Miracle-dz/UniFAR-FTUs huggingface dataset:
Chromosome-Level Genome Assembly of the Asian Red-Tail Catfish (Hemibagrus wyckioides)

Aquaculture plays a vital role in food security and economic stability worldwide (Houston et al., 2020). Selective breeding to genetically improve production traits has great potential in increasing the efficiency of aquaculture and reducing its environmental footprint (such as habitat destruction and infectious disease outbreaks). To achieve this, we require fish species with excellent economic traits and high-quality genomic data that can be applied at all stages of domestication for ongoing genetic improvement (Houston, et al., 2020). Siluriformes (catfish) is an order of major aquaculture species worldwide, especially in China, the United States, and Vietnam (De Silva and Phuong, 2011; Zhong et al., 2016; Kumar et al., 2020). Redtail catfish (Hemibagrus wyckioides), belonging to the family Bagridae, initially possess a white caudal fin that becomes bright red when it reaches approximately 15 cm. The red-tail catfish is the largest Bagridae fish in body size and weight, reaching 130 cm and 80 kg, respectively (Ng, 1999). Red-tail catfish were originally distributed throughout the Mekong River. In China, they are now only distributed in Yunnan Province. Here, it is a famous indigenous fish due to a variety of excellent economic traits such as high protein content, strong disease resistance, easy domestication, and better production performance; it also has ornamental value (Zhou et al., 2021). Therefore, it has recently become an important aquaculture species in China (Zhou et al., 2019; Zhou et al., 2021). H. wyckioides exhibits marked sex dimorphism in growth, with the males growing much faster than females. Sexual maturation takes over 3 years and a lack of selective breeding has resulted in a decline in the growth rate of red-tail catfish (Zhou et al., 2021). Thus, it is essential to construct a reference genome of H. wyckioides and establish a breeding program to improve the economic characteristics, maintaining and developing the industry, to ultimately create an economically viable local fishing industry.
Time Course of Severe Fever With Thrombocytopenia Syndrome Virus and Antibodies in Patients by Long-Term Follow-Up Study, China

Objectives: The objective was to describe the changes of severe fever with thrombocytopenia syndrome virus (SFTSV) and antibody in the disease course and explore the relationship between antibody titers and patients’ prognosis. Methods: The levels of SFTSV, virus-specific immunoglobulin M (IgM), immunoglobulin G (IgG) titers, and cytokines in 37 patients with severe fever with thrombocytopenia syndrome (SFTS) were measured dynamically by real-time PCR and ELISA during the disease course; IgG titers were followed up in 53 cases. The correlation analysis of antibody titers with individual serum cytokines was calculated using the Spearman test. Results: The average time of SFTSV duration in individual serum was 22.45 ± 7.6 days from onset. We found SFTSV turned negative within the 10th day from the onset in two patients. SFTSV-specific IgM seroconversion occurred as early as within 3 days from the onset, increased gradually within the first 2 months, decreased gradually 3 months later, and disappeared after 6 months in all the patients. The average time of SFTSV-specific IgG antibody seroconversion was at 17 days from onset in the patients; the time was later in severe cases than in mild cases (23 ± 1.4 vs. 14.3 ± 1.0 days, p < 0.0001). IgG titers were maintained at the peak levels during the periods from 6 months to 1 year and decreased from the second year gradually. Severe cases had higher IgG levels than mild cases and also had a slower decreasing trend. During follow-up, only one lost IgG antibody 7 years later; no chronic infection and sequela were found among the 53 patients. None of the patients had SFTSV reinfection even if they were bitten by ticks again. The correlation analysis showed a positive relationship between inflammatory factors and IgG antibody levels. Conclusion: IgM antibody has important value in early diagnosis of SFTS. A moderate inflammatory response is beneficial for production and duration of IgG antibodies.
Inverted CD8 T-Cell Exhaustion and Co-Stimulation Marker Balance Differentiate Aviremic HIV-2-Infected From Seronegative Individuals

