Miracle-dz/UniFAR-FTUs huggingface dataset:
Skin Application of Menthol Enhances Maximal Isometric Lifting Performance

Abstract Over, DM, Arjomandkhah, N, Beaumont, JD, Goodall, S, and Barwood, MJ. Skin application of menthol enhances maximal isometric lifting performance. J Strength Cond Res 37(3): 564–573, 2023—Topical application of menthol to the skin improves perception (i.e., makes subjects feel cooler) and changes submaximal neuromuscular recruitment facilitating force generation. We explored the effect of menthol (0.2% concentration; sprayed on the legs), on perception and maximal, dynamic (DLT) and isometric (IMLT) (weight) lifting tasks. Nine resistance-trained male subjects (mean ± SD: 24 ± 5 years; 75.7 ± 8.8 kg; 174 ± 10 cm; 5 repetition maximum deadlift [5RM] 132.3 ± 28.5 kg) were tested using a repeated measures design; we hypothesized that performance would improve. Before completing the DLT (i.e., deadlift performance 75% 1RM) and a midthigh pull dynamometer IMLT, subjects were sprayed with (∼125 ml) of menthol or control spray. Performance, electromyography (root mean squared [rmsEMG], rectus femoris [RF], biceps femoris [BF], and medial gastrocnemius [MG]), perceptions (leg thermal sensation [TSlegs] and comfort [TClegs] and perceived exertion [RPE] and readiness to train), heart rate, and skin temperature were measured. Data were compared using analysis of variance (effect size ηp2) and t test to a 0.05 alpha level supported by Bayesian analysis. Dynamic lifting task performance was unchanged, although BF rmsEMG was higher (i.e., greater muscle activation in final [10th] repetition). Isometric lifting task force production was higher in the menthol spray (148 ± 30 kgf) condition (control spray 140 ± 30 kgf; p = 0.035, ηp2 = 0.444) with corresponding higher rmsEMG (BF 3.8 ± 1.46 vs. control spray 2.9 ± 0.34 V; p = 0.049, ηp2 = 0.403). TSlegs was lower after menthol spray before IMLT; subjects felt slightly cool. Menthol spray enhances isometric weightlifting performance with corresponding changes in neuromuscular activity, partially supporting our hypothesis.
Association of dietary fiber with subjective sleep quality in hemodialysis patients: a cross-sectional study in China

Abstract Background Poor sleep quality is a common problem among hemodialysis (HD) patients. Dietary fiber is a key component of a healthy diet and is beneficial for a variety of health outcomes; however, evidence of an association between dietary fiber consumption and subjective sleep quality has not been established among HD patients. Therefore, we determined the association between dietary fiber consumption and the subjective sleep quality in Chinese maintenance HD patients, taking into account fiber type and source. Methods Dietary intake was assessed with a validated food frequency questionnaire in a cross-sectional study including 741 maintenance HD patients between December 2021 and January 2022. The daily intake of dietary fiber was categorized into three groups. The lowest tertile was used as the reference category. Sleep quality of patients was accurately calculated using the Pittsburgh sleep quality index standard questionnaire. Multivariable logistic regression model and restricted cubic spline analysis were performed to assess the relationship between dietary fiber consumption and poor sleep quality. Results Compared with the lowest tertile group of dietary fiber intake, the highest tertile group had a lower prevalence of poor sleep quality. After adjustment for potential confounders, a higher intake of total dietary fiber (ORtertile 3 (T3) to tertile 1 (T1)= 0.51, 95% CI: 0.31–0.85), total insoluble dietary fiber (ORT3 to T1 =0.54, 95% CI: 0.33–0.89), and soluble dietary fiber in vegetables (ORT3 to T1 =0.61, 95% CI: 0.40–0.93) were associated with a lower prevalence of poor sleep quality. Furthermore, significant linear trends were also observed (p < 0.05). No significant interactions were observed in subgroup analyses. Conclusion A higher intake of dietary fiber was inversely associated with the poor sleep quality. These findings support the current recommendations that dietary fiber is essential for health and well-being. Key messages This study was conducted because there was not prior evidence connecting sleep quality and dietary fiber consumption in hemodialysis patients. In the present study a cross-sectional design was used to assess the association between dietary fiber consumption and poor sleep quality. Intake of total dietary fiber, total insoluble dietary fiber, and soluble dietary fiber in vegetables were negatively associated with poor sleep quality among maintenance hemodialysis patients.
Phenotypic heterogeneity in 22q11.2 deletion syndrome: Copy Number Variants as genetic modifiers for congenital heart disease in a Brazilian cohort

