Miracle-dz/UniFAR-FTUs huggingface dataset:
Genetics, genomics, and diet interactions in obesity in the Latin American environment

Obesity is a chronic disease characterized by abnormal or excessive fat accumulation that could impact an individual’s health; moreover, the World Health Organization (WHO) has declared obesity a global epidemic since 1997. In Latin America, in 2016, reports indicated that 24.2% of the adult population was obese. The environmental factor or specific behaviors like dietary intake or physical activity have a vital role in the development of a condition like obesity, but the interaction of genes could contribute to that predisposition. Hence, it is vital to understand the relationship between genes and disease. Indeed, genetics in nutrition studies the genetic variations and their effect on dietary response; while genomics in nutrition studies the role of nutrients in gene expression. The present review represents a compendium of the dietary behaviors in the Latin American environment and the interactions of genes with their single nucleotide polymorphisms (SNPs) associated with obesity, including the risk allele frequencies in the Latin American population. Additionally, a bibliographical selection of several studies has been included; these studies examined the impact that dietary patterns in Latin American environments have on the expression of numerous genes involved in obesity-associated metabolic pathways.
Invisible clinical labor driving the successful integration of AI in healthcare

Artificial Intelligence and Machine Learning (AI/ML) tools are changing the landscape of healthcare decision-making. Vast amounts of data can lead to efficient triage and diagnosis of patients with the assistance of ML methodologies. However, more research has focused on the technological challenges of developing AI, rather than the system integration. As a result, clinical teams' role in developing and deploying these tools has been overlooked. We look to three case studies from our research to describe the often invisible work that clinical teams do in driving the successful integration of clinical AI tools. Namely, clinical teams support data labeling, identifying algorithmic errors and accounting for workflow exceptions, translating algorithmic output to clinical next steps in care, and developing team awareness of how the tool is used once deployed. We call for detailed and extensive documentation strategies (of clinical labor, workflows, and team structures) to ensure this labor is valued and to promote sharing of sociotechnical implementation strategies.
Predictive models for IOPs measured with NCT, GAT, and ORA among patients undergoing SMILE

Purpose: To develop predictive models for the intraocular pressure (IOP) of patients undergoing small incision lenticule extraction (SMILE) procedures, measured with a noncontact tonometer (NCT), Goldmann applanation tonometry (GAT), and an ocular response analyzer (ORA). Methods: In this prospective study, a total of 104 eyes (−6.23 ± 2.06 diopters) of 52 patients (24.38 ± 4.76 years) undergoing SMILE procedures were included. The intraocular pressure was measured (IOPNCT with NCT, IOPGAT with GAT, and IOPcc and IOPg with ORA) before surgery and at postoperative 6 months. Information on age, preoperative and attempted spherical equivalent (SE), ablation depth, preoperative values and postoperative changes in central corneal thickness (CCT), K1, K2, Km, corneal hysteresis (CH) and corneal resistance factor (CRF) values was collected in order to predict IOPs. Results: All surgeries were uneventful. At postoperative 6 months, the efficacy and safety index were 1.04 ± 0.15 and 1.08 ± 0.18, respectively. Significant decreases were detected in postoperative IOPNCT, IOPGAT, IOPcc, and IOPg compared to preoperative values (all p < 0.001). No relationship was found between any IOP and ablation depth, attempted SE, and preoperative SE, as well as CCTdifference (all p > 0.05). Predictive models for IOPs were constructed to predict preoperative values, and R 2 values were 67.5% (IOPNCT), 64.5% (IOPGAT), 78.7% (IOPcc), and 82.0% (IOPg). The prediction band of IOPNCT and IOPGAT was 7.4–15.1 mmHg and 8–16 mmHg, respectively. Conclusion: Predictive models for IOP measurements after SMILE procedures can be helpful in clinical practice.
Water-Vapor Maser Disk at the Nucleus of the Seyfert 2 Galaxy NGC 3079

