Miracle-dz/UniFAR-FTUs huggingface dataset:
Beyond isolation: OS verification as a foundation for correct applications

Verified systems software has generally had to assume the correctness of the operating system and its provided services (like networking and the file system). Even though there exist verified operating systems and file systems, the specifications for these components do not compose with applications to produce a fully verified high-performance software stack. In this position paper, we lay out our vision for what it would look like to have a verified OS with verified applications, all with good multi-core performance. We've explored a part of the verification by proving a page table correct already, but the larger goal is to lay out a vision for an ambitious project that supports an application verified from its high-level specification down to the hardware.
The Cell Wall Integrity MAP Kinase Signaling Pathway Is Required for Development, Pathogenicity, and Stress Adaption of the Pepper Anthracnose Fungus Colletotrichum scovillei

Abstract The cell wall integrity (CWI) signaling pathway plays important roles in the dissemination and infection of several plant pathogenic fungi. However, its roles in the pepper fruit anthracnose fungus Colletotrichum scovillei remain uninvestigated. In this study, the major components of the CWI signaling pathway—CsMCK1 (MAPKKK), CsMKK1 (MAPKK), and CsMPS1 (MAPK)—were functionally characterized in C. scovillei via homology-dependent gene replacement. The ΔCsmck1, ΔCsmkk1, and ΔCsmps1 mutants showed impairments in fungal growth, conidiation, and tolerance to CWI and salt stresses. Moreover, ΔCsmck1, ΔCsmkk1, and ΔCsmps1 failed to develop anthracnose disease on pepper fruits due to defects in appressorium formation and invasive hyphae growth. These results suggest that CsMCK1, CsMKK1, and CsMPS1 play important roles in mycelial growth, conidiation, appressorium formation, plant infection, and stress adaption of C. scovillei. These findings will contribute to a better understanding of the roles of the CWI signaling pathway in the development of pepper fruit anthracnose disease.
Designing meaningful continuous representations of T cell receptor sequences with deep generative models

T Cell Receptor (TCR) antigen binding underlies a key mechanism of the adaptive immune response yet the vast diversity of TCRs and the complexity of protein interactions limits our ability to build useful low dimensional representations of TCRs. To address the current limitations in TCR analysis we develop a capacity-controlled disentangling variational autoencoder trained using a dataset of approximately 100 million TCR sequences, that we name TCR-VALID. We design TCR-VALID such that the model representations are low-dimensional, continuous, disentangled, and sufficiently informative to provide high-quality TCR sequence de novo generation. We thoroughly quantify these properties of the representations, providing a framework for future protein representation learning in low dimensions. The continuity of TCR-VALID representations allows fast and accurate TCR clustering, benchmarked against other state-of-the-art TCR clustering tools and pre-trained language models.
Associations of sport participation with subjective well-being: a study consisting of a sample of Chinese school-attending students

Purpose Past studies have illustrated that the impact of sports participation on school-attending students’ well-being plays a significant role in the life course of adolescence, which is a golden period for developing sound psychological qualities. However, the relationship between sports participation and subjective well-being is not clear, particularly in Chinese primary and middle schools. Therefore, the current study was aimed to explore the relationship between sports participation and subjective well-being in elementary and middle schools in China. Method All involved children and adolescents were asked to conduct a self-report of their sociodemographic factors (e.g., sex, grade, and age), independence, and outcomes. The survey involved a two-stage sampling design (district school). Besides, in order to examine the relationship between participation in sports and subjective well-being, a self-report questionnaire was used. Logistic regression with 95% confidence interval and odds ratios (ORs), was conducted to investigate the relationship between sports participation and subjective well-being. Results A total of 67,281 participants in total provided complete data for the final analysis of the current study. The percentage of boys and girls was 51.9% and 48.1%, namely. The current study found that compared with children who never participate in sports, those children who participated sports in 1–3 times a month, 1–2 times a week, and 3 times a week and above were more likely to enjoy better well-being. Compared with children who never participate in sports, those children who in every grade participated sports in 1–3 times a month, 1–2 times a week, and 3 times a week and above were more likely to achieve better well-being. Conclusion Our current study offered the positive effect of sports participation on children and adolescents’ subjective well-being. For schools and governments, further studies are needed to focus on sports participation and positive feedback on adolescents’ mental health, and the three parties’ endeavors should be intervened.
The neural substrates responsible for food odor processing: an activation likelihood estimation meta-analysis

