Miracle-dz/UniFAR-FTUs huggingface dataset:
The association of household food insecurity and HIV infection with common mental disorders among newly diagnosed tuberculosis patients in Botswana

Abstract Objective: To determine the association between food insecurity and HIV infection with depression and anxiety among new tuberculosis (TB) patients. Design: Our cross-sectional study assessed depression, anxiety and food insecurity with Patient Health Questionnaire (PHQ-9), Zung Anxiety Self-Assessment Scale (ZUNG) and Household Food Insecurity Access Scale, respectively. Poisson regression models with robust variance were used to examine correlates of depression (PHQ-9 ≥ 10) and anxiety (ZUNG ≥ 36). Setting: Gaborone, Botswana. Participants: Patients who were newly diagnosed with TB. Results: Between January and December 2019, we enrolled 180 TB patients from primary health clinics in Botswana. Overall, 99 (55·0 %) were HIV positive, 47 (26·1 %), 85 (47·2 %) and 69 (38·5 %) indicated depression, anxiety and moderate to severe food insecurity, respectively. After adjusting for potential confounders, food insecurity was associated with a higher prevalence of depression (adjusted prevalence ratio (aPR) = 2·30; 95 % CI 1·40, 3·78) and anxiety (aPR = 1·41; 95 % CI 1·05, 1·91). Prevalence of depression and anxiety was similar between HIV-infected and HIV-uninfected participants. Estimates remained comparable when restricted to HIV-infected participants. Conclusions: Mental disorders may be affected by food insecurity among new TB patients, regardless of HIV status.
Automated Partitioning of Data-Parallel Kernels using Polyhedral Compilation

GPUs are well-established in domains outside of computer graphics, including scientific computing, artificial intelligence, data warehousing, and other computationally intensive areas. Their execution model is based on a thread hierarchy and suggests that GPU workloads can generally be safely partitioned along the boundaries of thread blocks. However, the most efficient partitioning strategy is highly dependent on the application’s memory access patterns, and usually a tedious task for programmers in terms of decision and implementation. We leverage this observation for a concept that automatically compiles single-GPU code to multi-GPU applications. We present the idea and a prototype implementation of this concept and validate both on a selection of benchmarks. In particular, we illustrate our use of 1) polyhedral compilation to model memory accesses, 2) a runtime library to track GPU buffers and identify stale data, 3) IR transformations for the partitioning of GPU kernels, and 4) a custom preprocessor that rewrites CUDA host code to utilize multiple GPUs. This work focuses on applications with regular access patterns on global memory and the toolchain to fully automatically compile CUDA applications without requiring any user intervention. Our benchmarks compare single-device CUDA binaries produced by NVIDIA’s reference compiler to binaries produced for multiple GPUs using our toolchain. We report speedups of up to 12.4x for 16 Kepler-class GPUs.
Influence of Ambidextrous Learning on Eco-Innovation Performance of Startups: Moderating Effect of Top Management’s Environmental Awareness

Ecological innovation is an inevitable trend for firms to enhance competitiveness and sustainably operate in the context of green economy. The previous literature has rarely discussed the influence of ambidextrous learning on the eco-innovation performance of startups and ignored the moderating effect of top management’s environmental awareness from the perspective of microscopic psychology. We have conducted a questionnaire survey on 212 firms established within 4 years in the Pearl River Delta of China, using the structure mode and the PROCESS by Hayes (2013) to analyze the influence of ambidextrous learning, such as exploratory learning and exploitative learning, by startups on eco-innovation performance and verify the moderating effect of top management’s environmental awareness. The results show that exploratory learning and exploitative learning have a positive and significant influence on eco-innovation performance, indicating that the organizational learning of startups is conducive to improving eco-innovation performance; under the moderating effect of top management’s environmental awareness, the influence of exploratory learning and exploitative learning on eco-innovation performance may differ. The results also show that in the process of organizing ambidextrous learning, startups should help raise the environmental awareness of top management to improve the eco-innovation performance, thus providing guidance for startups to carry out eco-innovation activities and for local governments to make decisions on green economy.
In silico Design of Phl p 6 Variants With Altered Fold-Stability Significantly Impacts Antigen Processing, Immunogenicity and Immune Polarization

