Miracle-dz/UniFAR-FTUs huggingface dataset:
High ATF4 Expression Is Associated With Poor Prognosis, Amino Acid Metabolism, and Autophagy in Gastric Cancer

Background The role of activating transcription factor 4 (ATF4) underlying gastric cancer (GC) remains unclear. The purpose of this study was to investigate the expression levels and biological functions of ATF4 in GC. Methods Expression of ATF4 was detected by quantitative PCR (qPCR), Western blotting, and immunohistochemistry. Cox regression was used for survival analysis and the construction of the nomogram. Immunofluorescence was used to identify the intracellular localization of ATF4. Knockdown and overexpression of ATF4 in GC cells followed by wound healing and Transwell assays, EdU and Calcein-AM/propidium iodide (PI) staining, and cell cycle detection were performed to examine its function in vitro. Transmission electron microscopy was performed to assess the autophagy levels upon ATF4 silencing. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis and gene set enrichment analysis (GSEA) were used to determine gene enrichment. SPSS 22.0 software, GraphPad Prism 7.0, and R version 3.6. 1 were used for statistical analysis. Results ATF4 expression was upregulated in GC cells and tissues compared with corresponding normal tissues. Survival analysis suggested that a high ATF4 expression was strongly associated with worse overall survival (OS) of GC patients (p < 0.001). The nomogram and the receiver operating characteristic (ROC) curves demonstrated that ATF4 was a highly sensitive and specific prognostic marker of GC [C-index = 0.797, area under the ROC curve (AUC) of 3-year OS = 0.855, and AUC of 5-year OS = 0.863]. In addition, ATF4 knockdown inhibited the cell proliferation, migration, invasion, and cell cycle progression of GC cells in vitro, while overexpression of ATF4 exerted the opposite effects. Bioinformatics analysis showed that ATF4 could promote GC progression possibly by regulating asparagine (Asn) metabolism and autophagy pathways. Further experiments indicated that ATF4 expression was significantly positively correlated with ASNS expression. The inhibition of cell clone formation in Asn-deprived conditions was more significant in the shATF4 group. Finally, we found that ATF4 promoted autophagy through regulating the mTORC1 pathway in GC cells. Conclusion These findings suggested that ATF4 can significantly promote GC development and serve as an independent prognostic factor for GC.
Safety, Immunogenicity and Antibody Persistence of Rift Valley Fever Virus Clone 13 Vaccine in Sheep, Goats and Cattle in Tanzania

Background: Vaccination is considered to be the best approach to control Rift Valley fever (RVF) in animals and consequently in humans. This study assessed the efficacy and safety of the RVF virus (RVFV) Clone 13 vaccine under field conditions. Methodology: A vaccine trial was conducted in sheep (230), goats (230), and cattle (140) in Ngorongoro district, Tanzania. Half of each of the animal species were vaccinated and the other half received the placebo. Animals were clinically monitored and bled before vaccination and at days 15, 30, 60, 180 and 360 (+/– 10) post-vaccination to measure Immunoglobulin M (IgM) and IgG antibody responses to RVFV. Survival analysis was conducted using cox-proportional hazard regression model to measure the time until an event of interest had occurred and to compare the cumulative proportion of events over time. Results: Of 600 animals included in the study, 120 animals were lost during the study, leaving a total of 480 (243 in the vaccinated group and 237 in the control group) for complete follow-up sampling. There was no adverse reaction reported at the injection site of the vaccine/placebo in all animals. Abortions, deaths, or body temperature variations were not associated with vaccination (p > 0.05). By day 15 post-inoculation, the IgG seroconversion in vaccinated goats, cattle and sheep was 27.0% (n = 115), 20.0% (n = 70) and 10.4% (n = 115), respectively. By day 30 post-inoculation, it was 75.0% (n = 113), 74.1% (n = 112) and 57.1% (n = 70) in vaccinated sheep, goats and cattle, respectively. By day 60 post-inoculation, IgG seroconversion in sheep, goats and cattle was 88.1% (n = 109), 84.3% (n = 108) and 64.60% (n = 65), respectively. By day 180, the IgG seroconversion in sheep, goats and cattle was 88.0% (n = 108), 83.8% (n = 105) and 66.1% (n = 62), respectively. By day 360, the IgG seroconversion in sheep, goats and cattle was 87.2% (n = 94), 85.6% (n = 90) and 66.1% (n = 59), respectively. Only five animals from the vaccinated group were RVFV IgM positive, which included four sheep and a goat. Conclusion: RVFV Clone 13 vaccine was well tolerated by sheep, goats, and cattle. The vaccine induced detectable, but variable levels of IgG responses, and of different duration. The vaccine is considered safe, with high immunogenicity in sheep and goats and moderate in cattle.
High-Resolution Image Analysis Reveals a Decrease in Lens Thickness and Cone Density in a Cohort of Young Myopic Patients

