Miracle-dz/UniFAR-FTUs huggingface dataset:
Patients’ priorities around drug-resistant tuberculosis treatment: A multi-national qualitative study from Mongolia, South Africa and Georgia

ABSTRACT We conducted qualitative research exploring the treatment experience of people with DR-TB. We held nine focus group discussions with 57 adults undergoing/recently completed treatment for DR-TB in Georgia, Mongolia and South Africa. Translated transcripts were analysed using thematic analysis. We identified three higher order themes: (1) Treatment experience and the role of good relationships with healthcare providers: Treatment duration, pill burden and side-effects were challenging aspects of treatment. Side-effects/symptoms that were visible signs of illness were particularly troubling. Good relations with clinical staff helped combat fear and uncertainty regarding treatment. (2) Mental distress and opportunities for wellbeing: The shame, stigma and isolation people experienced as a result of their DR-TB diagnosis was an important cause of mental distress. No longer being infectious enabled people to resume work and socialising. Positive emotions emerged with good treatment outcomes. (3) Fear and worry along the treatment journey: Participants expressed fears about TB: infecting others; whether they would be able to endure treatment; side-effects; health consequences of treatment. Worries mostly disappeared with successful treatment. Alongside measuring side-effects, time to culture conversion and cure rates, future trials of DR-TB treatments should capture how quickly visible symptoms resolve, quality of life measures, and mental health outcomes.
Associations of neutral pH, low-GDP peritoneal dialysis solutions with patient survival, transfer to haemodialysis and peritonitis

ABSTRACT Background Peritoneal dialysis (PD) solutions containing low levels of glucose degradation products (GDPs) are associated with attenuation of peritoneal membrane injury and vascular complications. However, clinical benefits associated with neutral-pH, low-GDP (N-pH/L-GDP) solutions remain unclear. Methods Using data from the Australia and New Zealand Dialysis and Transplant Registry, we examined the associations between N-pH/L-GDP solutions and all-cause mortality, cause-specific mortality, transfer to haemodialysis (HD) for ≥30 days and PD peritonitis in adult incident PD patients in Australia and New Zealand between 1 January 2005 and 31 December 2020 using adjusted Cox regression analyses. Results Of 12 814 incident PD patients, 2282 (18%) were on N-pH/L-GDP solutions. The proportion of patients on N-pH/L-GDP solutions each year increased from 11% in 2005 to 33% in 2017. During the study period, 5330 (42%) patients died, 4977 (39%) experienced transfer to HD and 5502 (43%) experienced PD peritonitis. Compared with the use of conventional solutions only, the use of any form of N-pH/L-GDP solution was associated with reduced risks of all-cause mortality {adjusted hazard ratio [aHR] 0.67 [95% confidence interval (CI) 0.61–0.74]}, cardiovascular mortality [aHR 0.65 (95% CI 0.56–0.77)], infection-related mortality [aHR 0.62 (95% CI 0.47–0.83)] and transfer to HD [aHR 0.79 (95% CI 0.72–0.86)] but an increased risk of PD peritonitis [aHR 1.16 (95% CI 1.07–1.26)]. Conclusions Patients who received N-pH/L-GDP solutions had decreased risks of all-cause and cause-specific mortality despite an increased risk of PD peritonitis. Studies assessing the causal relationships are warranted to determine the clinical benefits of N-pH/L-GDP solutions.
Cryptography based on the Matrices

In this work we introduce a new method of cryptography based on the matrices over a finite field $\mathbb{F}_{q}$, were $q$ is a power of a prime number $p$. The first time we construct the matrix $M=\left( \begin{array}{cc} A_{1} & A_{2} \\ 0 & A_{3} \\ \end{array} \right) $ were \ $A_{i}$ \ with $i \in \{1, 2, 3 \}$ is the matrix of order $n$ \ in \ $\mathcal{M}(\mathbb{F}_{q})$ - the set of matrices with coefficients in $\mathbb{F}_{q}$ - and $0$ is the zero matrix of order $n$. We prove that $M^{l}=\left( \begin{array}{cc} A_{1}^{l} & (A_{2})_{l} \\ 0 & A_{3}^{l} \\ \end{array} \right) $ were $(A_{2})_{l}=\sum\limits_{k=0}^{l-1} A_{1}^{l-1-k}A_{2}A_{3}^{k}$ for all $l\in \mathbb{N}^{\ast}$. After we will make a cryptographic scheme between the two traditional entities Alice and Bob.
Soft sensor development for Mooney viscosity prediction in rubber mixing process based on GMMDJITGPR algorithm

