Miracle-dz/UniFAR-FTUs huggingface dataset:
Cerebral hypometabolism mediates the effect of stroke volume on cognitive impairment in heart failure patients

Abstract Aims The present study aimed to phenotype the cerebral structural and glucose metabolic alterations in patients with heart failure (HF) using simultaneous positron emission tomography (PET)/magnetic resonance (MR) and to investigate their relationship to cardiac biomarkers and cognitive performance. Methods and results Forty‐two HF patients caused by ischaemic heart disease (mean age 67.2 ± 10.4, 32 males) and 32 age‐ and sex‐matched healthy volunteers (mean age 61.3 ± 4.8, 18 males) were included in this study. Participants underwent simultaneous cerebral fluorine‐18 (18F) fluorodeoxyglucose PET/MR followed by cardiac MR scan, and neuropsychological scores were obtained to assess cognitive performance. The grey matter volume (GMV) and standardized uptake value ratio (SUVR) were calculated to examine cerebral structural and metabolic alterations. Cardiac biomarkers included cardiac MR parameters and cardiac serum laboratory tests. Mediation analysis was performed to explore the associations among cerebral alterations, cardiac biomarkers, and cognitive performance. HF patients demonstrated notable cognitive impairment compared with normal controls (P < 0.001). Furthermore, HF patients exhibited regional brain hypometabolism in the bilateral calcarine cortex, caudate nucleus, thalamus, hippocampus, precuneus, posterior cingulate cortex, lingual and olfactory cortex, and GMV reduction in bilateral thalamus and hippocampus (cluster level at P < 0.05, Gaussian random field correction). The SUVR of the hypometabolic brain regions was correlated with the Montreal Cognitive Assessment (MoCA) scores (r = 0.55, P = 0.038) and cardiac stroke volume (r = 0.49, P = 0.002). Cerebral hypometabolism played a key role in the relationship between the decreased stroke volume and MoCA scores, with a mediation effect of 33.2%. Conclusions HF patients suffered cerebral metabolic and structural alterations in regions associated with cognition. The observed correlation between cardiac stroke volume and cognitive impairment underscored the potential influence of cerebral hypometabolism, suggesting that cerebral hypometabolism due to chronic systemic hypoperfusion may significantly contribute to cognitive impairment in HF patients.
The Neoproterozoic Quatipuru ophiolite and the Araguaia fold belt, central-northern Brazil, compared with correlatives in NW Africa

Abstract The Araguaia Belt, the northern branch of Neoproterozoic Tocantins tectonic province, developed during West Gondwana amalgamation as a result of collision between the Amazon and West African and/or São Francisco/Congo cratons. The external zone of the belt consists of ophiolitic slices and fragments, sedimentary rocks derived from magmatic arc sources, volcanic rocks, and part of a passive continental margin with low-grade metamorphic rocks, while the internal zone corresponds to a pile of low- to medium-grade metasedimentary rocks. The largest and best preserved ophiolitic bodies occur in the southern part of the belt, where the Quatipuru and Morro do Agostinho ophiolites are composed predominantly of mantle peridotites (mainly residual harzburgite) representing the base of the Moho transition zone. They contain chromitite pods, dunitic lensoid bodies and a suite of mafic–ultramafic dykes and/or sills resulting from partial melting, magma impregnation and diapiric up-rise. A Sm–Nd isochron age of 757±49 Ma indicates oceanic crust formation during the Early Neoproterozoic. NW African correlatives of the Araguaia Belt, the Mauritanide–Bassaride–Rokelide belt, show similarities with respect to lithostratigraphic units, the ages of basement and supracrustal rocks, the presence of Neoproterozoic ophiolitic slices and fragments, suture zones characterized by high gravity anomalies and centrifugal tectonic vergence. We conclude that these belts were probably formed around the same Neoproterozoic ocean or several small coeval oceans.
Effects of Phosphate Fertilizer on Fresh Yield of Green Manure

The application of phosphate fertilizer in green manure production is the important technique measure for raising its fresh grass yield.The results show that the seeds coated by phosphate fertilizer can increase its fresh grass yield by 25%～32% and 4～8kg/667m2 of phosphate application can gain the fresh yield.
A Role of Environmental Shear on the Organization Mode of Quasi-Stationary Convective Clusters during the Warm Season in Japan