In many species including humans, food odors appear to play a distinct role when compared with other odors. Despite their functional distinction, the neural substrates responsible for food odor processing remain unclear in humans. This study aimed to identify brain regions involved in food odor processing using activation likelihood estimation (ALE) meta-analysis. We selected olfactory neuroimaging studies conducted with sufficient methodological validity using pleasant odors. We then divided the studies into food and non-food odor conditions. Finally, we performed an ALE meta-analysis for each category and compared the ALE maps of the two categories to identify the neural substrates responsible for food odor processing after minimizing the confounding factor of odor pleasantness. The resultant ALE maps revealed that early olfactory areas are more extensively activated by food than non-food odors. Subsequent contrast analysis identified a cluster in the left putamen as the most likely neural substrate underlying food odor processing. In conclusion, food odor processing is characterized by the functional network involved in olfactory sensorimotor transformation for approaching behaviors to edible odors, such as active sniffing.
Plastome phylogenomics reveals an early Pliocene North- and Central America colonization by long-distance dispersal from South America of a highly diverse bromeliad lineage

Understanding the spatial and temporal frameworks of species diversification is fundamental in evolutionary biology. Assessing the geographic origin and dispersal history of highly diverse lineages of rapid diversification can be hindered by the lack of appropriately sampled, resolved, and strongly supported phylogenetic contexts. The use of currently available cost-efficient sequencing strategies allows for the generation of a substantial amount of sequence data for dense taxonomic samplings, which together with well-curated geographic information and biogeographic models allow us to formally test the mode and tempo of dispersal events occurring in quick succession. Here, we assess the spatial and temporal frameworks for the origin and dispersal history of the expanded clade K, a highly diverse Tillandsia subgenus Tillandsia (Bromeliaceae, Poales) lineage hypothesized to have undergone a rapid radiation across the Neotropics. We assembled full plastomes from Hyb-Seq data for a dense taxon sampling of the expanded clade K plus a careful selection of outgroup species and used them to estimate a time- calibrated phylogenetic framework. This dated phylogenetic hypothesis was then used to perform biogeographic model tests and ancestral area reconstructions based on a comprehensive compilation of geographic information. The expanded clade K colonized North and Central America, specifically the Mexican transition zone and the Mesoamerican dominion, by long-distance dispersal from South America at least 4.86 Mya, when most of the Mexican highlands were already formed. Several dispersal events occurred subsequently northward to the southern Nearctic region, eastward to the Caribbean, and southward to the Pacific dominion during the last 2.8 Mya, a period characterized by pronounced climate fluctuations, derived from glacial–interglacial climate oscillations, and substantial volcanic activity, mainly in the Trans-Mexican Volcanic Belt. Our taxon sampling design allowed us to calibrate for the first time several nodes, not only within the expanded clade K focal group but also in other Tillandsioideae lineages. We expect that this dated phylogenetic framework will facilitate future macroevolutionary studies and provide reference age estimates to perform secondary calibrations for other Tillandsioideae lineages.
Atrial arrhythmias following lung transplant: a single pediatric center experience