Purpose: To study the association between axial length (AL) and the thickness of the lens, retina, choroid, and cone density with swept-source optical coherence tomography (SS-OCT) and an adaptive optics (AO) fundus camera. Design: A prospective cross-sectional study. Methods: This study included 136 eyes in 68 subjects. SS-OCT was used to quantify the thickness of the lens, ganglion cell complex (GCC) layer, inner nuclear layer (INL), outer retinal layer (ORL), and choroid layer. Adaptive optics was used to quantify spatial features of the cone photoreceptors, including density, spacing, regularity, and dispersion. The associations among the AL and the thickness of lens, retina, choroid, and cone features were evaluated with linear regression. Results: With the severity of myopia, the increased AL was associated with thinning of the lens (P < 0.001, 95% CI: −100.42 to −49.76). The thickness of the ORL and choroid decreased significantly (all P < 0.001), whereas the thickness of the GCC and INL decreased only in the outer ring (both P < 0.01). There was a significant correlation between the cone density/spacing and AL (both P < 0.001). Although cone density was reduced from 25,160/mm2 to 19,134/mm2 in the inner region and from 17,458/mm2 to 13,896/mm2 in the outer region, the best-corrected visual acuity (BCVA) was 20/20 or greater. Conclusions: We found that the lens thickness (LT), ORL, and cone density decreased in myopia. While decreasing cone density and ORL thickness should be related to axial elongation, decreasing of LT might imply intrinsic physical accommodation. These results provide further morphological changes of myopia.
Gut Microbial Profile Is Associated With the Severity of Social Impairment and IQ Performance in Children With Autism Spectrum Disorder

Background and Objective: Autism spectrum disorder (ASD) refers to a heterogeneous set of neurodevelopmental disorders with diverse symptom severity and comorbidities. Although alterations in gut microbiota have been reported in individuals with ASD, it remains unclear whether certain microbial pattern is linked to specific symptom or comorbidity in ASD. We aimed to investigate the associations between gut microbiota and the severity of social impairment and cognitive functioning in children with ASD. Methods: A total of 261 age-matched children, including 138 children diagnosed with ASD, 63 with developmental delay or intellectual disability (DD/ID), and 60 typically developing (TD) children, were enrolled from the Shanghai Xinhua Registry. The children with ASD were further classified into two subgroups: 76 children diagnosed with ASD and developmental disorder (ASD+DD) and 62 with ASD only (ASD-only). The gut microbiome of all children was profiled and evaluated by 16S ribosomal RNA sequencing. Results: The gut microbial analyses demonstrated an altered microbial community structure in children with ASD. The alpha diversity indices of the ASD+DD and ASD-only subgroups were significantly lower than the DD/ID or TD groups. At the genus level, we observed a decrease in the relative abundance of Prevotella. Simultaneously, Bacteroides and Faecalibacterium were significantly increased in ASD compared with DD/ID and TD participants. There was a clear correlation between alpha diversity and the Childhood Autism Rating Scale (CARS) total score for all participants, and this correlation was independent of IQ performance. Similar correlations with the CARS total score were observed for genera Bacteroides, Faecalibacterium, and Oscillospira. However, there was no single genus significantly associated with IQ in all participants. Conclusions: Specific alterations in bacterial taxonomic composition and associations with the severity of social impairment and IQ performance were observed in children with ASD or ASD subgroups, when compared with DD/ID or TD groups. These results illustrate that gut microbiota may serve as a promising biomarker for ASD symptoms. Nevertheless, further investigations are warranted.
Live Birth Rate in Patients With Premature Ovarian Insufficiency During Long-Term Follow-Up Under Hormone Replacement With or Without Ovarian Stimulation