HIV-2 is less pathogenic compared to HIV-1. Still, disease progression may develop in aviremic HIV-2 infection, but the driving forces and mechanisms behind such development are unclear. Here, we aimed to reveal the immunophenotypic pattern associated with CD8 T-cell pathology in HIV-2 infection, in relation to viremia and markers of disease progression. The relationships between pathological differences of the CD8 T-cell memory population and viremia were analyzed in blood samples obtained from an occupational cohort in Guinea-Bissau, including HIV-2 viremic and aviremic individuals. For comparison, samples from HIV-1- or dually HIV-1/2-infected and seronegative individuals were obtained from the same cohort. CD8 T-cell exhaustion was evaluated by the combined expression patterns of activation, stimulatory and inhibitory immune checkpoint markers analyzed using multicolor flow cytometry and advanced bioinformatics. Unsupervised multidimensional clustering analysis identified a cluster of late differentiated CD8 T-cells expressing activation (CD38+, HLA-DRint/high), co-stimulatory (CD226+/-), and immune inhibitory (2B4+, PD-1high, TIGIThigh) markers that distinguished aviremic from viremic HIV-2, and treated from untreated HIV-1-infected individuals. This CD8 T-cell population displayed close correlations to CD4%, viremia, and plasma levels of IP-10, sCD14 and beta-2 microglobulin in HIV-2 infection. Detailed analysis revealed that aviremic HIV-2-infected individuals had higher frequencies of exhausted TIGIT+ CD8 T-cell populations lacking CD226, while reduced percentage of stimulation-receptive TIGIT-CD226+ CD8 T-cells, compared to seronegative individuals. Our results suggest that HIV-2 infection, independent of viremia, skews CD8 T-cells towards exhaustion and reduced co-stimulation readiness. Further knowledge on CD8 T-cell phenotypes might provide help in therapy monitoring and identification of immunotherapy targets.
[18F](2S,4R)-4-Fluoroglutamine as a New Positron Emission Tomography Tracer in Myeloma

The high glycolytic activity of multiple myeloma (MM) cells is the rationale for use of Positron Emission Tomography (PET) with 18F-fluorodeoxyglucose ([18F]FDG) to detect both bone marrow (BM) and extramedullary disease. However, new tracers are actively searched because [18F]FDG-PET has some limitations and there is a portion of MM patients who are negative. Glutamine (Gln) addiction has been recently described as a typical metabolic feature of MM cells. Yet, the possible exploitation of Gln as a PET tracer in MM has never been assessed so far and is investigated in this study in preclinical models. Firstly, we have synthesized enantiopure (2S,4R)-4-fluoroglutamine (4-FGln) and validated it as a Gln transport analogue in human MM cell lines, comparing its uptake with that of 3H-labelled Gln. We then radiosynthesized [18F]4-FGln, tested its uptake in two different in vivo murine MM models, and checked the effect of Bortezomib, a proteasome inhibitor currently used in the treatment of MM. Both [18F]4-FGln and [18F]FDG clearly identified the spleen as site of MM cell colonization in C57BL/6 mice, challenged with syngeneic Vk12598 cells and assessed by PET. NOD.SCID mice, subcutaneously injected with human MM JJN3 cells, showed high values of both [18F]4-FGln and [18F]FDG uptake. Bortezomib significantly reduced the uptake of both radiopharmaceuticals in comparison with vehicle at post treatment PET. However, a reduction of glutaminolytic, but not of glycolytic, tumor volume was evident in mice showing the highest response to Bortezomib. Our data indicate that [18F](2S,4R)-4-FGln is a new PET tracer in preclinical MM models, yielding a rationale to design studies in MM patients.
Presence of Antibodies to SARS-CoV-2 in Domestic Cats in Istanbul, Turkey, Before and After COVID-19 Pandemic

Recent studies demonstrated that domestic cats can be naturally and experimentally infected with severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). This study was performed to investigate the presence of SARS-CoV-2-specific antibodies within the domestic cat population in Istanbul, Turkey, before the coronavirus disease 2019 (COVID-19) and during the COVID-19 pandemic. Overall, from 155 cat sera analyzed, 26.45% (41/155) tested positive in the spike protein-ELISA (S-ELISA), 28.38% (44/155) in the receptor-binding domain-ELISA (RBD-ELISA), and 21.9% (34/155) in both, the S- and RBD-ELISAs. Twenty-seven of those were also positive for the presence of antibodies to feline coronavirus (FCoV). Among the 34 SARS-CoV-2-positive sera, three of those were positive on serum neutralization assay. Six of the 30 cats before COVID-19 and 28 of the 125 cats during COVID-19 were found to be seropositive. About 20% of ELISA-positive cats exhibited mainly respiratory, gastrointestinal, and renal signs and skin lesions. Hematocrit, hemoglobin, white blood cells, lymphocyte, and platelet numbers were low in about 30% of ELISA-positive cats. The number of neutrophils and monocytes were above normal values in about 20% of ELISA-positive cats. The liver enzyme alanine aminotransferase levels were high in 23.5% ELISA-positive cats. In conclusion, this is the first report describing antibodies specific to SARS-CoV-2 antigens (S and RBD) in cats in Istanbul, Turkey, indicating the risk for domestic cats to contract SARS-CoV-2 from owners and/or household members with COVID-19. This study and others show that COVID-19-positive pet owners should limit their contact with companion animals and that pets with respiratory signs should be monitored for SARS-CoV-2 infections.
Risk Factors Associated With Diabetic Retinopathy: A Cross-Sectional Study Within Palestinian Patients in Northern West Bank

