Miracle-dz/UniFAR-FTUs huggingface dataset:
Waist Circumference and All-Cause Mortality among Older Adults in Rural Indonesia

Waist circumference, a measure of abdominal obesity, is associated with all-cause mortality in general adult population. However, the link between abdominal obesity with all-cause mortality in the studies of older adults is unclear. This study aims to determine the association between waist circumference and all-cause mortality in older adults in Indonesia. The association between waist circumference and all-cause mortality was examined in 10,997 men and women aged 50 years and older, in the World Health Organization (WHO) and International Network of field sites for continuous Demographic Evaluation of Populations and their Health in developing countries (INDEPTH) collaboration Study on global AGEing and adult health (SAGE) in Purworejo District Central Java, Indonesia during 2007–2010. Multivariate Cox regression analysis with restricted cubic splines was used to assess the non-linear association between waist circumference and all-cause mortality. During the 3-year follow-up, a total of 511 men and 470 women died. The hazard ratio plot shows a pattern of U-shape relationship between waist circumference and all-cause mortality among rich women, though the result was significant only for women in the lower end of waist circumference distribution (p < 0.05). Poor men with a low waist circumference (5th percentile) have a two times higher mortality risk (HR = 2.1; 95% CI = 1.3, 3.3) relative to those with a waist circumference of 90 cm. Poor women with a low waist circumference (25th percentile) have a 1.4 times higher mortality risk (HR = 1.4; 95% CI = 1.1, 1.8) relative to those with a waist circumference of 80 cm. This study shows a significant association between low waist circumference measure and mortality, particularly among poor men and women. Though the association between large waist circumference and mortality was not significant, we observed a trend of higher mortality risk particularly among rich women with large waist circumference measure. Public health intervention should include efforts to improve nutritional status among older people and promoting healthy lifestyle behaviours including healthy food and active lifestyle.
Immune parameters and outcomes during Ebola virus disease.

BACKGROUND The West African Ebola virus epidemic from 2014-2016 highlighted the lack of knowledge about the pathogenicity of the virus and the factors responsible for outcome. A performant and rapid diagnosis is of crucial importance, as is overcoming the difficulty of providing high-quality patient management during such an extensive outbreak. Here, we propose to study the role of the immune mediators during Ebola virus disease and to define some molecules of importance in the outcome. METHODS Plasma from Guinean patients sampled during the outbreak were analyzed using RT-qPCR, magnetic bead assay, ELISA, and high-quality statistical analyses. We also performed a transcriptomic analysis in leukocytes samples. Therefore, we deeply characterized the immune responses involved in Ebola virus disease. RESULTS We evaluated the immune patterns depending on the outcome of the disease. Survivors presented an efficient and well-balanced immune response, whereas fatalities were characterized by an intense inflammatory response, overexpression of multiple cytokines, and a "chemokine storm. " The plasma concentration of most of the parameters tested increased until death. Statistical analyses also allowed us to define a panel of markers highly predictive of outcome. CONCLUSION The immune response observed in fatalities was highly similar to that characterizing septic shock syndrome. Our results suggest that immune responses can play a major pathogenic role during severe Ebola virus infection and argue in favor of therapeutic approaches that act on both viral replication and the induction of shock syndrome. FUNDING French Ministry of Foreign Affairs, the Agence Française de Développement, and the Institut Pasteur.
Transcriptomic responses of the marine cyanobacterium Prochlorococcus to viral lysis products

