Miracle-dz/UniFAR-FTUs huggingface dataset:
Risk variants of obesity associated genes demonstrate BMI raising effect in a large cohort

Obesity is highly polygenic disease where several genetic variants have been reportedly associated with obesity in different ethnicities of the world. In the current study, we identified the obesity risk or protective association and BMI raising effect of the minor allele of adiponectin, C1Q and collagen domain containing (ADIPOQ), cholesteryl ester transfer protein (CEPT), FTO alpha-ketoglutarate dependent dioxygenase (FTO), leptin (LEP), and leptin receptor (LEPR) genes in a large cohort stratified into four BMI-based body weight categories i.e., normal weight, lean, over-weight, and obese. Based on selected candidate genetic markers, the genotyping of all study subjects was performed by PCR assays, and genotypes and allele frequencies were calculated. The minor allele frequencies (MAFs) of all genetic markers were computed for total and BMI-based body weight categories and compared with MAFs of global and South Asian (SAS) populations. Genetic associations of variants with obesity risk were calculated and BMI raising effect per copy of the minor allele were estimated. The genetic variants with higher MAFs in obese BMI group were; rs2241766 (G = 0.43), rs17817449 (G = 0.54), rs9939609 (A = 0.51), rs1421085 (C = 0.53), rs1558902 (A = 0.63), and rs1137101 (G = 0.64) respectively. All these variants were significantly associated with obesity (OR = 1.03–4.42) and showed a high BMI raising effect (β = 0.239–0.31 Kg/m2) per copy of the risk allele. In contrast, the MAFs of three variants were higher in lean-normal BMI groups; rs3764261 A = 0.38, rs9941349 T = 0.43, and rs7799039 G = 0.40–0.43). These variants showed obesity protective associations (OR = 0.68–0.76), and a BMI lowering effect per copy of the protective allele (β = -0.103–0.155 Kg/m2). The rs3764261 variant also showed significant and positive association with lean body mass (OR = 2.38, CI = 1.30–4.34). Overall, we report six genetic variants of ADIPOQ, FTO and LEPR genes as obesity-risk markers and a CETP gene variant as lean mass/obesity protective marker in studied Pakistani cohort.
Systoles et applications selon Gromov

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Healthful and unhealthful provegetarian food patterns and micronutrient intake adequacy in the SUN cohort

Abstract Objective: To investigate the association between different versions of a provegetarian food pattern (FP) and micronutrient inadequacy. Design: Cross-sectional analysis. Dietary intake was assessed at baseline through a validated 136-item FFQ. Participants were classified according to groups of different versions of a provegetarian FP: overall, healthful and unhealthful. The prevalence of inadequate intake of vitamins B1, B2, B3, B6, B12, C, A, D, E, folic acid, Zn, I, Se, Fe, Ca, K, P, Mg and Cr was evaluated using the estimated average requirement (EAR) cut-point method and the probabilistic approach. Logistic regression analyses were conducted to estimate the probability of failing to meet EAR for either ≥ 3 or ≥ 6 micronutrients. Setting: Seguimiento Universidad de Navarra (SUN) cohort. Participants: 17 825 Spanish adults. Results: Overall, subjects in the highest group of the unhealthful provegetarian FP had the highest prevalence of inadequate dietary intake for every vitamin and mineral, compared to those in the lowest group. The adjusted OR of failing to meet ≥ 3 EAR (highest v. lowest group) was 0·65 (0·54, 0·69) for the overall, 0·27 (0·24, 0·31) for the healthful and 9·04 (7·57, 10·4) for the unhealthful provegetarian FP. Conclusion: A higher adherence to an overall and healthful provegetarian FP was inversely associated with the risk of failing to meet EAR values, whereas the unhealthful version was directly associated with micronutrient inadequacy. Provegetarian FP should be well planned, prioritising nutrient-dense plant foods and minimising ultra-processed and unhealthy ones.
Seasonal and Diel Communication Periods of Sympatric Pest Limonius Click Beetle Species (Coleoptera: Elateridae) in Western Canada

