Miracle-dz/UniFAR-FTUs huggingface dataset:
Lack of robust evidence for a Wolbachia infection in Anopheles gambiae from Burkina Faso

The endosymbiont Wolbachia can have major effects on the reproductive fitness, and vectorial capacity of host insects and may provide new avenues to control mosquito borne pathogens. Anopheles gambiae s.l is the major vector of malaria in Africa but the use of Wolbachia in this species has been limited by challenges in establishing stable transinfected lines and uncertainty around native infections. High frequencies of infection of Wolbachia have been previously reported in An. gambiae collected from the Valle du Kou region of Burkina Faso in 2011 and 2014. Here we re-evaluated the occurrence of Wolbachia in natural samples, collected from Valle du Kou over a 12-year time span, and in addition, expanded sampling to other sites in Burkina Faso. Our results showed that, in contrast to earlier reports, Wolbachia is present at an extremely low prevalence in natural population of An. gambiae. From 5,341 samples analysed only 29 were positive for Wolbachia by nested PCR representing 0.54% of prevalence. No positive samples were found with regular PCR. Phylogenetic analysis of 16S rRNA gene amplicons clustered across supergroup B, with some having similarity to sequences previously found in Anopheles from Burkina Faso. However, we cannot discount the possibility that the amplicon positive samples we detected were due to environmental contamination or were false positives. Regardless, the lack of a prominent native infection in An. gambiae s.l. is encouraging for applications utilising Wolbachia traninsfected mosquitoes for malaria control.
Behavioral Testing of Knowledge Graph Embedding Models for Link Prediction

Knowledge graph embedding (KGE) models are often used to encode knowledge graphs in order to predict new links inside the graph. The accuracy of these methods is typically evaluated by computing an averaged accuracy metric on a held-out test set. This approach, however, does not allow the identiﬁcation of where the models might systematically fail or succeed. To address this challenge, we propose a new evaluation framework that builds on the idea of (black-box) behavioral testing, a software engineering principle that enables users to detect system failures before deployment. With behavioral tests, we can speciﬁcally target and evaluate the behavior of KGE models on speciﬁc capabilities deemed important in the context of a particular use case. To this end, we leverage existing knowledge graph schemas to design behavioral tests for the link prediction task. With an extensive set of experiments, we perform and analyze these tests for several KGE models. Crucially, we for example ﬁnd that a model ranked second to last on the original test set actually performs best when tested for a speciﬁc capability. Such insights allow users to better choose which KGE model might be most suitable for a particular task. The framework is extendable to additional behavioral tests and we hope to inspire fellow researchers to join us in collaboratively growing this framework. The framework will be made publicly available upon acceptance.
Understanding the Role of SARS-CoV-2 ORF3a in Viral Pathogenesis and COVID-19

The ongoing SARS-CoV-2 pandemic has shocked the world due to its persistence, COVID-19-related morbidity and mortality, and the high mutability of the virus. One of the major concerns is the emergence of new viral variants that may increase viral transmission and disease severity. In addition to mutations of spike protein, mutations of viral proteins that affect virulence, such as ORF3a, also must be considered. The purpose of this article is to review the current literature on ORF3a, to summarize the molecular actions of SARS-CoV-2 ORF3a, and its role in viral pathogenesis and COVID-19. ORF3a is a polymorphic, multifunctional viral protein that is specific to SARS-CoV/SARS-CoV-2. It was acquired from β-CoV lineage and likely originated from bats through viral evolution. SARS-CoV-2 ORF3a is a viroporin that interferes with ion channel activities in host plasma and endomembranes. It is likely a virion-associated protein that exerts its effect on the viral life cycle during viral entry through endocytosis, endomembrane-associated viral transcription and replication, and viral release through exocytosis. ORF3a induces cellular innate and pro-inflammatory immune responses that can trigger a cytokine storm, especially under hypoxic conditions, by activating NLRP3 inflammasomes, HMGB1, and HIF-1α to promote the production of pro-inflammatory cytokines and chemokines. ORF3a induces cell death through apoptosis, necrosis, and pyroptosis, which leads to tissue damage that affects the severity of COVID-19. ORF3a continues to evolve along with spike and other viral proteins to adapt in the human cellular environment. How the emerging ORF3a mutations alter the function of SARS-CoV-2 ORF3a and its role in viral pathogenesis and COVID-19 is largely unknown. This review provides an in-depth analysis of ORF3a protein’s structure, origin, evolution, and mutant variants, and how these characteristics affect its functional role in viral pathogenesis and COVID-19.
Liquid Biopsy and Artificial Intelligence as Tools to Detect Signatures of Colorectal Malignancies: A Modern Approach in Patient’s Stratification