We observed a Seyfert 2/LINER galaxy NGC 3079 using the NRO 45-m telescope from 1992 to 2002, and the Very Long Baseline Array (VLBA) in 2001 December, at 22 GHz. The 45-m telescope detected weak red-shifted and systemic features as well as strong blue-shifted features. High spatial resolution observations with the VLBA indicated that the H 2 O maser spots are distributed along the north–south direction, showing blue-shifted velocities in the north and red-shifted in the south. We propose a nearly edge-on molecular gas disk in the nuclear region of NGC 3079, whose radius varies from 0.4 to 1.2 pc and whose thickness is 0.3 pc. The disk is rotating at V rot = 200–100kms − 1 , having a large velocity dispersion of ∆ V ≈ 50kms − 1 . The binding mass within the disk is ∼ 10 6 M (cid:3) . The disk is inclined such that the east side is nearest to us. The large luminosity of the maser emission and exceptionally strong blue-shifted features of NGC 3079 are probably the result of local shocks in the disk. Three continuum components are interpreted as jets emitted from the nucleus. The velocities of the components relative to the dynamical center of the masing disk are (0 . 09–0 . 17) c , < 0 . 005 c , and < 0 . 05 c .
Assessment of a diverse panel of transmitted/founder HIV-1 infectious molecular clones in a luciferase based CD8 T-cell mediated viral inhibition assay

Introduction Immunological protection against human immunodeficiency virus-1 (HIV-1) infection is likely to require both humoral and cell-mediated immune responses, the latter involving cytotoxic CD8 T-cells. Characterisation of CD8 T-cell mediated direct anti-viral activity would provide understanding of potential correlates of immune protection and identification of critical epitopes associated with HIV-1 control. Methods The present report describes a functional viral inhibition assay (VIA) to assess CD8 T-cell-mediated inhibition of replication of a large and diverse panel of 45 HIV-1 infectious molecular clones (IMC) engineered with a Renilla reniformis luciferase reporter gene (LucR), referred to as IMC-LucR. HIV-1 IMC replication in CD4 T-cells and CD8 T-cell mediated inhibition was characterised in both ART naive subjects living with HIV-1 covering a broad human leukocyte antigen (HLA) distribution and compared with uninfected subjects. Results & discussion CD4 and CD8 T-cell lines were established from subjects vaccinated with a candidate HIV-1 vaccine and provided standard positive controls for both assay quality control and facilitating training and technology transfer. The assay was successfully established across 3 clinical research centres in Kenya, Uganda and the United Kingdom and shown to be reproducible. This IMC-LucR VIA enables characterisation of functional CD8 T-cell responses providing a tool for rational T-cell immunogen design of HIV-1 vaccine candidates and evaluation of vaccine-induced T-cell responses in HIV-1 clinical trials.
Effects of challenge with Clostridium perfringens, Eimeria and both on ileal microbiota of yellow feather broilers

In the poultry industry worldwide, Clostridium perfringens has been causing major economic loss as it can cause necrotic enteritis (NE). The coccidial infection has been considered as the most important predisposing factor of NE caused by C. perfringens. In this study, we aimed to advance our knowledge on ileal microbiota of yellow feather broilers under C. perfringens and/or Eimeria challenge. Total of 80 healthy day old yellow feather broilers were randomly assigned to four groups including: Control, C. perfringens challenge group (C. Per), Eimeria challenge group (Cocc), and C. perfringens plus Eimeria challenge group (Comb). On day 14, the Cocc and Comb group broilers were orally gavaged 1 ml PBS solution containing 25,000 oocysts of Eimeria brunetti and 25,000 oocysts of Eimeria maxima. Starting on day 17, the C. Per and Comb group broilers were orally gavaged 10 mL of C. perfringens per bird (4 × 107 CFU/mL, ATCC® 13124™ Strain) every day for 6 days. 16S rRNA gene sequencing was performed on extracted DNA of ileal digesta samples. The results showed that C. perfringens alone did not affect the alpha diversity of ileal microbiome in yellow feather broilers but co-infection with Eimeria significantly decreased the diversity of ileal microbiota. C. perfringens and Eimeria challenge also decreased the relative abundance of beneficial bacteria including Bacteroidetes at the phylum level and Faecalibacterium at the genus level. At the species level, the relative abundance of Candidatus Arthromitus was significantly decreased in the Eimeria challenged groups. This microbial shift information of ileal microbiota under C. Perfringens and Eimeria challenge provide important reference data for the development of therapeutic approaches to necrotic enteritis in yellow-feather broiler chickens.
Analysis of the timing of endoscopic treatment for esophagogastric variceal bleeding in cirrhosis