Risk factors associated with diabetes mellitus (DM) have been widely researched worldwide, but the determinants of these factors among diabetic retinopathy (DR) in Palestine are currently unclear. We aimed to assess the prevalence of DR among DM in Northern West Bank and identify factors associated with DR natural history. Patients with Type 2 diabetes (T2D) (n = 300, age > 18 years) from a main diabetic center covering all northern provinces of Palestine were enrolled to this cross-sectional research. Demographic information including age, sex, and duration of T2D was obtained. Moreover, HbA1C, BMI, hypertension (HTN), controlled T2D, current smoking, and total cholesterol level were assessed. Potential correlations between these factors and DR diagnosed by ophthalmologist were evaluated using different tests on SPSS version 22. Prevalence of DR among our population was 30%; 47.8% of these patients showed mild non-proliferative DR (NPDR), 23.3% moderate NPDR, 16.7% severe NPDR, and 12.2% proliferative DR (PDR). Univariate logistic regression analysis showed age (p = 0.007), HTN (p = 0.022), uncontrolled T2D (p = 0.025), and duration of T2D (<0.001) were mostly associated with DR while multivariate logistic regression showed duration of T2D as the major and solely risk factor for prevalence of DR (p < 0.0001) and were positively correlated with severities of NPDR and being a strong predictor in the PDR (p = 0.001). We identified several important risk factors that affect DR, which could assist to develop effective strategies for metabolic disease prevention among populations in Palestine. Furthermore, our data suggest a necessity to control sugar serum levels and HTN.
Menstrual Cycle Phase, Hormonal Contraception, and Alcohol Consumption in Premenopausal Females: A Systematic Review

Women may be particularly vulnerable to alcohol harm, but many current theories fail to acknowledge the unique factors that influence female alcohol use. The biological mechanisms underlying female alcohol consumption have largely been unexplored, although recently the menstrual cycle has been highlighted as a potentially important factor. This systematic review, using a narrative synthesis, examined the association between the menstrual cycle phases on alcohol consumption and aimed to determine whether hormonal contraception influences this association. The review follows PRISMA and SWiM guidelines, registration number: CRD42018112744. Electronic searches were conducted in the relevant databases with keyword (e.g., “menstrua*”; “alcohol”). Thousand six hundred and sixty-two titles were identified, 16 of which were included in the review. Results were inconsistent regarding whether an association between menstrual cycle phase and alcohol consumption was found. Furthermore, there was inconsistency regarding which phase was associated with higher consumption, and different factors were reported to have moderated the direction, e.g., family history of alcohol use disorder (AUD), premenstrual syndrome (PMS). These conflicting results may be partly explained by variability in both study quality and design, and differences in measurement of cycle phase and alcohol consumption. More robust research is needed before conclusions can be drawn with regard to the role of the menstrual cycle and hormonal contraception on female drinking behavior. This review provides recommendations to strengthen research in this area.
Siglec-8 Signals Through a Non-Canonical Pathway to Cause Human Eosinophil Death In Vitro