Colorectal cancer (CRC) is the second most frequently diagnosed type of cancer and a major worldwide public health concern. Despite the global efforts in the development of modern therapeutic strategies, CRC prognosis is strongly correlated with the stage of the disease at diagnosis. Early detection of CRC has a huge impact in decreasing mortality while pre-lesion detection significantly reduces the incidence of the pathology. Even though the management of CRC patients is based on robust diagnostic methods such as serum tumor markers analysis, colonoscopy, histopathological analysis of tumor tissue, and imaging methods (computer tomography or magnetic resonance), these strategies still have many limitations and do not fully satisfy clinical needs due to their lack of sensitivity and/or specificity. Therefore, improvements of the current practice would substantially impact the management of CRC patients. In this view, liquid biopsy is a promising approach that could help clinicians screen for disease, stratify patients to the best treatment, and monitor treatment response and resistance mechanisms in the tumor in a regular and minimally invasive manner. Liquid biopsies allow the detection and analysis of different tumor-derived circulating markers such as cell-free nucleic acids (cfNA), circulating tumor cells (CTCs), and extracellular vesicles (EVs) in the bloodstream. The major advantage of this approach is its ability to trace and monitor the molecular profile of the patient’s tumor and to predict personalized treatment in real-time. On the other hand, the prospective use of artificial intelligence (AI) in medicine holds great promise in oncology, for the diagnosis, treatment, and prognosis prediction of disease. AI has two main branches in the medical field: (i) a virtual branch that includes medical imaging, clinical assisted diagnosis, and treatment, as well as drug research, and (ii) a physical branch that includes surgical robots. This review summarizes findings relevant to liquid biopsy and AI in CRC for better management and stratification of CRC patients.
Biomechanical Analysis of a Novel Double-Point Fixation Method for Displaced Intra-Articular Calcaneal Fractures

The development of minimally invasive procedures and implant materials has improved the fixation strength of implants and is less traumatic in surgery. The purpose of this study was to propose a novel “double-point fixation” for calcaneal fractures and compare its biomechanical stability with the traditional “three-point fixation. ” A three-dimensional finite element foot model with a Sanders type IIIAB calcaneal fracture was developed based on clinical images comprising bones, plantar fascia, ligaments, and encapsulated soft tissue. Double-point and three-point fixation resembled the surgical procedure with a volar distal radius plate and calcaneal locking plate, respectively. The stress distribution, fracture displacement, and change of the Böhler angle and Gissane’s angle were estimated by a walking simulation using the model, and the predictions between the double-point and three-point fixation were compared at heel-strike, midstance, and push-off instants. Double-point fixation demonstrated lower bone stress (103.3 vs. 199.4 MPa), but higher implant stress (1,084.0 vs. 577.9 MPa). The model displacement of double-point fixation was higher than that of three-point fixation (3.68 vs. 2.53 mm). The displacement of the posterior joint facet (0.127 vs. 0.150 mm) and the changes of the Böhler angle (0.9° vs. 1.4°) and Gissane’s angle (0.7° vs. 0.9°) in double-point fixation were comparably lower. Double-point fixation by volar distal radius plates demonstrated sufficient and favorable fixation stability and a lower risk of postoperative stress fracture, which may potentially serve as a new fixation modality for the treatment of displaced intra-articular calcaneal fractures.
Identification of the LOX Gene Family in Peanut and Functional Characterization of AhLOX29 in Drought Tolerance