In rubber mixing process, the key parameter (Mooney viscosity), which is used to evaluate the property of the product, can only be obtained with 4-6h delay offline. It is quite helpful for the industry, if the parameter can be estimate on line. Various data driven soft sensors have been used to prediction in the rubber mixing. However, it always not functions well due to the phase and nonlinear property in the process. The purpose of this paper is to develop an efficient soft sensing algorithm to solve the problem. Based on the proposed GMMD local sample selecting criterion, the phase information is extracted in the local modeling. Using the Gaussian local modeling method within Just-in-time (JIT) learning framework, nonlinearity of the process is well handled. Efficiency of the new method is verified by comparing the performance with various mainstream soft sensors, using the samples from real industrial rubber mixing process.
Ca2+‐activated K+ channels regulate cell volume in human glioblastoma cells

Glioblastoma (GBM), the most lethal form of brain tumors, bases its malignancy on the strong ability of its cells to migrate and invade the narrow spaces of healthy brain parenchyma. Cell migration and invasion are both critically dependent on changes in cell volume and shape driven by the transmembrane transport of osmotically important ions such as K+ and Cl−. However, while the Cl− channels participating in cell volume regulation have been clearly identified, the precise nature of the K+ channels involved is still uncertain. Using a combination of electrophysiological and imaging approaches in GBM U87‐MG cells, we found that hypotonic‐induced cell swelling triggered the opening of Ca2+‐activated K+ (KCa) channels of large and intermediate conductance (BKCa and IKCa, respectively), both highly expressed in GBM cells. The influx of Ca2+ mediated by the hypotonic‐induced activation of mechanosensitive channels was found to be a key step for opening both the BKCa and the IKCa channels. Finally, the activation of both KCa channels mediated by mechanosensitive channels was found to be essential for the development of the regulatory volume decrease following hypotonic shock. Taken together, these data indicate that KCa channels are the main K+ channels responsible for the volume regulation in U87‐MG cells.
G-type receptor-like kinase AsNIP43 interacts with rhizobia effector nodulation outer protein P and is required for symbiosis

Abstract In the Rhizobium-Legume symbiosis, the nodulation outer protein P (NopP) effector is one of the key regulators for rhizobial infection and nodule organogenesis. However, the molecular mechanism through which host legume plants sense NopP remains largely unknown. Here, we constructed an nopP deletion mutant of Mesorhizobium huakuii and found that nopP negatively regulates nodulation on Chinese milk vetch (Astragalus sinicus). Screening for NopP interacting proteins in host plants using the yeast 2-hybrid system identified NopP interacting protein 43 (AsNIP43), which encodes a G-type receptor-like kinase (LecRLK). The B-lectin domain at the N terminus of AsNIP43 was essential in mediating its interaction with NopP, which was confirmed in vitro and in vivo. Subcellular localization, co-localization, and gene expression analyses showed that AsNIP43 and NopP function tightly associated with earlier infection events. RNA interference (RNAi) knockdown of AsNIP43 expression by hairy root transformation led to decreased nodule formation. AsNIP43 plays a positive role in symbiosis, which was further verified in the model legume Medicago truncatula. Transcriptome analysis indicated that MtRLK (a homolog of AsNIP43 in M. truncatula) may function to affect defense gene expression and thus to regulate early nodulation. Taken together, we show that LecRLK AsNIP43 is a legume host target that interacts with rhizobia effector NopP is essential for rhizobial infection and nodulation.
Global, regional, and national burden of allergic disorders and their risk factors in 204 countries and territories, from 1990 to 2019: A systematic analysis for the Global Burden of Disease Study 2019

Asthma and atopic dermatitis (AD) are chronic allergic conditions, along with allergic rhinitis and food allergy and cause high morbidity and mortality both in children and adults. This study aims to evaluate the global, regional, national, and temporal trends of the burden of asthma and AD from 1990 to 2019 and analyze their associations with geographic, demographic, social, and clinical factors.
Identification of Staphylococcus aureus virulence-modulating RNA from transcriptomics data with machine learning