The clinical heterogeneity in 22q11.2 deletion syndrome (22q11.2DS) underlies complex genetic mechanisms including variants in other regions of the genome, known as genetic modifiers. Congenital heart disease (CHD) is one of the most relevant phenotypes in the syndrome and copy number variants (CNVs) outside the 22q11.2 region could play a role in its variable expressivity. Since those described loci account for a small proportion of the variability, the CNV analysis in new cohorts from different ancestry‐based populations constitutes a valuable resource to identify a wider range of modifiers. We performed SNP‐array in 117 Brazilian patients with 22q11.2DS, with and without CHD, and leveraged genome‐wide CNV analysis. After quality control, we selected 50 CNVs in 38 patients for downstream analysis. CNVs' genetic content and implicated biological pathways were compared between patients with and without CHD. CNV‐affected genes in patients with CHD were enriched for several functional terms related to ubiquitination, transcription factor binding sites and miRNA targets, highlighting the complexity of the phenotype's expressivity. Cardiac‐related genes were identified in both groups of patients suggesting that increasing risk and protective mechanisms could be involved. These genes and enriched pathways could indicate new modifiers to the cardiac phenotype in 22q11.2DS patients.
Periostin as an important biomarker of inflammatory phenotype T2 in Brazilian asthma patients

ABSTRACT Objective: The aim of this study was to assess the laboratory performance of periostin associated with a panel of biomarkers to identify the inflammatory phenotype of Brazilian asthma patients. Methods: We evaluated 103 Brazilian individuals, including 37 asthmatics and 66 nonasthmatic controls. Both groups underwent analyses for serum periostin, eosinophil levels in the peripheral blood, the fraction of exhaled nitric oxide (FeNO), total serum IgE, urinary leukotriene E4, and serum cytokines. Results: Higher levels of periostin (p = 0.005), blood eosinophils (p = 0.012), FeNO (p = 0.001), total IgE (p < 0.001), and IL-6 (p ≤ 0.001) were found in the asthmatic patients than the controls. Biomarker analyses by the ROC curve showed an AUC greater than 65%. Periostin (OR: 12,550; 95% CI: 2,498-63,063) and IL-6 (OR: 7,249; 95% CI: 1,737-30,262) revealed to be suitable asthma inflammation biomarkers. Blood eosinophils, FeNO, total IgE, IL-6, TNF, and IFN-g showed correlations with clinical severity characteristics in asthmatic patients. Periostin showed higher values in T2 asthma (p = 0.006) and TNF in non-T2 asthma (p = 0.029). Conclusion: The panel of biomarkers proposed for the identification of the inflammatory phenotype of asthmatic patients demonstrated good performance. Periostin proved to be an important biomarker for the identification of T2 asthma.
In silico analysis reveals hypoxia-induced miR-210-3p specifically targets SARS-CoV-2 RNA

Abstract Human coronaviruses (HCoVs) until the emergence of SARS in 2003 were associated with mild cold and upper respiratory tract infections. The ongoing pandemic caused by SARS-CoV-2 has enhanced the potential for infection and transmission as compared to other known members of this family. MicroRNAs (miRNA) are 21-25 nucleotides long non-coding RNA that bind to 3' UTR of genes and regulate almost every aspect of cellular function. Several human miRNAs have been known to target viral genomes, mostly to downregulate their expression and sometimes to upregulate also. In some cases, host miRNAs could be sequestered by the viral genome to create a condition for favourable virus existence. The ongoing SARS CoV-2 pandemic is unique based on its transmissibility and severity and we hypothesised that there could be a unique mechanism for its pathogenesis. In this study, we exploited in silico approach to identify human respiratory system-specific miRNAs targeting the viral genome of three highly pathogenic HCoVs (SARS-CoV-2 Wuhan strain, SARS-CoV, and MERS-CoV) and three low pathogenic HCoVs (OC43, NL63, and HKU1). We identified ten common microRNAs that target all HCoVs studied here. In addition, we identified unique miRNAs which targeted specifically one particular HCoV. miR-210-3p was the single unique lung-specific miRNA, which was found to target the NSP3, NSP4, and NSP13 genes of SARS-CoV-2. Further miR-210-NSP3, miR-210-NSP4, and miR-210-NSP13 SARS-CoV-2 duplexes were docked with the hAGO2 protein (PDB ID 4F3T) which showed Z-score values of −1.9, −1.7, and −1.6, respectively. The role of miR-210-3p as master hypoxia regulator and inflammation regulation may be important for SARS-CoV-2 pathogenesis. Overall, this analysis advocates that miR-210-3p be investigated experimentally in SARS-CoV-2 infection. Communicated by Ramaswamy H. Sarma
Hard-Constrained Deep Learning for Climate Downscaling