A role of environmental shear on the organization mode of warm-season quasi-stationary convective clusters (QSCCs) was statistically investigated by using operational weather radar and radiosonde data from May to October during 2005−2012. With the use of an ellipse-fitting method, the total number of QSCCs whose shape was determined was 2549. It was found that 87% of the QSCCs have an aspect ratio of larger than 1.4, suggesting that the elongated mode is dominant during the warm season in Japan. The elongated QSCCs were mostly oriented southwest–northeast. The analyses of the environmental shear direction with respect to the orientation of the elongated QSCCs showed that the wind shear direction at the lower troposphere is mainly parallel to the orientation of the elongated QSCCs. A comparison between the elongated and the circular QSCCs with the environmental parameters showed that the lower convective instability and stronger intensity of the low-level shear clearly characterize the elongated QSCC environments. A parameter combining convective instability and shear, bulk Richardson number, characterizes the environmental conditions for determining the organization mode of the QSCCs, suggesting that a back-building mechanism should play a role in generating the elongated QSCCs. (Citation: Unuma, T., and T. Takemi, 2016: A role of environmental shear on the organization mode of quasi-stationary convective clusters during the warm season in Japan. SOLA, 12, 111−115, doi:10.2151/sola.2016-025.)
Quantifying uniaxial prestress and waveguide effects on dynamic elastography estimates for a cylindrical rod

Dynamic elastography attempts to reconstruct quantitative maps of the viscoelastic properties of materials by noninvasively measuring mechanical wave motion in them. The target motion is typically transversely-polarized relative to the wave propagation direction, such as bulk shear wave motion. In addition to neglecting waveguide effects caused by small lengths in one dimension or more, many reconstruction strategies also ignore nonzero, non-isotropic static preloads. Significant anisotropic prestress is inherent to the functional role of some biological materials of interest, which also are small in size relative to shear wavelengths in one or more dimensions. A cylindrically shaped polymer structure with isotropic material properties is statically elongated along its axis while its response to circumferentially-, axially-, and radially-polarized vibratory excitation is measured using optical or magnetic resonance elastography. Computational finite element simulations augment and aid in the interpretation of experimental measurements. We examine the interplay between uniaxial prestress and waveguide effects. A coordinate transformation approach previously used to simplify the reconstruction of un-prestressed transversely isotropic material properties based on elastography measurements is adapted with partial success to estimate material viscoelastic properties and prestress conditions without requiring advanced knowledge of either.
GONADAL DEVELOPMENT OF GUDUSIA CHAPRA (HAMILTON - BUCHANAN) FROM RAJDHALA RESERVOIR, BANGLADESH

The present study deals with the histological changes during different developmental stages of gonads, and fecundity of chapila, Gudusia chapra (Hamilton-Buchanan) in Rajdhala reservoir in Netrakona district of Bangladesh. The gonadosomatic index (GSI) and the histology of gonads revealed that chapila spawns during February to August in the reservoir but the peak period was during March, with a second peak in July. The fecundity of G. chapra was found to range from 32,798 - 1,80,329 with a mean of 1,13,465 ± 19,876 during the period of study. The regression equation between total length (X) and fecundity (Y) of the fish was estimated as Y = -197150 + 25906X, r = 0.698, and between body weight (X) and fecundity (Y) as Y = 34181 + 4281.239X, r = 0.653.
Exploring the understanding, source of availability and level of access of cognitive enhancers among university students in the United Arab Emirates: A qualitative study

The use of prescription stimulants for cognitive enhancement by healthy university students, identified as the largest cohort of cognitive enhancer (CE) users, is of growing interest. The purpose of this study was to look at the understanding, perception, experience, and level of access of CEs among healthy university students in the United Arab Emirates (UAE).
A Novel High-Dimensional Kernel Joint Non-Negative Matrix Factorization With Multimodal Information for Lung Cancer Study