Introduction: Understanding, which factors determine the immunogenicity and immune polarizing properties of proteins, is an important prerequisite for designing better vaccines and immunotherapeutics. While extrinsic immune modulatory factors such as pathogen associated molecular patterns are well-understood, far less is known about the contribution of protein inherent features. Protein fold-stability represents such an intrinsic feature contributing to immunogenicity and immune polarization by influencing the amount of peptide-MHC II complexes (pMHCII). Here, we investigated how modulation of the fold-stability of the grass pollen allergen Phl p 6 affects its ability to stimulate immune responses and T cell polarization. Methods: MAESTRO software was used for in silico prediction of stabilizing or destabilizing point mutations. Mutated proteins were expressed in E. coli, and their thermal stability and resistance to endolysosomal proteases was determined. Resulting peptides were analyzed by mass spectrometry. The structure of the most stable mutant protein was assessed by X-ray crystallography. We evaluated the capacity of the mutants to stimulate T cell proliferation in vitro, as well as antibody responses and T cell polarization in vivo in an adjuvant-free BALB/c mouse model. Results: In comparison to wild-type protein, stabilized or destabilized mutants displayed changes in thermal stability ranging from −5 to +14°. While highly stabilized mutants were degraded very slowly, destabilization led to faster proteolytic processing in vitro. This was confirmed in BMDCs, which processed and presented the immunodominant epitope from a destabilized mutant more efficiently compared to a highly stable mutant. In vivo, stabilization resulted in a shift in immune polarization from TH2 to TH1/TH17 as indicated by higher levels of IgG2a and increased secretion of TNF-α, IFN-γ, IL-17, and IL-21. Conclusion: MAESTRO software was very efficient in detecting single point mutations that increase or reduce fold-stability. Thermal stability correlated well with the speed of proteolytic degradation and presentation of peptides on the surface of dendritic cells in vitro. This change in processing kinetics significantly influenced the polarization of T cell responses in vivo. Modulating the fold-stability of proteins thus has the potential to optimize and polarize immune responses, which opens the door to more efficient design of molecular vaccines.
Partial Amniote Sex Chromosomal Linkage Homologies Shared on Snake W Sex Chromosomes Support the Ancestral Super-Sex Chromosome Evolution in Amniotes

Squamate reptile chromosome 2 (SR2) is thought to be an important remnant of an ancestral amniote super-sex chromosome, but a recent study showed that the Siamese cobra W sex chromosome is also a part of this larger ancestral chromosome. To confirm the existence of an ancestral amniote super-sex chromosome and understand the mechanisms of amniote sex chromosome evolution, chromosome maps of two snake species [Russell’s viper: Daboia russelii (DRU) and the common tiger snake: Notechis scutatus (NSC)] were constructed using bacterial artificial chromosomes (BACs) derived from chicken and zebra finch libraries containing amniote sex chromosomal linkages. Sixteen BACs were mapped on the W sex chromosome of DRU and/or NSC, suggesting that these BACs contained a common genomic region shared with the W sex chromosome of these snakes. Two of the sixteen BACs were co-localized to DRU2 and NSC2, corresponding to SR2. Prediction of genomic content from all BACs mapped on snake W sex chromosomes revealed a large proportion of long interspersed nuclear element (LINE) and short interspersed nuclear element (SINE) retrotransposons. These results led us to predict that amplification of LINE and SINE may have occurred on snake W chromosomes during evolution. Genome compartmentalization, such as transposon amplification, might be the key factor influencing chromosome structure and differentiation. Multiple sequence alignments of all BACs mapped on snake W sex chromosomes did not reveal common sequences. Our findings indicate that the SR2 and snake W sex chromosomes may have been part of a larger ancestral amniote super-sex chromosome, and support the view of sex chromosome evolution as a colorful myriad of situations and trajectories in which many diverse processes are in action.
Differential Host Pro-Inflammatory Response to Mycobacterial Cell Wall Lipids Regulated by the Mce1 Operon