Background Outcomes after lung transplant (LTx) in children have slowly improved. Although atrial arrhythmia (AA) is a common and adverse complication following LTx among adults, there is limited data on pediatric recipients. We detail our pediatric single-center experience while providing further insights on occurrence and management of AA following LTx. Methods A retrospective analysis of LTx recipients at a pediatric LTx program from 2014 to 2022 was performed. We investigated timing of occurrence and management of AA following LTx, and its effect on post-LTx outcome. Results Three out of nineteen (15%) pediatric LTx recipients developed AA. The timing of occurrence was 9–10 days following LTx. Those patients in the older age group (age >12 years old) were the only ones who developed AA. Developing AA did not have a negative effect on hospital stay duration or short-term mortality. All LTx recipients with AA were discharged home on therapy that was discontinued at 6 months for those who was on mono-therapy without recurrence of AA. Conclusions AA is an early post-operative complication in older children and younger adults undergoing LTx at a pediatric center. Early recognition and aggressive management can mitigate any morbidity or mortality. Future investigations should explore factors that place this population at risk for AA in order to prevent this complication post-operatively.
Two plant-associated Bacillus velezensis strains selected after genome analysis, metabolite profiling, and with proved biocontrol potential, were enhancing harvest yield of coffee and black pepper in large field trials

Elimination of chemically synthesized pesticides, such as fungicides and nematicides, in agricultural products is a key to successful practice of the Vietnamese agriculture. We describe here the route for developing successful biostimulants based on members of the Bacillus subtilis species complex. A number of endospore-forming Gram-positive bacterial strains with antagonistic action against plant pathogens were isolated from Vietnamese crop plants. Based on their draft genome sequence, thirty of them were assigned to the Bacillus subtilis species complex. Most of them were assigned to the species Bacillus velezensis. Whole genome sequencing of strains BT2.4 and BP1.2A corroborated their close relatedness to B. velezensis FZB42, the model strain for Gram-positive plant growth-promoting bacteria. Genome mining revealed that at least 15 natural product biosynthesis gene clusters (BGCs) are well conserved in all B. velezensis strains. In total, 36 different BGCs were identified in the genomes of the strains representing B. velezensis, B. subtilis, Bacillus tequilensis, and Bacillus. altitudinis. In vitro and in vivo assays demonstrated the potential of the B. velezensis strains to enhance plant growth and to suppress phytopathogenic fungi and nematodes. Due to their promising potential to stimulate plant growth and to support plant health, the B. velezensis strains TL7 and S1 were selected as starting material for the development of novel biostimulants, and biocontrol agents efficient in protecting the important Vietnamese crop plants black pepper and coffee against phytopathogens. The results of the large-scale field trials performed in the Central Highlands in Vietnam corroborated that TL7 and S1 are efficient in stimulating plant growth and protecting plant health in large-scale applications. It was shown that treatment with both bioformulations resulted in prevention of the pathogenic pressure exerted by nematodes, fungi, and oomycetes, and increased harvest yield in coffee, and pepper.
Effect of fermentation using different lactic acid bacteria strains on the nutrient components and mineral bioavailability of soybean yogurt alternative

Introduction Analysis of the composition of yogurt alternatives (YAs) during fermentation provides critical information for evaluating its quality and nutritional attributes. Method We investigated the effects of homotypic (HO) and heterotypic (HE) lactic acid bacteria on the nutritional and mineral bioavailabilities of soybean YA (SYA) during fermentation. Result The acidic amino acid (Glu, Asp) and organic acid contents in HO-fermented YA were increased from 2.93, 1.71, and 7.43 mg/100 g to 3.23, 1.82, and 73.47 mg/100 g, respectively. Moreover, both HO and HE lactic acid bacteria fermentation enhanced mineral absorptivity. They altered the molecular speciation of minerals from a large molecular type (2,866 Da) to a small molecular type (1,500 Da), which was manifested in a time-dependent manner. Furthermore, YA substantially increased the bone mass in a zebrafish osteoporosis model, further highlighting the potential of lactic acid bacterial fermentation for mineral bioavailability. Discussion This study provides a foundation for understanding the effects of fermentation conditions on the composition and bioavailability of minerals in YA and can assist in its production.
What happens when a whole-school health promotion research trial ends? a case study of the SEHER program in India