Abstract In western North America, sympatric Limonius click beetle species produce limoniic acid [(E)-4-ethyloct-4-enoic acid] as a sex pheromone component (L. canus (LeConte), L. californicus (Mannerheim)) or respond to it as a sex attractant (L. infuscatus (Motschulsky)). We tested the hypothesis that these three congeners maintain species-specificity of sexual communication through nonoverlapping seasonal occurrence and/or contrasting diel periodicity of sexual communication. Using capture times of beetles in pheromone-baited traps as a proxy for sexual communication periods, our data show that L. canus and L. californicus have seasonally distinct communication periods. Most L. canus males (>90%) were captured in April and most L. californicus males (>95%) were captured in May/June/July. As almost exclusively L. infuscatus males were captured in two separate 24-hr trapping studies, with data recordings every hour, it remains inconclusive whether the three Limonius congeners communicate at different times of the day. Males of L. infuscatus responded to pheromone lures only during daytime hours and during the warmest period each day. Captures of L. infuscatus overlapping with those of L. canus in April and those of L. californicus in May/June imply the presence of reproductive isolating mechanisms other than seasonal separation of sexual communication periods.
Association of Carotid Plaque and Flow Velocity With White Matter Integrity in a Middle-aged to Elderly Population

Background and Objectives It is uncertain whether there is an association of carotid plaques (CPs) and flow velocities with peak width mean diffusivity (PSMD) and white matter hyperintensities (WMH) independent of shared risk factors. We aimed to study this association controlling for biomarkers of inflammation and cardiac dysfunction and typical cardiovascular risk factors and spatial distribution. Methods We included participants from the population-based Hamburg City Health Study, recruiting citizens between 45 and 74 years of age. Medical history was obtained from structured interviews and extended laboratory tests, physical examinations, MRI of the head, echocardiography, and abdominal and carotid ultrasound were performed. We performed multivariable regression analysis with PSMD and periventricular, deep, and total volume of WMH (pWMH, dWMH, tWMH) as dependent variables. PSMD was calculated as the difference between the 95th and 5th percentiles of MD values on the white skeleton in standard space. Volumes of WMH were determined by the application of a manually trained k-nearest neighbor segmentation algorithm. WMH measured within a distance of 1 cm from the surface of the lateral ventricles were defined as pWMH and above 1 cm as dWMH. Results Two thousand six hundred twenty-three participants were included. The median age was 65 years, and 56% were women. Their median tWMH was 946 mm3(IQR:419, 2,164), PSMD 2.24 mm2/s × 10−4 (IQR: 2.04, 2.47), peak systolic velocity (PSV) of internal carotid arteries 0.70m/second (IQR:0.60, 0.81), and 35% had CPs. Adjusted for age, sex, high-sensitive CRP, NT-proBNP, and commonly measured cardiovascular risk and systemic hemodynamic factors, both CPs (B = 0.15; CI: 0.04, 0.26; p = 0.006) and low PSV (B = −0.49; CI: −0.87, −0.11; p = 0.012) were significantly associated with a higher tWMH and PSMD. Low PSV (B = −0.48; CI: −0.87, −0.1; p = 0.013) was associated with pWMH and the presence of CP with pWMH (B = 0.15; CI: 0.04, 0.26; p = 0.008) and dWMH (B = 0.42; CI: 0.11, 0.74; p < 0.009). Discussion Low PSV and CP are associated with WMH and PSMD independent of cardiovascular risk factors and biomarkers of inflammation and cardiac dysfunction. This points toward pathophysiologic pathways underlying both large and small vessel disease beyond the common cardiovascular risk profile. Trial Registration Information The trial was submitted at clinicaltrials.gov, under NCT03934957 on January 4, 2019. The first participant was enrolled in February 2016.
Free-form deformation in a constructive solid geometry modeling system

Research in computer aided geometric design of free-form surfaces has provided elegant modeling techniques. However, there has been limited development of free-form design methods for solid geometric modeling. Most approaches have attempted to impose current free-form surface technology on solid modeling. This dissertation examines a new approach. This new technique proceeds by deforming solid geometric models in a free-form manner. This approach can be used with any existing solid modeling scheme such as constructive solid geometry or boundary representation. It can deform surface primitives of any type or degree such as planes, quadrics, parametric surface patches or implicitly defined surfaces. The deformation can be applied either globally or locally and can impose any desired degree of derivative continuity. The scheme is based on trivariate Bernstein polynomials. The deformation technique functions well in a constructive solid geometry modeling system. Implementation of such a system with specific design approaches are presented: primarily the polygonalization of deformed surfaces using adaptive subdivision and display by the use of a scan line hidden surface removal algorithm.
Diverse ancestry whole-genome sequencing association study identifies TBX5 and PTK7 as susceptibility genes for posterior urethral valves