Lipoxygenases (LOXs) are a gene family of nonheme iron-containing dioxygenases that play important roles in plant development and defense responses. To date, a comprehensive analysis of LOX genes and their biological functions in response to abiotic stresses in peanut has not been performed. In this study, a total of 72 putative LOX genes were identified in cultivated (Arachis hypogaea) and wild-type peanut (Arachis duranensis and Arachis ipaensis) and classified into three subfamilies: 9-LOX, type I 13-LOX and type II 13-LOX. The gene structures and protein motifs of these peanut LOX genes were highly conserved among most LOXs. We found that the chromosomal distribution of peanut LOXs was not random and that gene duplication played a crucial role in the expansion of the LOX gene family. Cis-acting elements related to development, hormones, and biotic and abiotic stresses were identified in the promoters of peanut LOX genes. The expression patterns of peanut LOX genes were tissue-specific and stress-inducible. Quantitative real-time PCR results further confirmed that peanut LOX gene expression could be induced by drought, salt, methyl jasmonate and abscisic acid treatments, and these genes exhibited diverse expression patterns. Furthermore, overexpression of AhLOX29 in Arabidopsis enhanced the resistance to drought stress. Compared with wide-type, AhLOX29-overexpressing plants showed significantly decreased malondialdehyde contents, as well as increased chlorophyll degradation, proline accumulation and superoxide dismutase activity, suggesting that the transgenic plants exhibit strengthened capacity to scavenge reactive oxygen species and prevent membrane damage. This systematic study provides valuable information about the functional characteristics of AhLOXs in the regulation of abiotic stress responses of peanut.
Adipogenic Transdifferentiation and Regulatory Factors Promote the Progression and the Immunotherapy Response of Renal Cell Carcinoma: Insights From Integrative Analysis

Background Adipogenic transdifferentiation was an important carcinogenic factor in various tumors, while studies on its role in clear cell renal cell carcinoma (ccRCC) were still relatively few. This study aimed to investigate its prognostic value and mechanism of action in ccRCC. Methods Gene expression profiles and clinical data of ccRCC patients were obtained from The Cancer Genome Atlas database. Nonnegative matrix factorization was used for clustering. Gene set variation analysis (GSVA) and gene set enrichment analysis (GSEA) were used to analyze the pathways and biological process activities. single-sample GSEA (ssGSEA) was utilized to quantify the relative abundance of each immune cell. Tumor Immune Estimation Resource (TIMER) was used to evaluate the proportion of various immune infiltrating cells across diverse cancer types. Real-Time PCR was performed to examine the gene expression. R software was utilized to analyze the expression and prognostic role of genes in ccRCC. Results A total of 49 adipose-related genes (ARGs) were screened for differential expression between normal and ccRCC tissues. Based on differentially expressed ARGs, patients with ccRCC were divided into two adipose subtypes with different clinical, molecular, and pathway characteristics. Patients in cluster A exhibited more advanced pathological stages, higher expressions of RARRES2 and immune checkpoint genes, higher immune infiltration scores, and less nutrient metabolism pathways. Adipose differentiation index (ADI) was constructed according to the above ARGs and survival data, and its robustness and accuracy was validated in different cohorts. In addition, it was found that the expression of ARGs was associated with immune cell infiltration and immune checkpoint in ccRCC, among which GBP2 was thought to be the most relevant gene to the tumor immune microenvironment and play a potential role in carcinogenesis and invasion of tumor cells. Conclusion Our analysis revealed the consistency of higher adipogenic transdifferentiation of tumor cells with worse clinical outcomes in ccRCC. The 16-mRNA signature could predict the prognosis of ccRCC patients with high accuracy. ARGs such as GBP2 might shed light on the development of novel biomarkers and immunotherapies of ccRCC.
Low FODMAP Diet and Probiotics in Irritable Bowel Syndrome: A Systematic Review With Network Meta-analysis