We analyzed data from 466 patients with premature ovarian insufficiency (POI) who wished to have a biological child and were followed up while undergoing hormone replacement (HR) therapy with or without ovarian stimulation (OS) between April 2014 and December 2020. OS was conducted in 6891 cycles in 429 patients (Group OS), whereas only HR (Group HR) was conducted in 1117 cycles in 37 patients. The follicle growth rate was 48.3% (207/429) per patient in Group OS and 5.4% (2/37) in Group HR (p<0.01). There were 51 live births (LBs) in 50 patients during follow-up. In Group OS, the LB rate was 5.8% (47/807) in cycles where in vitro fertilization (IVF) and embryo transfer were attempted (Group IVF), and 1.3% (3/236) in cycles where intrauterine insemination/timed intercourse was attempted (p<0.01). No pregnancies occurred in Group HR. Among the patients in Group IVF, the LB rate was significantly higher in patients aged <35 years at the initiation of follow-up than in patients who started at later ages (p<0.01). Among the cases who achieved an LB, 39 were patients with idiopathic POI (Group IVF-1, n=297) and seven were patients who had undergone surgical treatment for benign ovarian tumors (Group IVF-2, n=50); however, no LBs occurred in patients who had undergone treatment for malignancy (n=17), and only one in patients with chromosomal abnormalities (n=22). The LB rate per case in the patients in Group IVF-1 and those aged <35 years at the start of follow-up (Group IVF-1-a) was 24.1% (26/108), which was higher than those of the other age groups. The LB rate per case in the patients in Group IVF-1-a with <4 years of amenorrhea was 37.3% (19/51), and that in the patients in Group IVF-2 with <4 years of amenorrhea was 21.2% (7/33). These results suggest that infertility treatment is possible in some patients with POI, especially those that can be classified in Group IVF-1-a and Group IVF-2 with <4 years of amenorrhea. Therefore, OS combined with HR therapy should be considered for such patients before attempts at oocyte donation.
Dietary Intake and Adherence to the Recommendations for Healthy Eating in Patients With Type 1 Diabetes: A Narrative Review

Background: Medical nutrition therapy is essential for all people with diabetes, of any type or severity. Compliance with the recommended nutrition is an integral part of the treatment of type 1 diabetes (T1D). It remains unclear to what extent the dietary intake of patients with type 1 diabetes adheres to the recommendations for healthy eating. Objective: The primary aim of our study is to collect and analyze published articles on the nutrition of T1D patients in comparison with the general population and recommendations. Research Strategy and Methods: A literature search for articles, published between January 2006 and July 2021 was conducted, using electronic databases (PubMed and Google Scholar) for all available publications in English and Bulgarian. The process of study selection, identification, screening, eligibility and inclusion followed the PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analyses) recommendations for a flowchart. Based on the keywords search, 425 titles were retrieved, of which 27 were selected based on title and abstract. All papers were crosschecked and reviewed for selection by 3 independent reviewers. As a result, 19 titles were eligible and met inclusion criteria for a full review. Results: Energy intake tends to be lower in T1D patients or comparable to controls and in most cases within the general recommendations. The percentage of calories from protein is within the recommendations for children, adolescents and adults. Only two studies showed that T1D patients consume significantly less than the recommendation for total fat intake (<35E%). The median intake of carbohydrates is in the lower end of the recommended 45 to 60E%. The median intake of dietary fiber adjusted for total energy is too low for T1D patients and the general population. Conclusion: Study findings suggested a lack of knowledge or misunderstanding of diabetes dietary management. Patients with T1D, who are being consulted with a dietician as a part of their treatment plan may have better compliance to their recommended diet and as a result, are likely to have better health outcomes. Nutritional therapy should focus not only on glycemic control and pure carbohydrate counting but also on healthy eating and complication prevention.
The Mediating Effect of Self-Control on Depression and Tendencies of Eating Disorders in Adolescents

Self-control is very important for the adaptation among adolescents. It is associated with depression and tendencies of eating disorders. This study aimed to investigate the relationship between the two and the mediating role of self-control for adolescents. In total, 1,231 adolescents (11–18 years) participated in this study. Self-control, depression, and tendencies of eating disorders were evaluated using the Dual-Mode of Self-Control Scale (DMSC-S), 11-item Kutcher Adolescent Depression Scale (KADS-11), and Eating Attitudes Test (EAT-26). The correlations among these factors were analyzed using mediating effect models. Girls had higher scores on the both subscales (impulse system and control system) of DMSC-S (P < 0.001). Those between 15–18 years had higher scores on impulse system than those between 11–14 years (P < 0.001). A significant mediating effect (12.8%) of the impulse system was observed between depression and tendencies of eating disorders in adolescents.
Extracts From Red Eggplant: Impact of Ohmic Heating and Different Extraction Solvents on the Chemical Profile and Bioactivity