Background Health promotion interventions that are developed and evaluated by researchers and other external providers are at risk of not being sustained beyond the initial implementation period. When delivered by a lay school health worker, the SEHER study of a whole-school health promotion intervention in Bihar, India was found to be feasible, acceptable and effective in improving school climate and student health behaviors. The objective of this case study is to describe the decision-making processes, barriers, and enablers to continuing the SEHER intervention following its official closure. Methods For this exploratory qualitative case study, data were collected from four government-run secondary schools, two of which continued SEHER and two of which discontinued it after official closure. Thirteen school staff were interviewed, and 100 girls and boys (aged 15–18 years old) participated in eight focus groups discussing their experiences of the process of continuing the intervention (or discontinuing) following its official closure. Thematic analysis was conducted in NVivo 12 using grounded theory. Results No school sustained the intervention as originally delivered in the research trial. In two schools, the intervention was adapted by selecting sustainable components, whereas in two others it was discontinued altogether. We identified four interrelated themes that explained the complex decision-making process, barriers, and enablers related to program continuation: (1) understanding of the intervention philosophy among school staff; (2) school capabilities to continue with intervention activities; (3) school attitudes and motivation about implementing the intervention, and; (4) the education policy environment and governance structures. Suggestions for overcoming barriers included adequate resource allocation; training, supervision, and support from external providers and the Ministry of Education; and formal government approval to continue the intervention. Conclusion Sustaining this whole-school health promotion intervention in low-resource school settings in India depended on individual, school and government factors as well as external support. These findings suggest that health interventions will not necessarily become embedded in a school’s operations merely because they are designed as a whole-school approach or because they are effective. Research should identify the resources and processes required to balance planning for future sustainability while awaiting trial results about an intervention’s effectiveness.
Human cytomegalovirus in cancer: the mechanism of HCMV-induced carcinogenesis and its therapeutic potential

Cancer is one of the leading causes of death worldwide. Human cytomegalovirus (HCMV), a well-studied herpesvirus, has been implicated in malignancies derived from breast, colorectal muscle, brain, and other cancers. Intricate host-virus interactions are responsible for the cascade of events that have the potential to result in the transformed phenotype of normal cells. The HCMV genome contains oncogenes that may initiate these types of cancers, and although the primary HCMV infection is usually asymptomatic, the virus remains in the body in a latent or persistent form. Viral reactivation causes severe health issues in immune-compromised individuals, including cancer patients, organ transplants, and AIDS patients. This review focuses on the immunologic mechanisms and molecular mechanisms of HCMV-induced carcinogenesis, methods of HCMV treatment, and other studies. Studies show that HCMV DNA and virus-specific antibodies are present in many types of cancers, implicating HCMV as an important player in cancer progression. Importantly, many clinical trials have been initiated to exploit HCMV as a therapeutic target for the treatment of cancer, particularly in immunotherapy strategies in the treatment of breast cancer and glioblastoma patients. Taken together, these findings support a link between HCMV infections and cellular growth that develops into cancer. More importantly, HCMV is the leading cause of birth defects in newborns, and infection with HCMV is responsible for abortions in pregnant women.
Enhanced nitrogen removal via Yarrowia lipolytica-mediated nitrogen and related metabolism of Chlorella pyrenoidosa from wastewater