Sialic acid-binding immunoglobulin-like lectin (Siglec)-8 is a glycan-binding receptor bearing immunoreceptor tyrosine-based inhibitory and switch motifs (ITIM and ITSM, respectively) that is selectively expressed on eosinophils, mast cells, and, to a lesser extent, basophils. Previous work has shown that engagement of Siglec-8 on IL-5–primed eosinophils causes cell death via CD11b/CD18 integrin–mediated adhesion and NADPH oxidase activity and identified signaling molecules linking adhesion, reactive oxygen species (ROS) production, and cell death. However, the proximal signaling cascade activated directly by Siglec-8 engagement has remained elusive. Most members of the Siglec family possess similar cytoplasmic signaling motifs and recruit the protein tyrosine phosphatases SHP-1/2, consistent with ITIM-mediated signaling, to dampen cellular activation. However, the dependence of Siglec-8 function in eosinophils on these phosphatases has not been studied. Using Siglec-8 antibody engagement and pharmacological inhibition in conjunction with assays to measure cell-surface upregulation and conformational activation of CD11b integrin, ROS production, and cell death, we sought to identify molecules involved in Siglec-8 signaling and determine the stage of the process in which each molecule plays a role. We demonstrate here that the enzymatic activities of Src family kinases (SFKs), Syk, SHIP1, PAK1, MEK1, ERK1/2, PLC, PKC, acid sphingomyelinase/ceramidase, and Btk are all necessary for Siglec-8–induced eosinophil cell death, with no apparent role for SHP-1/2, SHIP2, or c-Raf. While most of these signaling molecules are necessary for Siglec-8–induced upregulation of CD11b integrin at the eosinophil cell surface, Btk is phosphorylated and activated later in the signaling cascade and is instead necessary for CD11b activation. In contrast, SFKs and ERK1/2 are phosphorylated far earlier in the process, consistent with their role in augmenting cell-surface levels of CD11b. In addition, pretreatment of eosinophils with latrunculin B or jasplakinolide revealed that actin filament disassembly is necessary and sufficient for surface CD11b integrin upregulation and that actin polymerization is necessary for downstream ROS production. These results show that Siglec-8 signals through an unanticipated set of signaling molecules in IL-5–primed eosinophils to induce cell death and challenges the expectation that ITIM-bearing Siglecs signal through inhibitory pathways involving protein tyrosine phosphatases to achieve their downstream functions.
Predictors of Mortality in Progressive Fibrosing Interstitial Lung Diseases

Background: Progressive fibrosing interstitial lung disease (PF-ILD) and idiopathic pulmonary fibrosis (IPF) share similar progression phenotype but with different pathophysiological mechanism. The purpose of this study was to assess clinical characteristics and outcomes of patients with PF-ILD in a single-center cohort. Methods: Patients with PF-ILD treated in Shanghai Pulmonary Hospital from Jan. 2013 to Dec. 2014 were retrospectively analyzed. Baseline characteristics and clinical outcomes were collected for survival analysis to identifying clinical predictors of mortality. Results: Among 608 patients with ILD, 132 patients met the diagnostic criteria for PF-ILD. In this single-center cohort, there were 51 (38.6%) cases with connective tissue disease-associated interstitial lung disease (CTD-ILD) and 45 (34.1%) with unclassifiable ILDs. During follow-up, 83 patients (62.9%) either died (N = 79, 59.8%) or underwent lung transplantations (N = 4, 3.0%) with a median duration follow-up time of 53.7 months. Kaplan-Meier survival curves revealed that the 1, 3 and 5-years survival of PF-ILD were 90.9, 58.8 and 48.1%, respectively. In addition, the prognosis of patients with PF-ILD was similar to those with IPF, while it was worse than non-PF-ILD ones. Multivariate Cox regression analysis demonstrated that high-resolution computed tomography (HRCT) scores (HR 1.684, 95% CI 1.017–2.788, p = 0.043) and systolic pulmonary artery pressure (SPAP) > 36.5 mmHg (HR 3.619, 95%CI 1.170–11.194, p = 0.026) were independent risk factors for the mortality of PF-ILD. Conclusion: Extent of fibrotic changes on HRCT and pulmonary hypertension were predictors of mortality in patients with PF-ILD.
Retinal Oxygen Metabolism and Haemodynamics in Patients With Multiple Sclerosis and History of Optic Neuritis

Vascular changes and alterations of oxygen metabolism are suggested to be implicated in multiple sclerosis (MS) pathogenesis and progression. Recently developed in vivo retinal fundus imaging technologies provide now an opportunity to non-invasively assess metabolic changes in the neural retina. This study was performed to assess retinal oxygen metabolism, peripapillary capillary density (CD), large vessel density (LVD), retinal nerve fiber layer thickness (RNFLT) and ganglion cell inner plexiform layer thickness (GCIPLT) in patients with diagnosed relapsing multiple sclerosis (RMS) and history of unilateral optic neuritis (ON). 16 RMS patients and 18 healthy controls (HC) were included in this study. Retinal oxygen extraction was modeled using O2 saturations and Doppler optical coherence tomography (DOCT) derived retinal blood flow (RBF) data. CD and LVD were assessed using optical coherence tomography (OCT) angiography. RNFLT and GCIPLT were measured using structural OCT. Measurements were performed in eyes with (MS+ON) and without (MS-ON) history for ON in RMS patients and in one eye in HC. Total oxygen extraction was lowest in MS+ON (1.8 ± 0.2 μl O2/min), higher in MS-ON (2.1 ± 0.5 μl O2/min, p = 0.019 vs. MS+ON) and highest in HC eyes (2.3 ± 0.6 μl O2/min, p = 0.002 vs. MS, ANOVA p = 0.031). RBF was lower in MS+ON (33.2 ± 6.0 μl/min) compared to MS-ON (38.3 ± 4.6 μl/min, p = 0.005 vs. MS+ON) and HC eyes (37.2 ± 4.7 μl/min, p = 0.014 vs. MS+ON, ANOVA p = 0.010). CD, LVD, RNFLT and GCIPL were significantly lower in MS+ON eyes. The present data suggest that structural alterations in the retina of RMS patients are accompanied by changes in oxygen metabolism, which are more pronounced in MS+ON than in MS-ON eyes. Whether these alterations promote MS onset and progression or occur as consequence of disease warrants further investigation. Clinical Trial Registration: ClinicalTrials.gov registry, NCT03401879.
Kernel Water Relations and Kernel Filling Traits in Maize (Zea mays L.) Are Influenced by Water-Deficit Condition in a Tropical Environment