Judging and identifying biological activities and biomarkers inside tissues from imaging features of diseases is challenging, so correlating pathological image data with genes inside organisms is of great significance for clinical diagnosis. This paper proposes a high-dimensional kernel non-negative matrix factorization (NMF) method based on muti-modal information fusion. This algorithm can project RNA gene expression data and pathological images (WSI) into a common feature space, where the heterogeneous variables with the largest coefficient in the same projection direction form a co-module. In addition, the miRNA-mRNA and miRNA-lncRNA interaction networks in the ceRNA network are added to the algorithm as a priori information to explore the relationship between the images and the internal activities of the gene. Furthermore, the radial basis kernel function is used to calculate the feature proportion between different kinds of genes mapped in the high-dimensional feature space and projected into the common feature space to explore the gene interaction in the high-dimensional situation. The original feature matrix is regularized to improve biological correlation, and the feature factors are sparse by orthogonal constraints to reduce redundancy. Experimental results show that the proposed NMF method is better than the traditional NMF method in stability, decomposition accuracy, and robustness. Through data analysis applied to lung cancer, genes related to tissue morphology are found, such as COL7A1, CENPF and BIRC5. In addition, gene pairs with a correlation degree exceeding 0.8 are found, and potential biomarkers of significant correlation with survival are obtained such as CAPN8. It has potential application value for the clinical diagnosis of lung cancer.
Genetic analysis and literature review of a Poirier–Bienvenu neurodevelopmental syndrome family line caused by a de novo frameshift variant in CSNK2B

Abstract Background Poirier–Bienvenu neurodevelopmental syndrome (POBINDS) is a rare autosomal dominant neurologic disorder caused by a heterozygous variant of CSNK2B, which is characterized by early onset epilepsy, hypotonia, varying degrees of intellectual disability (ID), developmental delay (DD), and facial dysmorphism. This study clarifies the molecular diagnosis and causative factors of a Chinese boy with POBINDS. Methods The clinical phenotypes and ancillary laboratory tests were collected and analyzed by trio whole exome sequencing (WES) and copy number variant sequencing (CNV‐seq) in the follow‐up proband's families. The candidate variant was validated by Sanger sequencing and bioinformatics software was used to further explore the effect of the de novo frameshift variant on the protein structure. Results The proband carries a de novo frameshift variant c. 453_c. 454insAC (p.H152fs*76) in CSNK2B. According to the ACMG genetic variant classification criteria and guidelines, the locus is a pathogenic variant (PVS1+PS2+PM2) and the associated disease was POBINDS. Protein structure prediction suggests significant differences in amino acid sequences before and after mutation. Conclusion A rare case of POBINDS caused by a novel frameshift variant in CSNK2B was diagnosed. The novel variant extends the variation spectrum of CSNK2B, which provides guidance for early clinical diagnosis, genetic counseling and treatment of this family. A review of the currently reported cases of POBINDS further enriches and summarizes the relationship between genotype and phenotype of POBINDS.
m6A‐related lncRNAs as potential biomarkers and the lncRNA ELFN1‐AS1/miR‐182‐5p/BCL‐2 regulatory axis in diffuse large B‐cell lymphoma

Abstract Diffuse large B‐cell lymphoma (DLBCL) is the most common lymphoid subtype. However, unsatisfactory survival outcomes remain a major challenge, and the underlying mechanisms are poorly understood. N6‐methyladenosine (m6A), the most common internal modification of eukaryotic mRNA, participates in cancer pathogenesis. In this study, m6A‐associated long non‐coding RNAs (lncRNA) were retrieved from publicly available databases. Univariate, LASSO, and multivariate Cox regression analyses were performed to establish an m6A‐associated lncRNA model specific to DLBCL. Kaplan–Meier curves, principal component analysis, functional enrichment analyses and nomographs were used to study the risk model. The underlying clinicopathological characteristics and drug sensitivity predictions against the model were identified. Risk modelling based on the three m6A‐associated lncRNAs was an independent prognostic factor. By regrouping patients using our model‐based method, we could differentiate patients more accurately for their response to immunotherapy. In addition, prospective compounds that can target DLBCL subtypes have been identified. The m6A‐associated lncRNA risk‐scoring model developed herein holds implications for DLBCL prognosis and clinical response prediction to immunotherapy. In addition, we used bioinformatic tools to identify and verify the ceRNA of the m6A‐associated lncRNA ELFN1‐AS1/miR‐182‐5p/BCL‐2 regulatory axis. ELFN1‐AS1 was highly expressed in DLBCL and DLBCL cell lines. ELFN1‐AS1 inhibition significantly reduced the proliferation of DLBCL cells and promoted apoptosis. ABT‐263 inhibits proliferation and promotes apoptosis in DLBCL cells. In vitro and in vivo studies have shown that ABT‐263 combined with si‐ELFN1‐AS1 can inhibit DLBCL progression.
Phosphoglycerate-kinase-1 Is a Potential Prognostic Biomarker in HNSCC and Correlates With Immune Cell Infiltration.