The availability of reliable, high-resolution climate and weather data is important to inform long-term decisions on climate adaptation and mitigation and to guide rapid responses to extreme events. Forecasting models are limited by computational costs and, therefore, often generate coarse-resolution predictions. Statistical downscaling, including super-resolution methods from deep learning, can provide an efficient method of upsampling low-resolution data. However, despite achieving visually compelling results in some cases, such models frequently violate conservation laws when predicting physical variables. In order to conserve physical quantities, here we introduce methods that guarantee statistical constraints are satisfied by a deep learning downscaling model, while also improving their performance according to traditional metrics. We compare different constraining approaches and demonstrate their applicability across different neural architectures as well as a variety of climate and weather data sets. Besides enabling faster and more accurate climate predictions through downscaling, we also show that our novel methodologies can improve super-resolution for satellite data and natural images data sets.
Immunotoxin-αCD40 therapy activates innate and adaptive immunity and generates a durable antitumor response in glioblastoma models

D2C7-immunotoxin (IT), a dual-specific IT targeting wild-type epidermal growth factor receptor (EGFR) and mutant EGFR variant III (EGFRvIII) proteins, demonstrates encouraging survival outcomes in a subset of patients with glioblastoma. We hypothesized that immunosuppression in glioblastoma limits D2C7-IT efficacy. To improve the response rate and reverse immunosuppression, we combined D2C7-IT tumor cell killing with αCD40 costimulation of antigen-presenting cells. In murine glioma models, a single intratumoral injection of D2C7-IT+αCD40 treatment activated a proinflammatory phenotype in microglia and macrophages, promoted long-term tumor-specific CD8+ T cell immunity, and generated cures. D2C7-IT+αCD40 treatment increased intratumoral Slamf6+CD8+ T cells with a progenitor phenotype and decreased terminally exhausted CD8+ T cells. D2C7-IT+αCD40 treatment stimulated intratumoral CD8+ T cell proliferation and generated cures in glioma-bearing mice despite FTY720-induced peripheral T cell sequestration. Tumor transcriptome profiling established CD40 up-regulation, pattern recognition receptor, cell senescence, and immune response pathway activation as the drivers of D2C7-IT+αCD40 antitumor responses. To determine potential translation, immunohistochemistry staining confirmed CD40 expression in human GBM tissue sections. These promising preclinical data allowed us to initiate a phase 1 study with D2C7-IT+αhCD40 in patients with malignant glioma (NCT04547777) to further evaluate this treatment in humans. Description Immunotoxin-mediated tumor cell killing and αCD40-mediated immune cell activation generate cures in mouse brain tumor models. Slamming GBM with T cells An immunotoxin (IT), D2C7-IT, has demonstrated efficacy in a subset of patients with glioblastoma (GBM) but has been limited due to the immunosuppressive tumor microenvironment. To improve response to treatment, Parker et al. have combined D2C7-IT with anti-CD40 treatment to treat and cure glioma-bearing mice. They found that this treatment increased intratumoral Slamf6+CD8+ T cells, stimulated CD8+ T cell proliferation, and decreased terminally exhausted CD8+ T cells. In addition, they demonstrate that CD40 expression is present in GBM tissue from patients, which has warranted further evaluation in a phase I clinical trial (NCT04547777). —DH
Tree-based adaptive measurement design for compressive imaging under device constraints