Marine phytoplankton contributes to about one half of global primary production, and a significant proportion of their photosynthetically fixed organic carbon is released after viral infection as dissolved organic matter (DOM). This DOM pool is known to be consumed by heterotrophic microorganisms; however, its impact on the uninfected co-occurring phytoplankton remains largely unknown. Here, we conducted transcriptomic analyses to study the effects of viral lysis products on the unicellular cyanobacterium Prochlorococcus, which is the most abundant photosynthetic organism on Earth. While Prochlorococcus growth was not affected by viral lysis products, many tRNAs increased in abundance, which was also seen after amino acid addition, suggesting that amino acids are one of the compounds in viral lysis products that affected the expression of tRNA genes. The decreased transcript abundances of N metabolism genes also suggested that Prochlorococcus responded to organic N compounds, consistent with abundant amino acids in viral lysis products. The addition of viral lysis products to Prochlorococcus reduced the maximum photochemical efficiency of photosystem II and CO2 fixation while increased its respiration rate, consistent with differentially expressed genes related to photosynthesis and respiration. One of the highest positive fold-changes was observed for the 6S RNA, a non-coding RNA functioning as a global transcriptional regulator in bacteria. The high level of 6S RNA might be responsible for some of the observed transcriptional responses. Taken together, our results revealed the transcriptional regulation of Prochlorococcus in response to viral lysis products and suggested its metabolic potential to utilize organic N compounds. Importance Photosynthetic microorganisms called phytoplankton are abundant in the oceans and contribute to about one half of global CO2 fixation. Phytoplankton are frequently infected by viruses and after infection their organic carbon is released into the ocean as dissolved organic matter (DOM). Marine DOM is important for the marine food web because it supports the growth of heterotrophic microorganisms. However, the impact of viral DOM on the uninfected phytoplankton is largely unknown. In this study, we conducted transcriptomic analyses and identified many differentially expressed genes when viral DOM was added to the marine cyanobacterium Prochlorococcus. One effect of viral DOM is that the carbon fixation of Prochlorococcus was reduced by ~16%, which might affect carbon cycling in the world’s oceans since Prochlorococcus is the most abundant photosynthetic organism on Earth.
Tutorial on Filtering, Restoration, and State Estimation

This tutorial is dedicated to our long-suuering 442 students, and to the excellent authors from whom I shamelessly cribbed this work. It is a pure cut-and-paste job from my favorite sources on this material. This is not my own work { think of me as an editor working without his authors' permissions. Readers should know that original authors are usually easier to understand than rehashed versions. If this presentation helps you, good. If not it at least helped me sort a few things out. I assume knowledge of all necessary linear systems theory, diierential equations, statistics , control theory, etc. We start with the ideas of ltering, smoothing, prediction, and state estimation. Wiener ltering and its associated intellectual framework follows, with a brief foray into ARMA ltering. The idea of recursive estimation is introduced to give some motivation for the slog ahead, and then we start with basic concepts in maximum likelihood, maximum a posteriori, and least-squares estimation. The strategy is to work toward the Kalman Filtering equations by showing how they are simply related to general least-squares estimation. After Kalman ltering, some simpler versions of recursive lters are presented. There are appendices on the orthogonality principle, the matrix inversion lemma, singular value decomposition, partial C and LISP code, and a worked example.
Dinorcassane Diterpenoid from Boesenbergia rotunda Rhizomes Collected in Lower Myanmar

A new dinorcassane diterpenoid, seikphoochinal A (1), and four known compounds, pinostrobin (2), 4′,7‐dimethylkaempferol (3), and galanals A (4) and B (5), were isolated from the chloroform‐soluble crude extract of wild type Boesenbergia rotunda rhizomes collected in Lower Myanmar. The chemical structures of these compounds were identified, using a combination of spectroscopic methods. The presence of the diterpenoids 1, 4, and 5 demonstrated the structural diversity of wild type B. rotunda. Among the isolates, compounds 4 and 5 exhibited significant antiproliferative activities against a small panel of human cancer cell lines, including lung (LK‐2, A549), stomach (ECC4), breast (MCF7), cervix (HeLa), and prostate (DU145).
A novel method for measuring learning opportunities provided by parents to young children with autism spectrum disorder

The aim of this study was to develop a measurement approach to assess the learning opportunities provided by parents to their young children with autism spectrum disorder during a free play task and to examine the relationship between learning opportunities and child performance on measures of cognition, autism spectrum disorder symptoms, and language. Participants were 91 children with autism spectrum disorder ages 12–24 months and their parents. Ordinary least squares regression was used. Results showed that children whose parents provided more learning opportunities had significantly higher cognitive scores and significantly higher vocabulary comprehension and production. The psychometric properties of the measurement approach were investigated and results indicated that it may be psychometrically sound.
Upregulation of Anandamide Hydrolysis in the Basolateral Complex of Amygdala Reduces Fear Memory Expression and Indices of Stress and Anxiety