ABSTRACT The virulence factors of Staphylococcus aureus are tightly controlled by two-component systems (TCSs) and small RNA (sRNA). TCSs have been well studied over the past several decades, but our understanding of sRNA functions lags far behind that of TCS functions. Here, we studied the biological role of sRNA from 506 S. aureus RNA-seq datasets using independent component analysis (ICA). We found that a previously neglected sRNA, Sau-41, functions in the Agr system. Sau-41 is located within the PSMα operon and controlled by the Agr system. It was predicted to share 22-base complementarity with RNAIII, a major regulator of S. aureus virulence. The EMSA results demonstrated that Sau-41 directly binds to RNAIII. Furthermore, our results found that Sau-41 is capable of repressing S. aureus haemolysin activity by downregulating α-haemolysin and δ-toxin. The repression of α-haemolysin was attributed to the competition between the 5’ UTR of hla and Sau-41 for binding RNAIII. We observed that Sau-41 mitigated S. aureus virulence in an orthopaedic implant infection mouse model and alleviated osteolysis. Together, our results indicate that Sau-41 is a virulence-regulating RNA and suggest that Sau-41 might be involved in a negative feedback mechanism to control the Agr system. This work is a demonstration of using ICA in sRNA identification by mining high-throughput data and could be extended to other organisms as well.
Safety of nonthermal atmospheric pressure plasma for tooth bleaching evaluated in terms of microhardness and mineral content

The purpose of this study was to evaluate the influence of bleaching with nonthermal atmospheric pressure plasma and 15% hydrogen peroxide (HP) or 15% carbamide peroxide (CP). Sixty human enamel and dentin slabs were randomly assigned to six groups as follows: Group 1 was a control group and did not receive any treatment; Group 2 was exposed only to plasma, as a negative control; Group 3 was treated with 15% HP; Group 4 was treated with 15% HP plus plasma; Group 5 was treated with 15% CP alone; and Group 6 was treated with 15% CP plus plasma during 30 min bleaching treatments. A microhardness measurement was conducted according to a microhardness tester. The amount of calcium (Ca), phosphorus (P), chloride (Cl), sodium (Na), magnesium (Mg), and zinc (Zn) in the enamel and dentin was quantified with an electron probe microanalyzer (EPMA). The data were analyzed by using the Student’s t test and one-way analysis of variance (ANOVA), complemented by Tukey’s test. The statistical analysis did not show any significant differences in microhardness values and six mineral contents in all groups (p > 0.05). Therefore, we believe that the application of nonthermal atmospheric pressure plasma is a safe energy source for tooth bleaching.
Single‐cell RNA‐seq and bulk RNA‐seq explore the prognostic value of exhausted T cells in hepatocellular carcinoma

Abstract Hepatocellular carcinoma (HCC) remains a worldwide health problem. Mounting evidence indicates that exhausted T cells play a critical role in the progress and treatment of HCC. Therefore, a detailed characterisation of exhausted T cells and their clinical significance warrants further investigation in HCC. Based on the GSE146115, we presented a comprehensive single‐cell Atlas in HCC. Pseudo‐time analysis revealed that tumour heterogeneity progressively increased, and the exhausted T cells gradually appeared during tumour progression. Functional enrichment analysis revealed that the evolutionary process of exhausted T cells mainly contained the pathway of cadherin binding, proteasome, cell cycle, and T cell receptor regulation of apoptosis. In the International Cancer Genome Consortium database, we divided patients into three clusters with the T cell evolution‐associated genes. We found that the exhausted T cells are significantly related to poor outcomes through immunity and survival analysis. In The Cancer Genome Atlas database, the authors enrolled weighted gene co‐expression network analysis, univariate Cox analysis, and Lasso Cox analysis, then screened the 19 core genes in T cells evolution and built a robust prognostic model. This study offers a fresh view on evaluating the patients' outcomes from an exhausted T cells perspective and might help clinicians develop therapeutic systems.
INTERFLEX: Stata module to estimate multiplicative interaction models with diagnostics and visualization

interflex performs diagnostics and visualizations of multiplicative interaction models. Besides conventional linear interaction models, it provides two additional estimation strategies--linear regression based on pre-specified bins and locally linear regressions based on Gaussian kernel reweighting--to estimate the conditional marginal effect of a treatment variable on an outcome variable across different values of a moderating variable. These approaches relax the linear interaction effect assumption and safeguard against excessive extrapolation.
Generating candidates in global optimization algorithms using complementary energy landscapes.

