to the ordered behenic acid monolayer. This threshold is shown to strongly depend on the cation and the subphase pH. Above the threshold, the superstructure is independent of both the cation concentration and the pH. Below the threshold, the ions are disordered but induce a condensing effect on the fatty acid molecules, which is more or less pronounced depending on the ions. Moreover, the combination of isotherms and GI.
Clinical and laboratory importance of detecting Helicobacter pylori coccoid forms for the selection of treatment

Helicobacter pylori grows and multiplies in the gastrointestinal tract (GIT) in about half of the world’s population. The prevalence of diseases associated with this bacterium is steadily increasing, which makes it necessary to search for optimal therapy aimed at eradication of this bacterium. Such diseases, for example, include gastric ulcer (GU) and chronic gastritis (CG). Unfortunately, modern possibilities for eradication therapy do not always make it possible to cure patients, and relapses often occur if it is cured. Nowadays, a particular topical issue has arisen, which concerns the resistance of Helicobacter pylori to therapies, because the effectiveness of medication used in clinics decreases every year. One of the mechanisms favouring tolerance to antibiotics is the transformation into a different morphological form – coccoid. This form of the bacterium was discovered quite a long time ago. Nevertheless, the question of its importance in clinical practice remains open to this day. Modern studies are aimed at understanding the role of coccoid forms of H. pylori in the survival of the population of these bacteria and at clarifying their role in the pathogenesis of gastrointestinal diseases. It is not known whether it is necessary to evaluate the contamination of a given morphological form of a bacterium of the gastric mucosa in clinical practice and its influence on the development of diseases etc. This article presents an overview and analysis of modern ideas about H. pylori coccoid forms and answers to the main questions posed in the last 10 years regarding the study of coccoid forms. Additionally, our results present a comparison of expression of virulence factors in coccoid and spiral forms of H. pylori.