Eggplants contain a multitude of biocompounds with nutritional and/or biological activities. The objective of this work was to study the nutritional, chemical and bioactive value of red eggplant from Rotonda, Italy. Ohmic heating (OH) was compared to conventional heating, as different solvents were used (water, ethanol 30, 50, and 90% and methanol) for biocompounds extraction. Extracts were evaluated for their total phenolic compounds, antioxidant and antibacterial activities, and its toxicity was assessed in cells, L929 and Caco-2. The nutritional characterization of Rotonda's eggplant demonstrated that it is rich in carbohydrates (65%), fiber (12.5%), proteins (13%), lipids (7.6%) and minerals. Potassium is the mineral with the highest concentration in the red eggplant (27.24 mg/g). Phenolic composition of the obtained extracts was dependent on the extraction method, as well as on the solvent. The use of OH method increased the extraction of biocompounds, especially when using 50% of ethanol as solvent. The main phenolic compounds found in the extracts of this eggplant variety were ellagic acid, p-coumaricic acid, epicatechin, narginin, taxifolin and kaempferol. Antioxidant activity was positively correlated with the total amounts of phenolics. Red Eggplant extracts showed activity against Gram-negative bacteria (E. coli and S. enterica), however, they did not demonstrate activity against Gram-positive bacteria. The extracts obtained did not show cytotoxic effects in fibroblast and colorectal studied cells. Ohmic heating is a sustainable technology that increases the extraction yield of biocompounds, with reduced energy consumption and the resulting extracts show low toxicity and high biological activity.
Association of CCR5Δ32 Deletion and Human Cytomegalovirus Infection With Colorectal Cancer in Tunisia

Background and objectives: Human cytomegalovirus (HCMV) and genetic polymorphisms of the chemokine receptor 5 have been suggested as factors associated with the progression of colorectal cancer (CRC). The aim of the study was to evaluate the associations of both CCR5Δ32 genetic deletion and/or HCMV virus infection with CRC in Tunisia. Materials and methods: The association between HCMV and CRC was validated by Nested PCR technology performed for HCMV and HCMV-specific serum IgG and IgM antibodies were investigated by enzyme-linked immunosorbent assay. Experiments were carried out on 40 tumor and 35 peri-tumor tissues, 100 blood from CRC patients and on 140 blood samples from healthy subjects and finaly serum samples of 80 patients with CRC and 100 healthy individuals. A conventional PCR has been optimized for the detection of CCR5Δ32 in100 CRC patients and 100 healthy subjects. Results: Our results show that HCMV is significantly active in 93% of patients compared to 60% in controls (p < 0.0001, OR = 8.85, 95% CI: 3.82 -20.50). Compared to the healthy controls, the titers of IgG and IgM antiCMV antibodies in CRC patients were significantly higher than in healthy subjects (p value < 0,0001 for IgG and IgM). Statistical analysis revealed a lack of association between CCR5Δ32 mutation and colorectal cancer (p = 0.788, OR = 1.265, 95% CI: 0.228-7.011). Conclusion: our data confirmed that the HCMV infection was related to the development of CRC and that CRC cells may be infected more favorably by HCMV. Given the importance of the CCR5 in inflammation and therefore CRC progression, further studies still needed to evaluate CCR5 role as a potential candidate gene for CRC susceptibility under other polymorphisms.
Neutrophil Expression of T and B Immunomodulatory Molecules in HIV Infection