Background Existing guidelines recommend endoscopic treatment within 12 h or 12–24 h for patients with esophagogastric variceal bleeding (EGVB) in cirrhosis. In addition, research findings on the optimal time for endoscopy are inconsistent. Aim The aim of this study was to investigate the relationship between the timing of endoscopy and clinical outcomes in cirrhotic patients with EGVB and to analyze the risk factors for the composite outcomes after endoscopic treatment. Methods From January 2019 to June 2020, 456 patients with cirrhotic EGVB who underwent endoscopy were matched by a 1:1 propensity score. Finally, 266 patients were divided into two groups, including 133 patients within 12 h (urgent endoscopy group) of admission and after 12 h (non-urgent endoscopy group). Baseline data and clinical outcomes were compared. Logistic regression model analysis was used to determine risk factors for 30 days rebleeding and mortality. Results In 266 patients, the overall 30 days rebleeding rate and mortality were 10.9% (n = 29) and 3.4% (n = 9), respectively. Patients who underwent endoscopic treatment within 12 h had significantly higher 30 days rebleeding outcomes than those who underwent treatment beyond 12 h (15 vs. 6.8%, p = 0.003). However, 30 days mortality did not differ significantly between the two groups (3 vs. 3.8%, p = 0.736). Logistic regression analysis showed that age and shock on admission were independent risk factors for the composite outcome of 30 days rebleeding and mortality in patients with EGVB. Conclusion The 30 days rebleeding rate in patients with cirrhotic EGVB treated with urgent endoscopy was significantly higher than that in patients treated with non-urgent endoscopy, but there was no significant difference in 30 days mortality.
MM/PB(GB)SA benchmarks on soluble proteins and membrane proteins

Predicting protein-ligand binding free energy rapidly and accurately remains a challenging question in modern drug discovery. Molecular mechanics/Poisson-Boltzmann (Generalized Born) surface area (MM/PB(GB)SA) has emerged as an essential tool for accelerating cost-efficient binding free energy calculation. This study presents benchmarks with three membrane-bound protein systems and six soluble protein systems. Different parameters were sampled for different benchmarks to explore the highest accuracy. These include ligand charges, protein force fields, extra points, GB models, nonpolar optimization methods, internal dielectric constants and membrane dielectric constants. Comparisons of accuracy were made between MM/PB(GB)SA, docking and free energy perturbation (FEP). The results reveal a competitive performance between MM/PB(GB)SA and FEP. In summary, MM/PB(GB)SA is a powerful approach to predict ligand binding free energy rapidly and accurately. Parameters of MM/PB(GB)SA calculations, such as the GB models and membrane dielectric constants, need to be optimized for different systems. This method can be served as a powerful tool for drug design.
Modulations of static and dynamic functional connectivity among brain networks by electroacupuncture in post-stroke aphasia

Introduction Post-stroke aphasia (PSA) is a language disorder caused by left hemisphere stroke. Electroacupuncture (EA) is a minimally invasive therapeutic option for PSA treatment. Tongli (HT5) and Xuanzhong (GB39), two important language-associated acupoints, are frequently used in the rehabilitation of patients with PSA. Preliminary evidence indicated functional activation in distributed cortical areas upon HT5 and GB39 stimulation. However, research on the modulation of dynamic and static functional connectivity (FC) in the brain by EA in PSA is lacking. Method This study aimed to investigate the PSA-related effects of EA stimulation at HT5 and GB39 on neural processing. Thirty-five participants were recruited, including 19 patients with PSA and 16 healthy controls (HCs). The BOLD signal was analyzed by static independent component analysis, generalized psychophysiological interactions, and dynamic independent component analysis, considering variables such as age, sex, and years of education. Results The results revealed that PSA showed activated clusters in the left putamen, left postcentral gyrus (PostCG), and left angular gyrus in the salience network (SN) compared to the HC group. The interaction effect on temporal properties of networks showed higher variability of SN (F = 2.23, positive false discovery rate [pFDR] = 0.017). The interaction effect on static FC showed increased functional coupling between the right calcarine and right lingual gyrus (F = 3.16, pFDR = 0.043). For the dynamic FC, at the region level, the interaction effect showed lower variability and higher frequencies of circuit 3, with the strongest connections between the supramarginal gyrus and posterior cingulum (F = 5.42, pFDR = 0.03), middle cingulum and PostCG (F = 5.27, pFDR = 0.036), and triangle inferior frontal and lingual gyrus (F = 5.57, pFDR = 0.026). At the network level, the interaction effect showed higher variability in occipital network–language network (LN) and cerebellar network (CN) coupling, with stronger connections between the LN and CN (F = 4.29, pFDR = 0.042). Dynamic FC values between the triangle inferior frontal and lingual gyri were anticorrelated with transcribing, describing, and dictating scores in the Chinese Rehabilitation Research Center for Chinese Standard Aphasia Examination. Discussion These findings suggest that EA stimulation may improve language function, as it significantly modulated the nodes of regions/networks involved in the LN, SN, CN, occipital cortex, somatosensory regions, and cerebral limbic system.
Implicit spatial sequential learning facilitates attentional selection in covert visual search. An event-related potentials study