Global optimization of atomistic structure relies on the generation of new candidate structures in order to drive the exploration of the potential energy surface (PES) in search of the global minimum energy structure. In this work, we discuss a type of structure generation, which locally optimizes structures in complementary energy (CE) landscapes. These landscapes are formulated temporarily during the searches as machine learned potentials (MLPs) using local atomistic environments sampled from collected data. The CE landscapes are deliberately incomplete MLPs that rather than mimicking every aspect of the true PES are sought to become much smoother, having only a few local minima. This means that local optimization in the CE landscapes may facilitate the identification of new funnels in the true PES. We discuss how to construct the CE landscapes and we test their influence on the global optimization of a reduced rutile SnO2(110)-(4 × 1) surface and an olivine (Mg2SiO4)4 cluster for which we report a new global minimum energy structure.
Allosteric modulator potentiates β2AR agonist–promoted bronchoprotection in asthma models

Asthma is a chronic inflammatory disease associated with episodic airway narrowing. Inhaled β2-adrenergic receptor (β2AR) agonists (β2-agonists) promote — with limited efficacy — bronchodilation in asthma. All β2-agonists are canonical orthosteric ligands that bind the same site as endogenous epinephrine. We recently isolated a β2AR-selective positive allosteric modulator (PAM), compound-6 (Cmpd-6), which binds outside of the orthosteric site and modulates orthosteric ligand functions. With the emerging therapeutic potential of G-protein coupled receptor allosteric ligands, we investigated the impact of Cmpd-6 on β2AR-mediated bronchoprotection. Consistent with our findings using human β2ARs, Cmpd-6 allosterically potentiated β2-agonist binding to guinea pig β2ARs and downstream signaling of β2ARs. In contrast, Cmpd-6 had no such effect on murine β2ARs, which lack a crucial amino acid in the Cmpd-6 allosteric binding site. Importantly, Cmpd-6 enhanced β2 agonist–mediated bronchoprotection against methacholine-induced bronchoconstriction in guinea pig lung slices, but — in line with the binding studies — not in mice. Moreover, Cmpd-6 robustly potentiated β2 agonist–mediated bronchoprotection against allergen-induced airway constriction in lung slices obtained from a guinea pig model of allergic asthma. Cmpd-6 similarly enhanced β2 agonist–mediated bronchoprotection against methacholine-induced bronchoconstriction in human lung slices. Our results highlight the potential of β2AR-selective PAMs in the treatment of airway narrowing in asthma and other obstructive respiratory diseases.
Genetic polymorphism and forensic efficiency of 21 autosomal STR loci from Shandong Han population in Northern China

Abstract Background Highly polymorphic autosomal STR loci are useful for understanding population structure better and for forensic application, however the non-CODIS STR loci in the Han population of Shandong, located in Northern China, are not well-characterised. Aim To investigate population genetic polymorphism and forensic efficiency of 21 autosomal STR loci from the Shandong Han population in Northern China and reveal the genetic relationships with other populations both at home and abroad. Subjects and methods In this study, population genetic data of 21 autosomal STR loci included in the Goldeneye DNA ID 22NC Kit that includes four CODIS loci and 17 non-CODIS loci were determined for 523 unrelated Han individuals in Shandong. Results Significant deviations from Hardy–Weinberg equilibrium were not observed. A total of 233 alleles were detected with allele frequencies ranging from 0.0010 to 0.3728. The combined power of discrimination was 0.99999999999999999999999990011134, and the combined power of exclusion was 0.99999999788131. Furthermore, in an analysis of population differentiation Nei’s standard genetic distance and multidimensional scaling analysis, which were conducted based on the overlapping 15 STR loci, revealed that the Shandong Han population was most closely related to populations in close geographic proximity. Conclusions This study demonstrated that the 21 autosomal STR loci included in the GoldeneyeTM DNA ID 22NC system are highly polymorphic and suitable for forensic identification and paternity testing in the Shandong Han population. Additionally, the present results enrich the population genetic database.
Ontogenetic change in effectiveness of chemical defence against different predators in Oxycarenus true bugs