Increased anandamide (AEA) signaling through inhibition of its catabolic enzyme fatty acid amide hydrolase (FAAH) in the basolateral complex of amygdala (BLA) is thought to buffer against the effects of stress and reduces behavioral signs of anxiety and fear. However, examining the role of AEA signaling in stress, anxiety, and fear through pharmacological depletion has been challenging due to the redundant complexity of its biosynthesis and the lack of a pharmacological synthesis inhibitor. We developed a herpes simplex viral vector to rapidly yet transiently overexpress FAAH specifically within the BLA to assess the impact of suppressing AEA signaling on stress, fear, and anxiety in male rats. Surprisingly, FAAH overexpression in BLA dampened stress-induced corticosterone release, reduced anxiety-like behaviors, and decreased conditioned fear expression. Interestingly, depleting AEA signaling in the BLA did not prevent fear conditioning itself or fear reinstatement. These effects were specific to the overexpression of FAAH because they were reversed by intra-BLA administration of an FAAH inhibitor. Moreover, the fear-suppressive effects of FAAH overexpression were also mitigated by intra-BLA administration of a low dose of a GABAA receptor antagonist, but not an NMDA/AMPA/kainate receptor antagonist, suggesting that they were mediated by an increase in GABAergic neurotransmission. Our data suggest that a permissive AEA tone within the BLA might gate GABA release and that loss of this tone through elevated AEA hydrolysis increases inhibition in the BLA, which in turn reduces stress, anxiety, and fear. These data provide new insights on the mechanisms by which amygdalar endocannabinoid signaling regulates emotional behavior. SIGNIFICANCE STATEMENT Amygdala endocannabinoid signaling is involved in the regulation of stress, anxiety, and fear. Our data indicate that viral-mediated augmentation of anandamide hydrolysis within the basolateral amygdala reduces behavioral indices of stress, anxiety, and conditioned fear expression. These same effects have been previously documented with inhibition of anandamide hydrolysis in the same brain region. Our results indicate that the ability of anandamide signaling to regulate emotional behavior is nonlinear and may involve actions at distinct neuronal populations, which could be influenced by the basal level of anandamide. Modulation of anandamide signaling is a current clinical therapeutic target for stress-related psychiatric illnesses, so these data underscore the importance of fully understanding the mechanisms by which anandamide signaling regulates amygdala-dependent changes in emotionality.
Multiview Latent Space Learning With Feature Redundancy Minimization

Multiview learning has received extensive research interest and has demonstrated promising results in recent years. Despite the progress made, there are two significant challenges within multiview learning. First, some of the existing methods directly use original features to reconstruct data points without considering the issue of feature redundancy. Second, existing methods cannot fully exploit the complementary information across multiple views and meanwhile preserve the view-specific properties; therefore, the degraded learning performance will be generated. To address the above issues, we propose a novel multiview latent space learning framework with feature redundancy minimization. We aim to learn a latent space to mitigate the feature redundancy and use the learned representation to reconstruct every original data point. More specifically, we first project the original features from multiple views onto a latent space, and then learn a shared dictionary and view-specific dictionaries to, respectively, exploit the correlations across multiple views as well as preserve the view-specific properties. Furthermore, the Hilbert–Schmidt independence criterion is adopted as a diversity constraint to explore the complementarity of multiview representations, which further ensures the diversity from multiple views and preserves the local structure of the data in each view. Experimental results on six public datasets have demonstrated the effectiveness of our multiview learning approach against other state-of-the-art methods.
Evidence for Strong Kinship Influence on the Extent of Linkage Disequilibrium in Cultivated Common Beans

Phaseolus vulgaris is an important grain legume for human consumption. Recently, association mapping studies have been performed for the species aiming to identify loci underlying quantitative variation of traits. It is now imperative to know whether the linkage disequilibrium (LD) reflects the true association between a marker and causative loci. The aim of this study was to estimate and analyze LD on a diversity panel of common beans using ordinary r² and r2 extensions which correct bias due to population structure (rS²), kinship (rV²), and both (rVS²). A total of 10,362 single nucleotide polymorphisms (SNPs) were identified by genotyping by sequencing (GBS), and polymorphisms were found to be widely distributed along the 11 chromosomes. In terms of r2, high values of LD (over 0.8) were identified between SNPs located at opposite chromosomal ends. Estimates for rV² were lower than those for rS². Results for rV² and rVS² were similar, suggesting that kinship may also include information on population structure. Over genetic distance, LD decayed to 0.1 at a distance of 1 Mb for rVS². Inter-chromosomal LD was also evidenced. This study showed that LD estimates decay dramatically according to the population structure, and especially the degree of kinship. Importantly, the LD estimates reported herein may influence our ability to perform association mapping studies on P. vulgaris.
Synaptotagmin 5 regulates Ca2+-dependent Weibel–Palade body exocytosis in human endothelial cells