Water deficit is a major limiting condition for adaptation of maize in tropical environments. The aims of the current observations were to evaluate the kernel water relations for determining kernel developmental progress, rate, and duration of kernel filling, stem reserve mobilization in maize. In addition, canopy temperature, cell membrane stability, and anatomical adaptation under prolonged periods of pre- and post-anthesis water deficit in different hybrids was quantified to support observations related to kernel filling dynamics. In this context, two field experiments in two consecutive years were conducted with five levels of water regimes: control (D1), and four water deficit treatments [V10 to V13 (D2); V13 to V17 (D3); V17 to blister stage (D4); blisters to physiological maturity (D5)], on three maize hybrids (Pioneer 30B80, NK 40, and Suwan 4452) in Expt. 1. Expt. 2 had four water regimes: control (D1), three water deficit treatments [V10 to anthesis (D2); anthesis to milk stage (D3); milk to physiological maturity (D4)], and two maize hybrids (NK 40 and Suwan 4452). Water deficit imposed at different stages significantly reduced maximum kernel water content (MKWC), kernel filling duration (KFD), final kernel weight (FKW), and kernel weight ear–1 while it increased kernel water loss rate (KWLR), kernel filling rate (KFR), and stem weight depletion (SWD) across maize hybrids in both experiments. The lowest MKWC under water deficit was at D3 in both experiments, indicating that lower KFR results in lowest FKW in maize. Findings indicate that the MKWC (R2 = 0.85 and 0.41) and KFR (R2 = 0.62 and 0.37) were positively related to FKW in Expt. 1 and 2, respectively. The KFD was reduced by 5, 7, 7, and 11 days under water deficit at D3, D4 in Expt. 2 and D4, D5 in Expt. 1 as compared to control, respectively. Water deficit at D5 in Expt. 1 and D4 in Expt. 2 increased KWLR, KFR, and SWD. In Expt. 2, lower canopy temperature and electrical conductivity indicated cell membrane stability across water regimes in NK 40. Hybrid NK 40 under water deficit had significantly higher cellular adaptation by increasing the number of xylem vessel while reducing vessel diameter in leaf mid-rib and attached leaf blade. These physiological adjustments improved efficient transport of water from root to the shoot, which in addition to higher kernel water content, MKWC, KFD, KFR, and stem reserve mobilization capacity, rendered NK 40 to be better adapted to water-deficit conditions under tropical environments.
Enhanced Quality Factors of Surface Lattice Resonances in Plasmonic Arrays of Nanoparticles

Key in the application of plasmonics is the realization of low loss or high quality (Q) factor resonances. Nanoparticle arrays are systems capable of sustaining remarkably high Q‐factor resonances through the hybridization of plasmonic and photonic modes, known as surface lattice resonances (SLRs). SLRs result from the coupling of localized surface plasmon resonances (LSPRs) to in‐plane orders of diffraction known as Rayleigh anomalies (RAs). To date, the highest Q‐factors have been achieved with the (±1, 0) diffraction orders. However, these Q‐factors are highly sensitive to the angle of excitation. Here, a strategy is presented to generate high Q‐factor SLRs with low dispersion by coupling LSPRs to the (0, ±1) diffraction orders. 2D arrays of silver nanoparticles are investigated experimentally and numerically, and it is shown that the Q‐factor of SLRs critically depends on the quality of the metal film, the detuning between RAs and LSPRs, and the absorption of adhesive layer used between the substrate and the metallic nanoparticles. These silver nanoparticle arrays can achieve Q‐factors higher than 330 in the visible range. These extraordinarily high Q‐factors could be increased to values above 1500 if no adhesive layer is used, which could significantly improve sensors and enhance nonlinearities in plasmonic systems.