We look at the design of projective measurements for compressive imaging based upon image priors and device constraints. If one assumes that image patches from natural imagery can be modeled as a low rank manifold, we develop an optimality criterion for a measurement matrix based upon separating the canonical elements of the manifold prior. We then characterize this manifold based upon prior training imagery under a treebased framework which can be implemented adaptively. We also illustrate how these adaptive measurements can incorporate prior knowledge regarding the constrains of the device being used to collect the measurements. Simulated performance results are presented and compared against a standard imaging paradigm as well as more conventional compressive imaging techniques.
PROCEEDINGS OF THE 3RD INTERNATIONAL CONFERENCE ON MOLECULAR SIMULATION The observation of the longitudinal wave velocity in a model supercooled liquid

We have improved the non-equilibrium molecular dynamics measurement for the longitudinal wave (LW) velocity (the speed of sound) and have applied it to a model system in 2D and 3D. The LW velocity at temperature of the glass or supercooled liquid state reaches the range of 12s1=t in the 2D system and 7s1=t in the 3D system, with a gradual increase with increasing temperature under the isochoric and adiabatic conditions. In our previous paper [4] we analysed that the cooperative motion in intermediate time and length scales propagates with a speed depending on temperature and found that its dependency is opposed to that of the LWs. It suggests that the cooperative motion spreads over the system in a different way of sound.
Origin and development of the claustrum in rhesus macaque

Understanding the claustrum’s functions has recently progressed thanks to new anatomical and behavioral studies in rodents, which suggest that it plays an important role in attention, salience detection, slow-wave generation, and neocortical network synchronization. Nevertheless, knowledge about the origin and development of the claustrum, especially in primates, is still limited. Here, we show that neurons of rhesus macaque claustrum primordium are generated between embryonic day E48 and E55 and express some neocortical molecular markers, such as NR4A2, SATB2, and SOX5. However, in the early stages, it lacks TBR1 expression, which separates it from other surrounding telencephalic structures. We also found that two waves of neurogenesis (E48 and E55) in the claustrum, corresponding to the birthdates of layers 6 and 5 of the insular cortex, establish a “core” and “shell” cytoarchitecture, which is potentially a basis for differential circuit formation and could influence information processing underlying higher cognitive functions of the claustrum. In addition, parvalbumin-positive interneurons are the dominant interneuron type in the claustrum in fetal macaque, and their maturation is independent of that in the overlaying neocortex. Finally, our study reveals that the claustrum is likely not a continuance of subplate neurons of the insular cortex, but an independent pallial region, suggesting its potentially unique role in cognitive control. Significance Statement The claustrum is believed to have a role in many high cognitive functions. However, the origin and development of this mysterious structure remain unknown, and the understanding of its relationship with the neocortex is ambiguous. Here we examined neuron origin and development of claustrum in rhesus macaque during the prenatal and postnatal periods. We found that the claustrum is formed as an independent telencephalic area as early as E55, and it seems not related to the subplate of the insula, although it shares some molecular characteristics with the neocortex. The claustrum excitatory neurons are generated sequentially around E48 and E55 and build a “core and shell” structure that may be a basic computing neuronal circuit unit underlying higher cognitive functions.
TLR7 activation at epithelial barriers promotes emergency myelopoiesis and lung antiviral immunity

Monocytes are heterogeneous innate effector leukocytes generated in the bone marrow and released into circulation in a CCR2-dependent manner. During infection or inflammation myelopoiesis is modulated to rapidly meet demand for more effector cells. Danger signals from peripheral tissues can influence this process. Herein we demonstrate that repetitive TLR7 stimulation via the epithelial barriers drove a potent emergency bone marrow monocyte response. This process was unique to TLR7 activation and occurred independently of the canonical CCR2 and CX3CR1 axes or prototypical cytokines. The monocytes egressing the bone marrow had an immature Ly6C-high profile and differentiated into vascular Ly6C-low monocytes and tissue macrophages in multiple organs. They displayed a blunted cytokine response to further TLR7 stimulation and reduced lung viral load after RSV and influenza virus infection. These data provide insights into the emergency myelopoiesis likely to occur in response to the encounter of single-stranded RNA viruses at barrier sites.
Inferring context-dependent computations through linear approximations of prefrontal cortex dynamics