Introduction While most studies on implicit sequential learning focus on object learning, the hidden structure of target location and onset time can also be a subject of implicitly gathered knowledge. In our study, we wanted to investigate the effect of implicitly learned spatial and temporal sequential predictability on performance in a localization task in a paradigm in which covert selective attention is engaged. We were also interested in the neural mechanism of the facilitating effect of the predictable spatio-temporal context on visual search processes. Specifically, with the use of an event-related potential technique, we wanted to verify whether perceptual, attentional, and motor processes can be enhanced by the predictive spatio-temporal context of visual stimuli. Methods We analyzed data from 15 young, healthy adults who took part in an experimental electroencephalographic (EEG) study and performed a visual search localization task. Predictable sequences of four target locations and/or target onset times were presented in separate blocks of trials that formed the Space, Space- Time, and Time conditions. One block of trials with randomly presented stimuli served as a control condition. Results The behavioral results revealed that participants successfully learned only the spatial dimension of target predictability. Although spatial predictability was a response-relevant dimension, we found that attentional selection–instead of motor preparation–was the facilitation mechanism in this type of visual search task. This was manifested by a shorter latency and more negative amplitude of the N2pc component and the lack of an effect on the sLRP component. We observed no effect of predictability on perceptual processing (P1 component). Discussion We discuss these results with reference to the current knowledge on sequential learning. Our findings also contribute to the current debate on the predictive coding theory.
Nitrogen inclusion in carbon nanotubes initiated by boron doping and chlorination: Their use as electrocatalysts for oxygen reduction reaction

The use of carbon nanostructures doped with heteroatoms as electrocatalysts for oxygen reduction reaction (ORR) has attracted intense research in recent years because they are highly conductive, have good durability, and are highly electro-active. One of the strategies to modify the characteristics of carbon nanomaterials (CNMs) to render them suitable for certain applications is to dope them with boron (B) and nitrogen (N). The effect of doping CNMs with boron has been a subject of little study, and hence, it is not well understood, as compared to nitrogen doping studies. In this study, nitrogen was unintentionally doped into carbon nanotubes (CNTs) by chlorination and decomposition of triphenylborane in a catalytic vapor deposition (CVD) reactor. N-doping resulted from the use of nitrogen as a carrier gas. Microscopic and spectroscopic techniques revealed that N bonding of carbon nanostructures together with the presence of defects played pivotal roles in determining the extent of ORR performance of produced CNMs. The introduction of N in the carbon matrix during B molecule decomposition resulted in the reduction in the amount of B doped into the matrix, due to competitive incorporation of N which inhibited B introduction. The presence of pyridinic N species was responsible for a 2e− ORR performance.
Mild COVID-19 induces early, quantifiable, persistent troponin I elevations in elder men