ABSTRACT Elevations of intracellular free Ca2+ concentration ([Ca2+]i) are a potent trigger for Weibel–Palade body (WPB) exocytosis and secretion of von Willebrand factor (VWF) from endothelial cells; however, the identity of WPB-associated Ca2+-sensors involved in transducing acute increases in [Ca2+]i into granule exocytosis remains unknown. Here, we show that synaptotagmin 5 (SYT5) is expressed in human umbilical vein endothelial cells (HUVECs) and is recruited to WPBs to regulate Ca2+-driven WPB exocytosis. Western blot analysis of HUVECs identified SYT5 protein, and exogenously expressed SYT5–mEGFP localised almost exclusively to WPBs. shRNA-mediated knockdown of endogenous SYT5 (shSYT5) reduced the rate and extent of histamine-evoked WPB exocytosis and reduced secretion of the WPB cargo VWF-propeptide (VWFpp). The shSYT5-mediated reduction in histamine-evoked WPB exocytosis was prevented by expression of shRNA-resistant SYT5–mCherry. Overexpression of SYT5–EGFP increased the rate and extent of histamine-evoked WPB exocytosis, and increased secretion of VWFpp. Expression of a Ca2+-binding defective SYT5 mutant (SYT5-Asp197Ser–EGFP) mimicked depletion of endogenous SYT5. We identify SYT5 as a WPB-associated Ca2+ sensor regulating Ca2+-dependent secretion of stored mediators from vascular endothelial cells. Summary: How elevations of intracellular free Ca2+ concentration are detected by Weibel–Palade bodies (WPBs) remains unclear. Here, we show that synaptotagamin 5 is a WPB-associated Ca2+-sensor regulating exocytosis.
The Prognostic Value of Renal Function in Acute Pulmonary Embolism—A Multi-Centre Cohort Study

Abstract Background Haemodynamic alterations caused by acute pulmonary embolism (PE) may affect multi-organ function including kidneys. This multi-centre, multinational cohort study aimed to validate the prognostic significance of estimated glomerular filtration rate (eGFR) and its potential additive value to the current PE risk assessment algorithms. Methods The post hoc analysis of pooled prospective cohort studies: 2,845 consecutive patients (1,424 M/1,421 F, 66 ± 17 years) with confirmed acute PE and followed up for 180 days. We tested prognostic value of pre-specified eGFR level ≤60 mL/min/1.73 m2 calculated on admission according to the Modification of Diet in Renal Disease study equation. The primary outcome was all-cause 30-day mortality; the secondary outcomes were PE-related mortality, 180-day all-cause mortality, bleeding and composite outcome (PE-related death, thrombolysis or embolectomy). Results Two hundred and twenty-three patients (8%; 95% confidence interval [CI]: 7–9%) died within the first 30 days after the diagnosis. The eGFR on admission was significantly lower in non-survivors than in survivors (64 ± 34 vs. 75 ± 3 mL/min/1.73 m2, p < 0.0001). Independent predictors for a fatal outcome included: cancer, systolic blood pressure, older age, hypoxia, eGFR, heart rate and coronary artery disease. The eGFR of ≤60 mL/min/1.73 m2 independently predicted all-cause mortality (hazard ratio: 2.3; 95% CI: 1.7–3.0, p < 0.0001), PE-related outcome and clinically relevant bleedings (odds ratio: 0.90 per 10 mL/min/1.73 m2, 95% CI: 0.85–0.95, p = 0.0002). The eGFR assessment significantly improved prognostic models proposed by European guidelines with net re-classification improvement of 0.42 (p < 0.0001). Conclusion The eGFR of ≤60 mL/min/1.73 m2 not only independently predicted higher 30- and 180-day all-cause mortality and bleeding events, but when added to the current European Society of Cardiology risk stratification algorithm improved identification of both low- and high-risk patients. Therefore, eGFR calculation should be implemented in the risk assessment of acute PE.
miR-384 targets metadherin gene to suppress growth, migration, and invasion of gastric cancer cells