BACKGROUND/AIM Head and neck squamous cell carcinoma (HNSCC) is the sixth leading cancer worldwide, with a high recurrence rate and a low cure rate. Phosphoglycerate kinase 1 (PGK1), an essential enzyme in the aerobic glycolysis pathway, is a prognostic marker for a variety of cancers. However, it remains unclear whether a PGK1-based immune signature can be used as a prognostic biomarker in HNSCC patients. MATERIALS AND METHODS We explored the potential oncogenic mechanisms of PGK1 by multiple bioinformatics analyses combined with multiple databases, including the correlation between PGK1 and prognosis, and the infiltration of immune cells in HNSCC. Functional enrichment analyses were further performed to investigate the potential role of PGK1 in HNSCC. RESULTS The expression of PGK1 was significantly higher in HNSCC tissues compared to normal tissues. High expression of PGK1 was associated with poor prognosis in HNSCC, and multivariate cox regression analysis showed that PGK1 could be an independent prognostic factor in HNSCC. Pathway analysis revealed that PGK1 may regulate the pathogenesis of HNSCC through the immune signaling pathway. Moreover, PGK1 expression significantly correlated with the infiltration level of 16 types of immune cells. CONCLUSION The current study reports that PGK1 expression was increased in HNSCC and that high PGK1 expression was closely associated with poor prognosis and immune cell infiltration, which could serve as a promising independent prognostic biomarker and potential immunotherapeutic target for HNSCC.
Patient‐ and xenograft‐derived organoids recapitulate pediatric brain tumor features and patient treatments

Brain tumors are the leading cause of cancer‐related death in children. Experimental in vitro models that faithfully capture the hallmarks and tumor heterogeneity of pediatric brain cancers are limited and hard to establish. We present a protocol that enables efficient generation, expansion, and biobanking of pediatric brain cancer organoids. Utilizing our protocol, we have established patient‐derived organoids (PDOs) from ependymomas, medulloblastomas, low‐grade glial tumors, and patient‐derived xenograft organoids (PDXOs) from medulloblastoma xenografts. PDOs and PDXOs recapitulate histological features, DNA methylation profiles, and intratumor heterogeneity of the tumors from which they were derived. We also showed that PDOs can be xenografted. Most interestingly, when subjected to the same routinely applied therapeutic regimens, PDOs respond similarly to the patients. Taken together, our study highlights the potential of PDOs and PDXOs for research and translational applications for personalized medicine.
Taphonomic Control on Microstructure in Early Neoproterozoic Reefal Stromatolites and Thrombolites

Abstract Early Neoproterozoic reefs of the Little Dal Group, Northwest Territories, are built by stromatolites and thrombolites containing calcified filamentous cyanobacteria and interstitial cement. Micritic and microcrystalline carbonate grew in or on extracellular cyanobacterial sheaths, preserving filaments when mineralization was early relative to sheath degradation, or grumeaux when mineralization was later. Filamentous microstructure is volumetrically predominant in the reefs; less common are micritic and grumelous microstructures already known from late Proterozoic stromatolites and Phanerozoic thrombolites. Textural intergradation of filamentous-calcimicrobial microstructure with these non-filamentous microstructures reflects microstructural variation developed through differential preservation at the scale of individual filaments and laminae. Textural gradients from filaments to grumeaux, and from calcimicrobial to stromatolitic and thrombolitic microstructure types, imply that a wide variety of microbialite microstructure types can be derived from a single progenitor community. This suggests that taphonomic variables may be as important in the development of microbialite microstructure as the biology of the microbial mat community. It also challenges recent suggestions that the Neoproterozoic increase in thromboids was related to the rise of multicellular organisms. These conclusions have broad implications for the interpretation of fossil microbialites, many of which might have been more closely related in origin than hitherto suspected.
EFFECT OF SALT STRESS ON GROWTH AND YIELD ATTRIBUTES OF MUNGBEAN