The cell wall of wild-type (WT) Mycobacterium tuberculosis (Mtb), an etiologic agent of tuberculosis (TB) and a Mtb strain disrupted in a 13-gene operon mce1 (Δmce1) varies by more than 400 lipid species. Here, we examined Mtb lipid-induced response in murine macrophage, as well as in human T-cell subpopulations in order to gain an insight into how changes in cell wall lipid composition may modulate host immune response. Relative to WT Mtb cell wall lipids, the non-polar lipid extracts from Δmce1 enhanced the mRNA expression of lipid-sense nuclear receptors TR4 and PPAR-γ and dampened the macrophage expression of genes encoding TNF-α, IL-6, and IL-1β. Relative to untreated control, WT lipid-pre-stimulated macrophages from healthy individuals induced a higher level of CD4−CD8− double negative T-cells (DN T-cells) producing TNF-α. Conversely, compared to WT, stimulation with Δmce1 lipids induced higher mean fluorescence intensity (MFI) in IL-10-producing DN T cells. Mononuclear cells from TB patients stimulated with WT Mtb lipids induced an increased production of TNF-α by CD8+ lymphocytes. Taken together, these observations suggest that changes in mce1 operon expression during a course of infection may serve as a strategy by Mtb to evade the host pro-inflammatory responses.
WhatsApp and Google Drive Influence on Pre-service Students’ Learning

The use of technology and all that it entails, such as applications and social networks, has led to a transformation of education in all aspects. Communication and the monitoring of training processes are being transformed through these new elements gradually incorporated into the classrooms. The aim of the study is to analyze the impact of WhatsApp and Google Drive on the monitoring of training practices among pre-service students using a traditional, face-to-face methodology. A quasi-experimental design was carried out on a sample of 123 Spanish pre-service students. The data were collected by means of a questionnaire. The results show that the follow-up of external practices of future teachers using WhatsApp and Google Drive is effective in comparison with the face-to-face follow-up, although no significant differences are shown in the students’ grades. Conclusions show that applying a monitoring method with these technological tools leads to an increase in students’ motivation mainly as it allows a more direct interaction between the teacher and the student. It is important to select the monitoring method and the target student in the didactic development. Hence, these educational applications enable active learning where the learner is the main protagonist and can be supported and monitored.
A Combinatorial Reporter Set to Visualize the Membrane Contact Sites Between Endoplasmic Reticulum and Other Organelles in Plant Cell

The membrane contact sites (MCSs) enable interorganelle communication by associating organelles at distances of tens of nanometers over extended membrane surfaces and serve to maintain cellular homeostasis through efficient exchange of metabolites, lipid, and calcium between organelles, organelle fission, and movement. Most MCSs and a growing number of tethering proteins especially those involved in mediating the junctions between endoplasmic reticulum (ER) and other organelles have been extensively characterized in mammal and yeast. However, the studies of plant MCSs are still at stages of infancy, at least one reason might be due to the lack of bona fide markers for visualizing these membrane junctions in plant cells. In this study, a series of genetically encoded reporters using split super-folder GFP protein were designed to detect the possible MCSs between ER and three other cellular compartments including chloroplast, mitochondria and plasma membrane (PM) in plant cell. By expressing these genetically encoded reporter in Arabidopsis protoplasts as well as Nicotiana benthamiana leaf, we could intuitively observe the punctate signal surrounding chloroplast upon expression of ER-chloroplast MCS reporter, punctate signal of ER-mitochondria MCS reporter and punctate signal close to the PM upon expression of ER-PM MCS reporter. We also showed that the ER-chloroplast MCSs were dynamic structures that undergo active remodeling with concomitant occurrence of chloroplast dysfunction inside plant cells. This study demonstrates that ER associates with various organelles in close proximity in plant cells and provides tools that might be applicable for visualizing MCSs in plants.
Otic Neurogenesis Is Regulated by TGFβ in a Senescence-Independent Manner