Objective MicroRNA-384 (miR-384) has been reported to function as a tumor suppressor in multiple cancers; however, its role in gastric cancer (GC) remains unclear. Methods We measured expression levels of miR-384 in GC cell lines and in a normal gastric cell line (GES-1). The association between miR-384 and the metadherin gene (MTDH) was assessed by luciferase reporter assay and western blot. The effects of the miR-384/MTDH axis on GC cell behaviors were measured by CCK-8, wound-healing, and transwell invasion assays. Results miR-384 was significantly downregulated in GC cell lines compared with normal gastric cells. MTDH was identified as a direct target of miR-384 by bioinformatics analysis, luciferase assay, and western blot. Functional assays demonstrated that miR-384 inhibited GC cell proliferation, migration, and invasion through targeting MTDH. Conclusion These results reveal that miR-384 acts as a tumor suppressor in GC and suggest that the miR-384/MTDH axis may be a potential therapeutic target for GC.
Global photosynthetic capacity is optimized to the environment

Abstract Earth system models (ESMs) use photosynthetic capacity, indexed by the maximum Rubisco carboxylation rate (V cmax), to simulate carbon assimilation and typically rely on empirical estimates, including an assumed dependence on leaf nitrogen determined from soil fertility. In contrast, new theory, based on biochemical coordination and co‐optimization of carboxylation and water costs for photosynthesis, suggests that optimal V cmax can be predicted from climate alone, irrespective of soil fertility. Here, we develop this theory and find it captures 64% of observed variability in a global, field‐measured V cmax dataset for C3 plants. Soil fertility indices explained substantially less variation (32%). These results indicate that environmentally regulated biophysical constraints and light availability are the first‐order drivers of global photosynthetic capacity. Through acclimation and adaptation, plants efficiently utilize resources at the leaf level, thus maximizing potential resource use for growth and reproduction. Our theory offers a robust strategy for dynamically predicting photosynthetic capacity in ESMs.
Risk factors for atrioventricular block after transcatheter aortic valve implantation: a single-centre analysis including assessment of aortic calcifications and follow-up.

Aims To assess the contribution of aortic valve calcification to the occurrence of transient or permanent atrioventricular block (AVB) and the need for permanent pacemaker implantation (PPI) after transcatheter aortic valve implantation (TAVI) in a large single-centre cohort. Methods and results We retrospectively analysed pre-operative contrast-enhanced multidetector computed tomography scans of patients who underwent TAVI in our centre between 2012 and 2016. Calcium volume was calculated for each aortic cusp above (aortic valve), and below [left ventricular outflow tract (LVOT)] the basal plane. Clinical and procedural data as well as pre-operative electrocardiograms were evaluated. Multivariate analysis was performed to evaluate risk factors for transient and permanent AVB. A total of 342 patients receiving a balloon-expandable prosthesis were included in the study. Overall incidence of transient and permanent AVB was 4% (n = 14) and 7.6% (n = 26), respectively. On logistic regression analysis, baseline right bundle branch block [odds ratio (OR) 7.36, 95% confidence interval (CI) 2.6-20.6; P < 0.01], degree of oversizing (OR 1.04, 95% CI 1.01-1.07 P = 0.02), prior percutaneous coronary intervention (OR 2.8, 95% CI 1.1-7.3), and LVOT calcification beneath the non-coronary cusp (OR for an increase of 10 mm3 = 1.06, 95% CI 1-1.1; P = 0.03) were found to be independently associated with permanent AVB and PPI, whereas calcification of LVOT beneath the right coronary cusp (OR for an increase of 10 mm3 = 1.16, 95% CI 1.02-1.3; P = 0.02) and balloon post-dilation (OR 3.8, 95% CI 1.2-11.8; P = 0.02) were associated with reversible AVB. Conclusion Left ventricular outflow tract calcifications are associated with transient and non-reversible AVB after TAVI, and its evaluation could help in predicting onset and reversibility of AVB.