Many prey species change their antipredator defence during ontogeny, which may be connected to different potential predators over the life cycle of the prey. To test this hypothesis, we compared reactions of two predator taxa – spiders and birds – to larvae and adults of two invasive true bug species, Oxycarenus hyalinipennis and Oxycarenus lavaterae (Heteroptera: Oxycarenidae) with life‐stage‐specific chemical defence mechanisms. The reactions to larvae and adults of both true bug species strikingly differed between the two predator taxa. The spiders were deterred by the defences of adult bugs, but the larval defences were ineffective against them. By contrast, birds attacked the larvae considerably less often than the adult bugs. The results indicate a predator‐specific ontogenetic change in defence effectiveness of both Oxycarenus species. The change in defence is likely linked to the life‐stage‐specific composition of secretions in both species: whereas secretions of larvae are dominated by unsaturated aldehydes, secretions of adults are rich in terpenoids, which probably serve dual function of defensive chemicals and pheromones. Our results highlight the variation in defence between different life stages and the importance of testing responses of different types of predators.
Urchin grazing of kelp gametophytes in warming oceans

Sea urchins can cause extensive damage to kelp forests, and their overgrazing can create extensive barren areas, leading to a loss of biodiversity. Barrens may persist when the recruitment of kelp, which occurs through the microscopic haploid gametophyte stage, is suppressed. However, the ecology of kelp gametophytes is poorly understood, and here we investigate if grazing by juvenile urchins on kelp gametophytes can suppress kelp recruitment and if this is exacerbated by climate change. We compared grazing of Ecklonia radiata gametophytes by two species of juvenile urchins, the tropical Tripneustes gratilla and the temperate Centrostephanus rodgersii, at winter (19°C), summer (23°C), and ocean warming (26°C) temperatures for the low‐latitude range edge of E. radiata, which is vulnerable to ocean warming. We examined the rate of recovery of gametophytes following grazing and determined whether they survived and formed sporophytes after ingestion by sea urchins. Both T. gratilla and C. rodgersii grazed E. radiata gametophytes, reducing their abundance compared to no grazing controls. Surprisingly, temperature did not influence grazing rates, but gametophytes did not recover from grazing in the ocean warming (26°C) treatment. Gametophytes survived ingestion by both species of sea urchin and formed sporophytes after ingestion by T. gratilla, but not C. rodgersii. These results suggest complex grazer–gametophyte interactions, in which both negative (reduced abundance and poor recovery with warming) and positive (facilitated recruitment) effects are possible. Small grazers may play a more important role in kelp ecosystem function than previously thought and should be considered in our understanding of alternate stable states.
Improving access to transcatheter aortic valve implantation across Europe by restructuring cardiovascular services: An expert council consensus statement

Transcatheter aortic valve implantation (TAVI) is recommended for a growing range of patients with severe aortic stenosis in the European Society of Cardiology and European Association for Cardio‐Thoracic Surgery (ESC/EACTS) 2021 Guidelines update. However, guideline implementation programs are needed to ensure the application of clinical recommendations which will favorably influence disease outcomes. An Expert Council was convened to identify whether cardiology services across Europe are set up to address the growing needs of patients with severe aortic stenosis for increased access to TAVI by identifying the key challenges faced in growing TAVI programs and mapping associated solutions. Wide variation exists across Europe in terms of TAVI availability and capacity to deliver the increased demand for TAVI in different countries. The recommendations of this Expert Council focus on the short‐to‐medium‐term aspects where the most immediate, actionable impact can be achieved. The focus on improving procedural efficiency and optimizing the patient pathway via clinical practice and patient management demonstrates how to mitigate the current major issues of shortfall in catheterization laboratory, workforce, and bed capacity. Procedural efficiencies may be achieved through steps including streamlined patient assessment, the benchmarking of standards for minimalist procedures, standardized approaches around patient monitoring and conduction issues, and the implementation of nurse specialists and dedicated TAVI coordinators to manage organization, logistics, and early mobilization. Increased collaboration with wider stakeholders within institutions will support successful TAVI uptake and improve patient and economic outcomes. Further, increased education, collaboration, and partnership between cardiology centers will facilitate sharing of expertise and best clinical practice.