Background: Probiotic and low fermentable oligosaccharide, disaccharide, monosaccharide, and polyol (FODMAP) diet are two commonly used management approaches for patients with irritable bowel syndrome (IBS). We aimed to evaluate the most effective combinations and components among different probiotics or low FODMAP diet through component network meta-analysis (NMA). Methods: We searched Embase, Ovid Medline, and Web of Science from inception to 21 January 2021. Randomized controlled trials (RCTs) examining the efficacy of probiotics and low FODMAP diet for IBS were included, with placebo, sham diet, or conventional treatments as controls. Binary outcomes were compared among treatments using the relative ratio (RR). A minimally contextualized framework recommended by the GRADE group was used to evaluate the certainty of evidence. The primary efficacy outcome was the relief of global IBS symptoms, and the secondary efficacy outcome was the reduction in IBS symptom scores or abdominal pain scores. Key Results: We included 76 RCTs (n = 8058) after screening 1940 articles. Eight RCTs were classified as low risk of bias. Standard network meta-analysis (NMA) showed that Lactobacillus (RR 1.74, 95% CI 1.22–2.48) and Bifidobacterium (RR 1.76, 95% CI 1.01–3.07) were the most effective for the primary efficacy outcome (high certainty evidence); component NMA showed that Bacillus (RR 5.67, 95% CI 1.88 to 17.08, p = 0.002) and Lactobacillus (RR 1.42, 95% CI 1.07 to 1.91, p = 0.017) were among the most effective components. The results of standard NMA and CNMA analysis of the improvement of overall IBS symptom scores or abdominal pain scores were consistent with this finding. Conclusion: Lactobacillus was the most effective component for the relief of IBS symptoms; Bifidobacterium and Bacillus were possibly effective and need further verification. Systematic Review Registration: website, identifier registration number.
Prevalence and Risk Factors for Human T-Cell Lymphotropic Virus (HTLV) in Blood Donors in Brazil—A 10-Year Study (2007–2016)

It is unknown whether HTLV-1/2 prevalence has been stable or changing with time in Brazil. We present a 10-year (2007–2016) analysis of HTLV-1/2 infection in first-time blood donors from four blood banks in Brazil. The Brazilian blood centers participating in this multicenter Recipient Epidemiology and Donor Evaluation Study (REDS) are located in Recife in the Northeast and in São Paulo, Rio de Janeiro and Belo Horizonte located in the Southeast of the country. A previous REDS study using the same database from 2007 to 2009 showed that the prevalence per 100,000 donors was 222 in Recife, 83 in Belo Horizonte and 101 in São Paulo. From 2007 to 2016, HTLV-1/2 prevalence was calculated by year, blood center and birth cohort. Covariates included age, gender, schooling, self-reported skin color and type of donation. From 1,092,174 first-blood donations, in the general analysis, HTLV-1/2 infection predominated in females, donors over 50 years of age, black skin color and less educated. The average prevalence was 228 per 100,000 donors in Recife, 222 in Rio de Janeiro, 104 in Belo Horizonte and 103 in São Paulo. In the 10-year analysis, HTLV-1/2 prevalence was stable, but a trend was observed toward an increase in HTLV-1/2 infection among younger people (p < 0.001), males (p = 0.049), those with white skin color (p < 0.001), and higher education (p = 0.014). Therefore, this 10-year surveillance of the infection showed stable HTLV-1/2 prevalence overall but a trend toward increased prevalence among the younger and more educated donors despite Brazilian policies to control sexually transmitted infections being in place for more than 10 years.
Preventing Sleep Disruption With Bright Light Therapy During Chemotherapy for Breast Cancer: A Phase II Randomized Controlled Trial