We investigated the optimum co-culture ratio with the highest biological nitrogen removal rate, revealing that chemical oxygen demand, total nitrogen (TN), and ammoniacal nitrogen (NH3-N) removal was increased in the Chlorella pyrenoidosa and Yarrowia lipolytica co-culture system at a 3:1 ratio. Compared with the control, TN and NH3-N content in the co-incubated system was decreased within 2–6 days. We investigated mRNA/microRNA (miRNA) expression in the C. pyrenoidosa and Y. lipolytica co-culture after 3 and 5 days, identifying 9885 and 3976 differentially expressed genes (DEGs), respectively. Sixty-five DEGs were associated with Y. lipolytica nitrogen, amino acid, photosynthetic, and carbon metabolism after 3 days. Eleven differentially expressed miRNAs were discovered after 3 days, of which two were differentially expressed and their target mRNA expressions negatively correlated with each other. One of these miRNAs regulates gene expression of cysteine dioxygenase, hypothetical protein, and histone-lysine N-methyltransferase SETD1, thereby reducing amino acid metabolic capacity; the other miRNA may promote upregulation of genes encoding the ATP-binding cassette, subfamily C (CFTR/MRP), member 10 (ABCC10), thereby promoting nitrogen and carbon transport in C. pyrenoidosa. These miRNAs may further contribute to the activation of target mRNAs. miRNA/mRNA expression profiles confirmed the synergistic effects of a co-culture system on pollutant disposal.
Family psychoeducation to improve outcome in caregivers and patients with schizophrenia: a randomized clinical trial

Introduction Schizophrenia is recognized for its severe impact on both patients and caregivers. In a 12-month follow-up randomized clinical trial, we aimed to measure the efficacy of a brief family psychoeducation program in terms of reducing relapse risk and improving medication adherence in patients, as well as reducing caregiver burden, depression and increasing knowledge of the illness. Methods A total of 25 days of patients with schizophrenia (DSM-IV-TR) and family primary caregivers were recruited in a single regional psychiatric outpatient facility located in Bordeaux. In the active group, caregivers received a psychoeducational intervention consisting of six sessions spread over 1.5 months, while the control group was placed on a waiting list. Sociodemographic, symptom severity (PANSS) and medication adherence (MARS) from patients were assessed at baseline and relapse rates was recorded during the 12 months follow-up period. Caregivers’ burden (ZBI), depression (CES-D), quality of life (S-CGQoL), knowledge of the disease (KAST) and therapeutic alliance (4PAS-C) were assessed at baseline, three and 6 months. Results On the 25 patients included, the mean age was 33.3 years (SD = 9.7) with a mean duration of disease of 7.48 years (SD = 7.1). On the 25 caregivers included, the mean age was 50.6 years (SD = 14.0). Twenty-one were female (84.0%), 12 were married (48.0%) and 11 lived alone (44.0%). For patients, the family psychoeducation intervention significantly reduced the risk of relapse with a significant effect found at 12 months follow-up (p = 0.014). No change was observed on medication adherence. For caregivers, the intervention reduced the burden (p = 0.031), decreased the depression (p = 0.019), and increased the knowledge on schizophrenia (p = 0.024). Analyzes for repeated measures showed a statistically significant difference in therapeutic alliance (p = 0.035). Conclusion As confirmed by previous studies, the brief multifamily program (consisting of six sessions over a period of 1.5 months) was found to be effective in improving outcomes for caregivers (e.g., burden, depression, knowledge) and patients (e.g., preventing relapse) in the context of routine care. Given its short duration, this program is expected to be easily implementable within the community. Clinical trial registration https://clinicaltrials.gov/, NCT03000985.
Does a robot’s gaze aversion affect human gaze aversion?

Gaze cues serve an important role in facilitating human conversations and are generally considered to be one of the most important non-verbal cues. Gaze cues are used to manage turn-taking, coordinate joint attention, regulate intimacy, and signal cognitive effort. In particular, it is well established that gaze aversion is used in conversations to avoid prolonged periods of mutual gaze. Given the numerous functions of gaze cues, there has been extensive work on modelling these cues in social robots. Researchers have also tried to identify the impact of robot gaze on human participants. However, the influence of robot gaze behavior on human gaze behavior has been less explored. We conducted a within-subjects user study (N = 33) to verify if a robot’s gaze aversion influenced human gaze aversion behavior. Our results show that participants tend to avert their gaze more when the robot keeps staring at them as compared to when the robot exhibits well-timed gaze aversions. We interpret our findings in terms of intimacy regulation: humans try to compensate for the robot’s lack of gaze aversion.