Cellular senescence has classically been associated with aging. Intriguingly, recent studies have also unraveled key roles for senescence in embryonic development, regeneration, and reprogramming. Developmental senescence has been reported during embryonic development in different organisms and structures, such as the endolymphatic duct during inner ear development of mammals and birds. However, there is no study addressing the possible role of senescence on otic neurogenesis. TGFβ/SMAD is the best-known pathway linked to the induction of developmentally programmed cell senescence. Here, we studied if TGFβ2 induces cellular senescence during acoustic-vestibular-ganglion (AVG) formation. Using organotypic cultures of AVG, and characterizing different stages of otic neurogenesis in the presence of TGFβ2 and a selective TGF-β receptor type-I inhibitor, we show that TGFβ2 exerts a powerful action in inner ear neurogenesis but, contrary to what we recently observed during endolymphatic duct development, these actions are independent of cellular senescence. We show that TGFβ2 reduces proliferation, and induces differentiation and neuritogenesis of neuroblasts, without altering cell death. Our studies highlight the roles of TGFβ2 and cellular senescence in the precise regulation of cell fate within the developing inner ear and its different cell types, being their mechanisms of action highly cell-type dependent.
A Deep Network Model on Dynamic Functional Connectivity With Applications to Gender Classification and Intelligence Prediction

Increasing evidence has suggested that the dynamic properties of functional brain networks are related to individual behaviors and cognition traits. However, current fMRI-based approaches mostly focus on statistical characteristics of the windowed correlation time course, potentially overlooking subtle time-varying patterns in dynamic functional connectivity (dFC). Here, we proposed the use of an end-to-end deep learning model that combines the convolutional neural network (CNN) and long short-term memory (LSTM) network to capture temporal and spatial features of functional connectivity sequences simultaneously. The results on a large cohort (Human Connectome Project, n = 1,050) demonstrated that our model could achieve a high classification accuracy of about 93% in a gender classification task and prediction accuracies of 0.31 and 0.49 (Pearson’s correlation coefficient) in fluid and crystallized intelligence prediction tasks, significantly outperforming previously reported models. Furthermore, we demonstrated that our model could effectively learn spatiotemporal dynamics underlying dFC with high statistical significance based on the null hypothesis estimated using surrogate data. Overall, this study suggests the advantages of a deep learning model in making full use of dynamic information in resting-state functional connectivity, and highlights the potential of time-varying connectivity patterns in improving the prediction of individualized characterization of demographics and cognition traits.
Health-Related Quality of Life, Family Climate and Sense of Coherence of Families in Which a Parent Has Deafblindness

Introduction: The consequences of living with deafblindness can be vast and have been described as concerning difficulties with communication, restrictions in the activities of daily living and a lack of independence. Deafblindness has also been associated with poor health-related quality of life. Little is known about parenting when having deafblindness or how the health and family climate of families in which a parent has deafblindness are affected. Aim: The aim of the study was to describe the health-related quality of life, sense of coherence and family climate in families where a parent has a deafblindness. Methods: A total of 38 individuals, of which 14 were parents with deafblindness and 6 were partners to the parent with deafblindness, and 18 children, were included. The participants answered questionnaires about their health-related quality of life, family climate and sense of coherence (comprehensibility, manageability, and meaningfulness). The Swedish age-relevant versions of the questionnaires were used. Due to the small number of participants, descriptive statistics were used to explore the results from the questionnaires. Results: The results revealed a pattern indicating that the health-related quality of life was affected, parents with deafblindness reported the poorest health-related quality of life. Sense of coherence was reported by all the family members as either moderate or low. The Family climate questionnaire revealed the positive aspect of closeness across family members, however negative aspects of chaos and expressiveness in the families were reported, mainly by, but not restricted to, the parents with deafblindness. Discussion: This study includes a small sample, too small to draw far-reaching conclusions. However, some interesting results need to be highlighted and discussed. When considering the family as a system, it is reasonable to assume that the family members contribute in different ways to how health and wellbeing is experienced in the family. Deafblindness is a unique disability that affects not only the individual but also the whole family. This fact needs to be considered when support is offered to individuals with deafblindness. All members of families where a parent has deafblindness have to be asked about their needs and about how they experience the situation.
Classification of Muscle-Invasive Bladder Cancer Based on Immunogenomic Profiling