Objective Evaluate the expression of B and T cell immunomodulatory molecules in polymorphonuclear neutrophils (PMN) in HIV-infected patients. Methods HIV load, bacterial translocation and neutrophils’ expression of T [programmed death ligand, interleukin-10+, arginase 1+] and B [BAFF, APRIL] molecules were analyzed in different cohorts and time points: a control group of 25 healthy individuals and two groups of HIV-infected patients. Group 1 of patients included 35 untreated patients, studied at baseline and after antiretroviral therapy (ART). Group 2 was composed of 25 patients with undetectable viral load after a median of 101 months of ART prior to inclusion in the study. Results Compared with the control group, group 1 patients showed increased bacterial translocation and their PMN had a significantly higher expression of T and B-cell immunomodulatory molecules, both at baseline and after 12 months of ART. Group 2 patients showed reduced bacterial translocation levels when compared with group 1 patients after 12 months of treatment. PMN expression of B-cell modulators was similar between group 2 patients and healthy controls, although the expression of T-cell modulators remained increased. Conclusion In HIV-infected patients, the expression of B-cell stimulatory and T-cell suppressive molecules by neutrophils was increased at baseline and after a limited time of therapy. After a prolonged period of ART, only PMNs expression of T-cell immunosuppressive molecules remained elevated.
Construction and Validation of a Combined Ferroptosis and Hypoxia Prognostic Signature for Hepatocellular Carcinoma

Background: Ferroptosis, as a unique programmed cell death modality, has been found to be closely related to the occurrence and development of hepatocellular carcinoma (HCC). Hypoxia signaling pathway has been found to be extensively involved in the transformation and growth of HCC and to inhibit anti-tumor therapy through various approaches. However, there is no high-throughput study to explore the potential link between ferroptosis and hypoxia, as well as their combined effect on the prognosis of HCC. Methods: We included 370 patients in The Cancer Genome Atlas (TCGA) database and 231 patients in the International Cancer Genome Consortium (ICGC) database. Univariate COX regression and Least Absolute Shrinkage and Selection Operator approach were used to construct ferroptosis-related genes (FRGs) and hypoxia-related genes (HRGs) prognostic signature (FHPS). Kaplan–Meier method and Receiver Operating Characteristic curves were analyzed to evaluate the predictive capability of FHPS. CIBERSOR and single-sample Gene Set Enrichment Analysis were used to explore the connection between FHPS and tumor immune microenvironment. Immunohistochemical staining was used to compare the protein expression of prognostic FRGs and HRGs between normal liver tissue and HCC tissue. In addition, the nomogram was established to facilitate the clinical application of FHPS. Results: Ten FRGs and HRGs were used to establish the FHPS. We found consistent results in the TCGA training cohort, as well as in the independent ICGC validation cohort, that patients in the high-FHPS subgroup had advanced tumor staging, shorter survival time, and higher mortality. Moreover, patients in the high-FHPS subgroup showed ferroptosis suppressive, high hypoxia, and immunosuppression status. Finally, the nomogram showed a strong prognostic capability to predict overall survival (OS) for HCC patients. Conclusion: We developed a novel prognostic signature combining ferroptosis and hypoxia to predict OS, ferroptosis, hypoxia, and immune status, which provides a new idea for individualized treatment of HCC patients.
Unobserved, re-defined, unknown or removed failure modes in competing risks

Recently the nonparametric predictive approach to inference for competing risks was introduced by Maturi et al. (2010, J. Risk Reliab. 224, 11–26). In this paper further results for such inferences are presented, with focus on four important and closely related aspects. First, the effect of defined failure modes which thus far have not yet caused failures is studied. Second, the effect of re-defining (groups of) failure modes is considered, followed by a discussion of possible unknown, so undefined, failure modes. Finally, the effect of removal of failure modes is illustrated.
Propagation characteristics of finite-width conductor-backed coplanar waveguides with periodic electromagnetic bandgap cells

Wave propagation along the finite-width conductor-backed coplanar waveguide (FW-CBCPW) with periodically loaded one-dimensional electromagnetic bandgap (EBG) cells proposed earlier by the authors is investigated theoretically and experimentally in this paper. The full-wave simulation in conjunction with Floquet's theorem is employed to find the dispersion diagram for characterizing the guided and leaky waves over a wide frequency range. For examining the guided-wave mode, the equivalent-circuit model is established to obtain the analytical formula of the Bloch impedance. The remarkable slow-wave factor 1.9-2.9 times higher than that of a conventional FW-CBCPW is presented. When operating frequency is sufficiently high, the leaky-wave mode is emitted so that the structure radiates in the backward direction. Good agreement among the results of the full-wave simulation, equivalent-circuit model, published data, and measurement supports the usefulness of the proposed full-wave simulation and also validates the analytical formula. By properly adjusting the circuit configuration, the periodic EBG structure with controllable propagation characteristics, which include the bandgap zone, the slow-wave factor, and the Bloch impedance for the guided wave, as well as the radiation main beam for the leaky wave, may be achieved.