A pot experiment was performed at the Bangladesh Institute of Nuclear Agriculture (BINA) experimental farm, Mymensingh, during the period from 06 October 2003 to 08 January 2004 to observe the response of three mungbean genotypes (Binamoog-4 and twoadvanced line BMX 92007-3 and BMX 94010-11) under different salt stress (control, 3.89 deci-Siemen per metre (ds m -1 ) and 7.82 ds m -1 ). The experiment was laid out following Randomized Complete Block Design where each treatment replicated three times. All morphophysiological characters such as plant height, number of leaf, leaf area, yield contributing characters such as number of pods plant -1 , number of seeds pod -1 , 1000 seed weight, harvest index were reduced with the increase of salinity levels as compared to control. However, the content of Na + in leaves increased with increasing salinity levels. Plant height and yield attributes like number of pods plant -1 , number of seeds pod -1 , 1000 seed weight, harvest index were the highest in advanced line BMX 94010-11 compared to those in Binamoog-4 and advanced line BMX 92007-3. Potassium content in leaves was not varied among the genotypes but leaves of Binamoog-4 contain the highest amount of K + compared to that in BMX 94010-11 and BMX 92007-3. Interaction effect between the genotypes and salinity levels appeared significant for most of the studied characters. From the study it can be opined that salt stress reduced all the parameters under different salinity levels. Again among the genotypes advanced line BMX 94010-11 was found as relatively salt tolerant.
Evidence of survival bias in the association between APOE-ϵ4 and age of ischemic stroke onset

Large genome-wide association studies (GWAS) employing case-control study designs have now identified tens of loci associated with ischemic stroke (IS). As a complement to these studies, we performed GWAS in a case-only design to identify loci influencing age at onset (AAO) of ischemic stroke. Analyses were conducted in a Discovery cohort of 10,857 ischemic stroke cases using a linear regression framework. We meta-analyzed all SNPs with p-value < 1x10-5 in a sex-combined or sex-stratified analysis using summary data from two additional replication cohorts. In the women-only meta-analysis, we detected significant evidence for association of AAO with rs429358, an exonic variant in APOE that encodes for the APOE-{Jukcy}4 allele. Each copy of the rs429358:T>C allele was associated with a 1.29 years earlier stroke AOO (meta p-value = 2.48x10-11). This APOE variant has previously been associated with increased mortality and ischemic stroke AAO. We hypothesized that the association with AAO may reflect a survival bias attributable to an age-related decline in mortality among APOE-{Jukcy}4 carriers and have no association to stroke AAO per se. Using a simulation study, we found that a variant associated with overall mortality might indeed be detected with an AAO analysis. A variant with a two-fold increase on mortality risk would lead to an observed effect of AAO that is comparable to what we found. In conclusion, we detected a robust association of the APOE locus with stroke AAO and provided simulations to suggest that this association may be unrelated to ischemic stroke per se but related to a general survival bias.
Long-read RNA-seq atlas of novel microglia isoforms elucidates disease-associated genetic regulation of splicing

Microglia, the innate immune cells of the central nervous system, have been genetically implicated in multiple neurodegenerative diseases. We previously mapped the genetic regulation of gene expression and mRNA splicing in human microglia, identifying several loci where common genetic variants in microglia-specific regulatory elements explain disease risk loci identified by GWAS. However, identifying genetic effects on splicing has been challenging due to the use of short sequencing reads to identify causal isoforms. Here we present the isoform-centric microglia genomic atlas (isoMiGA) which leverages the power of long-read RNA-seq to identify 35,879 novel microglia isoforms. We show that the novel microglia isoforms are involved in stimulation response and brain region specificity. We then quantified the expression of both known and novel isoforms in a multi-ethnic meta-analysis of 555 human microglia short-read RNA-seq samples from 391 donors, the largest to date, and found associations with genetic risk loci in Alzheimer's disease and Parkinson's disease. We nominate several loci that may act through complex changes in isoform and splice site usage.