There is a significant heterogeneity in the immunotherapeutic responsiveness of each muscle-invasive bladder cancer (MIBC) patient. In our research, we aimed to identify a novel classification of MIBC based on immunogenomic profiling that may facilitate the reasonable stratification of prognosis and response to immunotherapy. The single-sample gene-set enrichment analysis (ssGSEA) was used to analyze the RNA-seq data of 29 important immune signatures from TCGA. Unsupervised hierarchical clustering was performed to identify an immunogenomic classification of MIBC. Then, we assessed the features of the classification in prognosis, immune infiltration, tumor-infiltration lymphocytes, HLA genes, and PD-L1 expression level. A total of 399 MIBC samples were included and three subtypes named Immunity_High, Immunity_Medium, and Immunity_Low were identified. The Immunity_High had a significant advantage in overall survival over the Immunity_Medium and Immunity_Low (p = 0.046 and p = 0.024). From Immunity_Low to Immunity_High, immune cell infiltration and stromal content showed an upward trend (p < 0.001). Meanwhile, Immunity_High was associated with a significantly higher proportion of TILs including dendritic cells resting, macrophages M1, mast cells resting, T cells CD4 memory activated, and T cells CD8+. And the expression levels of all HLA genes and PD-L1 of Immunity_High were the highest, consistent (p < 0.001). Two hundred ninety eight MIBC patients treated with immunotherapy from the IMvigor210 were included to form an independent validation cohort to verify the robustness of immunogenomic classification and the ability to predict the response to immunotherapy. This classification had potential clinical implications for predicting prognosis and immunotherapeutic responsiveness of MIBC patients.
The Role of 68Ga-PSMA Positron Emission Tomography/Computerized Tomography for Preoperative Lymph Node Staging in Intermediate/High Risk Patients With Prostate Cancer: A Diagnostic Meta-Analysis

Purpose: To evaluate the accuracy of 68Ga-PSMA positron emission tomography/computerized tomography (PET/CT) for preoperative lymph node staging using histopathological results of pelvic lymph node dissection (PLND) as reference standard in patients with intermediate/high risk of prostate cancer. Material and Methods: A systematic search of PubMed, Embase, and the Cochrane Library was completed up to May 2020. We included studies investigating accuracy of 68Ga-PSMA PET/CT in primary lymph node staging before radical prostatectomy and PLND. The pooled sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV), diagnostic odds ratio (DOR), and the summary receiver operating characteristic (SROC) curve with an area under the curve (AUC) were synthesized. Results: Eleven studies comprising 904 patients were identified. Based on per-patient analysis, the pooled sensitivity and specificity reached 0.63 (95% CI: 0.46–0.78) and 0.93 (95% CI: 0.88–0.96), respectively, with the DOR of 22 (95% CI: 10–47). An overall accuracy was revealed by the SROC curve with AUC of 0.91 (95% CI: 0.88–0.93). Using the lymph node as unit, the pooled sensitivity and specificity were 0.70 (95% CI: 0.49–0.85) and 0.99 (95% CI: 0.96–1.00), respectively. And the DOR reached 167 (95% CI: 40–695) with an AUC of 0.96 (95% CI: 0.94–0.98). The pooled PPV and NPV all reached above 0.8 on basis of per-patient or per-node analysis. Conclusions: 68Ga-PSMA PET/CT represented as a promising test for preoperative lymph node staging and patients without lymph node metastatic status can rarely be misdiagnosed. However, its sensitivity ought to be improved before forgoing PLND.
Bioorthogonal Non-canonical Amino Acid Tagging Combined With Flow Cytometry for Determination of Activity in Aquatic Microorganisms

In this study, we have combined bioorthogonal non-canonical amino acid tagging (BONCAT) and flow cytometry (FCM) analysis, and we demonstrate the applicability of the method for marine prokaryotes. Enumeration of active marine bacteria was performed by combining the DNA stain SYBR Green with detection of protein production with BONCAT. After optimization of incubation condition and substrate concentration on monoculture of Escherichia coli, we applied and modified the method to natural marine samples. We found that between 10 and 30% of prokaryotes in natural communities were active. The method is replicable, fast, and allow high sample throughput when using FCM. We conclude that the combination of BONCAT and FCM is an alternative to current methods for quantifying active populations in aquatic environments.