The complex neural population activity of prefrontal cortex (PFC) is a hallmark of cognitive processes. How these rich dynamics emerge and support neural computations is largely unknown. Here, we infer mechanisms underlying the context-dependent selection and integration of sensory inputs by fitting dynamical models to PFC population responses of behaving monkeys. A class of models implementing linear dynamics driven by external inputs accurately captured the PFC responses within each context, achieving performance comparable to models without linear constraints. Two distinct mechanisms of input selection and integration were equally consistent with the data. One implemented context-dependent recurrent dynamics, as previously proposed, and relied on transient input amplification. The other relied on the subtle contextual modulation of the inputs, providing quantitative constraints on the attentional effects in sensory areas required to explain flexible PFC responses and behavior. Both mechanisms consistently revealed properties of inputs and recurrent dynamics missing in more simplified, incomplete descriptions of PFC responses. By revealing mechanisms consistent with rich cortical dynamics, our modeling approach provides a principled and general framework to link neural population activity and computation.
A novel cryopreservation and biobanking strategy to study lymphoid tissue stromal cells in human disease

Non-hematopoietic lymph node stromal cells (LNSCs) regulate lymphocyte trafficking, survival, and function for key roles in host defense, autoimmunity, alloimmunity, and lymphoproliferative disorders. However, study of LNSCs in human diseases is complicated by a dependence on viable lymphoid tissues, which are most often excised prior to establishment of a specific diagnosis. Here, we demonstrate that cryopreservation can be used to bank lymphoid tissue for the study of LNSCs in human disease. Using human tonsils, lymphoid tissue fragments were cryopreserved for subsequent enzymatic digestion and recovery of viable non-hematopoietic cells. Flow cytometry and single-cell transcriptomics identified comparable proportions of LNSC cell types in fresh and cryopreserved tissue. Moreover, cryopreservation had little effect on transcriptional profiles, which showed significant overlap between tonsils and lymph nodes. The presence and spatial distribution of transcriptionally defined cell types was confirmed by in situ analyses. Our broadly applicable approach promises to greatly enable research into the roles of LNSC in human disease.
Innate receptors with high specificity for HLA class I–peptide complexes

Genetic studies associate killer-cell immunoglobulin-like receptors (KIR) and their HLA class I ligands with a variety of human diseases. The basis for these associations, and the relative contribution of inhibitory and activating KIR to NK cell responses are unclear. As KIR binding to HLA-I is peptide-dependent, we performed systematic screens totaling over 3,500 specific interactions to determine the specificity of five KIR for peptides presented by four HLA-C ligands. Inhibitory KIR2DL1 was largely peptide sequence agnostic, binding approximately 60% of hundreds of HLA-peptide complexes tested. Inhibitory KIR2DL2, KIR2DL3, and activating KIR2DS1 and KIR2DS4 bound only 10%, down to 1% of HLA-peptide complexes tested, respectively. Activating KIR2DS1, previously described as weak, had high binding affinity for HLA-C with high peptide sequence specificity. Our data revealed MHC-restricted peptide recognition by germ-line encoded NK receptors and imply that NK cell responses can be shaped by HLA-I bound immunopeptidomes in the context of disease or infection.
SoyOmics: A deeply integrated database on soybean multi-omics

As one of the most important crops to supply majority plant oil and protein for the whole world, soybean is facing an increasing global demand. Up to now, vast multi-omics data of soybean were generated, thereby providing valuable resources for functional study and molecular breeding. Nevertheless, it is tremendously challenging for researchers to deal with these big multi-omics data, particularly considering the unprecedented rate of data growth. Therefore, we collect the reported high-quality omics, including assembly genomes, graph pan-genome, resequencing and phenotypic data of representative germplasms, transcriptomic and epigenomic data from different tissues, organs and accessions, and construct an integrated soybean multi-omics database, named SoyOmics (https://ngdc.cncb.ac.cn/soyomics). By equipping with multiple analysis modules and toolkits, SoyOmics is of great utility to facilitate the global scientific community to fully use these big omics datasets for a wide range of soybean studies from fundamental functional investigation to molecular breeding.