Purpose The goal of this study was to examine whether daily increased morning light exposure would maintain or improve sleep and the circadian pattern of relatively more activity in the day and less during the night in women undergoing chemotherapy for breast cancer. Patients and Methods Participants were 39 women with newly diagnosed breast cancer, randomized to either 30-mins of daily morning bright white light (BWL) or dim red light (DRL). Sleep/wake was measured objectively for 72-h with wrist actigraphy and subjectively with the Pittsburgh Sleep Quality Index (PSQI) prior to and during chemotherapy cycles 1 and 4. The study was registered with the National Institutes of Health ClinicalTrials.gov (Clinical Trials number: NCT00478257). Results Results from actigraphy suggested that compared to the DRL group, women in the BWL group had longer night-time sleep, fewer sleep disturbances during the night, and had fewer and shorter daytime naps at the end of cycle 4 of chemotherapy as well as exhibiting less activity at night and more activity during the day by the end of cycle 4. Results from PSQI indicated that components of sleep quality improved but daytime dysfunction deteriorated during cycle 4 treatment in the BWL group; meanwhile the DRL group used more sleep medications in the treatment weeks which might have led to the improved sleep quality during the recovery weeks of both cycles. Conclusion These results suggest that bright white light therapy administered every morning on awakening may protect women undergoing chemotherapy for breast cancer from nighttime sleep and daytime wake disruption. Randomized clinical trials in larger samples are needed to confirm these findings.
Tracking of Diversity and Evolution in the Brown Rot Fungi Monilinia fructicola, Monilinia fructigena, and Monilinia laxa

Monilinia species are among the most devastating fungi worldwide as they cause brown rot and blossom blight on fruit trees. To understand the molecular bases of their pathogenic lifestyles, we compared the newly assembled genomes of single strains of Monilinia fructicola, M. fructigena and M. laxa, with those of Botrytis cinerea and Sclerotinia sclerotiorum, as the closest species within Sclerotiniaceae. Phylogenomic analysis of orthologous proteins and syntenic investigation suggest that M. laxa is closer to M. fructigena than M. fructicola, and is closest to the other investigated Sclerotiniaceae species. This indicates that M. laxa was the earliest result of the speciation process. Distinct evolutionary profiles were observed for transposable elements (TEs). M. fructicola and M. laxa showed older bursts of TE insertions, which were affected (mainly in M. fructicola) by repeat-induced point (RIP) mutation gene silencing mechanisms. These suggested frequent occurrence of the sexual process in M. fructicola. More recent TE expansion linked with low RIP action was observed in M. fructigena, with very little in S. sclerotiorum and B. cinerea. The detection of active non-syntenic TEs is indicative of horizontal gene transfer and has resulted in alterations in specific gene functions. Analysis of candidate effectors, biosynthetic gene clusters for secondary metabolites and carbohydrate-active enzymes, indicated that Monilinia genus has multiple virulence mechanisms to infect host plants, including toxins, cell-death elicitor, putative virulence factors and cell-wall-degrading enzymes. Some species-specific pathogenic factors might explain differences in terms of host plant and organ preferences between M. fructigena and the other two Monilinia species.
Family Relationships Under Work From Home: Exploring the Role of Adaptive Processes

Work-from-home (WFH) influences both work and life, and further impacts family relationships. The current study explored the impacts of WFH on family relationships during the COVID-19 pandemic and identified effective adaptive processes for maintaining family relationships under WFH. Using the Vulnerability-Stress-Adaptation (VSA) model, the study examined the roles of adaptive processes (spending time with family members and balancing work and life) and demographic differences (gender, age, marital status, and education level) in the relation between WFH and family relationships. Path analysis results based on an online survey (N = 150) suggested that, overall, WFH improved family relationships through proper adaptive processes. WFH had a positive relation to time spent with family members, and this relation was especially salient for workers with lower education levels. While there was no statistically significant overall relation between WFH and work-life balance, older workers tended to engage in increased work-life balance during WFH. Both adaptive processes were positively related to family relationship quality. The findings advance the understanding of family relationships and WFH and provide practical recommendations to enhance family relationships under WFH.