Importance Elderly patients, especially men, are at risk of increased morbidity from coronavirus disease 2019 (COVID-19). Long-term data on troponin I levels in longitudinal observational studies of outpatients with mild to moderate COVID-19 are scarce. Objective This controlled cohort study aimed to evaluate the course of troponin I concentrations over a long period in convalescent COVID-19 outpatients with mild to moderate symptoms. Setting and participants In this cohort study, individuals with PCR-confirmed, mild to moderate SARS-CoV-2 infection as well as control individuals with confirmed negative PCR and negative SARS-CoV-2 serology were included. Study visits were performed from April 2020 through July 2021 (initialized during the first wave of the corona pandemic in Switzerland). A study visit in patients comprised blood draws every week in the first month and additionally after 8 weeks. This course was repeated in patients observed long-term. Results This study enrolled 278 individuals from the Canton of St. Gallen, Switzerland, aged 12–92 years (59.5% women), who had mild to moderate COVID-19 symptoms (outpatients only) and a diagnosis confirmed by positive RT-PCR. Fifty-four of the participants with confirmed SARS-CoV-2 infection were followed for 14 months with repeat cycles of the testing protocol. In addition, 115 symptomatic patients that were PCR and serology negative were enrolled in the same time period as a control group. In COVID-19 patients, low-level troponin I concentrations (cTnI) were significantly increased from baseline until week 9 after positive RT-PCR diagnosis in men older than 54 years [ΔcTnI = 5.0 ng/L (median); 95% CI 4.1–6.0; p = 0.02]. The troponin I concentration remained elevated throughout 14 months in men older than 54 years within the cohort with a prolonged observation period. This statistically significant change in troponin I concentration was not dependent on co-morbidities in this group. ALT, Creatinine, BNP, and D-Dimer values after convalescence did not differ in comparison to the control cohort. Conclusion In this analysis of individuals with confirmed SARS-CoV-2 infection, hs troponin I levels of men aged 54 or older significantly increased after infection. They remained elevated for at least 14 months after diagnosis. This suggests the possibility of an ongoing, long-term, low-grade myocardial injury. Further studies with focus on elderly patients and a prolonged observational period are necessary to elucidate whether the phenomenon observed is associated with detectable structural changes to the heart muscle or is without further clinical consequences.
Canagliflozin reverses Th1/Th2 imbalance and promotes podocyte autophagy in rats with membranous nephropathy

Idiopathic membranous nephropathy is the main cause of chronic kidney disease (CKD). Studies have shown sodium–glucose co-transporter 2 (SGLT2) inhibitors significantly delay renal outcomes in patients with CKD, but the exact mechanism remains unknown. In this study, we investigated the mechanism by which the SGLT2 inhibitor canagliflozin attenuates podocyte injury by reversing the imbalance in Helper T cell 1 (Th1)/Helper T cell 2 (Th2) in peripheral blood of rats with membranous nephropathy (MN). MN rats were gavaged with canagliflozin (10 mg/kg/d) and losartan (10 mg/kg/d), respectively, for eight weeks. Compared with the MN group, the urinary ratio of total protein and the creatinine levels of the canagliflozin group decreased significantly. Canagliflozin improved the glomerulus pathological damage, increased the expression levels of podocyte marker proteins. The protective effect of canagliflozin on kidneys was more obvious than that of losartan. Treatment with canagliflozin increased the proportion of Th1 cells by 2.3 times, decreased the proportion of Th2 cells by 68.5%, and significantly restrained the synthesis of immunoglobulin G1 in B-cells and glomerulus subepithelial immune complex deposition. Co-culture of B-cells derived from MN rats with podocytes triggered the activation of phosphorylation of mTOR and ULK1 of podocytes, inhibited podocyte autophagy and resulted in podocyte injury. B-cells derived from canagliflozin treatment rats reversed these effects above. In conclusion, canagliflozin exerts a protective effect on kidneys by reversing the imbalance in Th1/Th2 cells in MN rats and restoring the autophagy of podocytes inhibited by the abnormal immunoglobulin G secretion from B-cells.
Responses to dichotic tone-in-noise stimuli in the inferior colliculus

Human listeners are more sensitive to tones embedded in diotic noise when the tones are out-of-phase at the two ears (N0Sπ) than when they are in-phase (N0S0). The difference between the tone-detection thresholds for these two conditions is referred to as the binaural masking level difference (BMLD) and reflects a benefit of binaural processing. Detection in the N0Sπ condition has been explained in modeling studies by changes in interaural correlation (IAC), but this model has only been directly tested physiologically for low frequencies. Here, the IAC-based hypothesis for binaural detection was examined across a wide range of frequencies and masker levels using recordings in the awake rabbit inferior colliculus (IC). IAC-based cues were strongly correlated with neural responses to N0Sπ stimuli. Additionally, average rate-based thresholds were calculated for both N0S0 and N0Sπ conditions. The rate-based neural BMLD at 500 Hz matched rabbit behavioral data, but the trend of neural BMLDs across frequency differed from that of humans.