Posterior urethral valves (PUV) are the commonest cause of end-stage renal disease in children, but the genetic architecture of this rare disorder remains unknown. We performed a sequencing-based genome-wide association study (seqGWAS) in 132 unrelated male PUV cases and 23,727 controls of diverse ancestry, identifying statistically significant associations with common variants at 12q24.21 (p=7.8 × 10−12; OR 0.4) and rare variants at 6p21.1 (p=2.0 × 10-8; OR 7.2), that were replicated in an independent European cohort of 395 cases and 4151 controls. Fine mapping and functional genomic data mapped these loci to the transcription factor TBX5 and planar cell polarity gene PTK7, respectively, the encoded proteins of which were detected in the developing urinary tract of human embryos. We also observed enrichment of rare structural variation intersecting with candidate cis-regulatory elements, particularly inversions predicted to affect chromatin looping (p=3.1 × 10-5). These findings represent the first robust genetic associations of PUV, providing novel insights into the underlying biology of this poorly understood disorder and demonstrate how a diverse ancestry seqGWAS can be used for disease locus discovery in a rare disease.
Ruelle's Perron-Frobenius theorem and the central limit theorem for additive functionals of one-dimensional Gibbs states

The central limit problem for sums of stationary sequences has such a long history (dating back to Markov and Bernstein, at least) that one might have hoped the final chapter had by now been written. Alas, this is not the case. It is now known that the central limit theorem will generally hold for a stationary sequence when there is a certain degree of "mixing" present. A variety of general results specifying sufficient conditions for the validity of the central limit theorem are presented in the treatise by Ibragimov and Linnik (1971), and further references to the literature are made there. So far as I have been able to discern, there are four methods for obtaining such results: (i) Markov's method of moments; (ii) Bernstein's method of approximation by i.i. d. sequences; (iii) Doeblin's method of finding "regeneration times"; and (iv) a martingale method which is apparently due to Gordin (1969). Although these methods are very powerful, enabling one to work with very general AMS subject classification. Primary 60F05; Secondary 60F10, 60G10.
Impact of a collaboration revolving around virtual capacity evaluations

Abstract Objective To assess the impact of virtual capacity assessments on access to medical care, community supports, and transitions to higher levels of care. Study Setting Virtual capacity evaluations of homebound suspected elder abuse/neglect/financial exploitation victims identified via exclusion criteria and initiated by Cuyahoga County adult protective services (APS) and conducted with Cleveland Clinic Geriatric Medicine. Study Design A retrospective chart review was conducted in conjunction with APS using their database to determine the outcomes of individuals who underwent virtual capacity evaluation from May 2020 through September 2021. Variables collected included completion of a statement of expert evaluation, guardianship assignment, offering community services, transfer to a higher level of care, and establishment of primary care. Data Collection/Extraction Data were extracted from medical records and the APS database. Outcomes were measured as percentages. Principal Findings Fifty‐four individuals underwent evaluation. Statements of expert evaluation were completed in 38 cases (70%). Guardianship was assigned in 28 cases (52%). Community services were offered to 51 (89%). Thirty‐one (57%) remained at home. At baseline, only 23 (43%) were receiving primary care. Post evaluation, 44 (81%) were connected or reconnected to their medical provider. Conclusion Of individuals who underwent our virtual capacity evaluations, most were able to remain at home, offered community services for support, and linked to primary care.
PhaSepDB in 2022: annotating phase separation-related proteins with droplet states, co-phase separation partners and other experimental information

Abstract Phase separation (PS) proteins form droplets to regulate myriad membraneless organelles (MLOs) and cellular pathways such as transcription, signaling transduction and protein degeneration. PS droplets are usually liquid-like and can convert to hydrogel/solid-like under certain conditions. The PS behavior of proteins is regulated by co-PS partners and mutations, modifications, oligomerizations, repeat regions and alternative splicing of the proteins. With growing interest in PS condensates and associated proteins, we established PhaSepDB 1.0, which provided experimentally verified PS proteins and MLO-related proteins. The past few years witnessed a surge in PS-related research works; thus, we kept updating PhaSepDB. The current PhaSepDB contains 1419 PS entries, 770 low-throughput MLO-related entries and 7303 high-throughput MLO-related entries. We provided more detailed annotations of PS proteins, including PS verification experiments, regions used in experiments, phase diagrams of different experimental conditions, droplet states, co-PS partners and PS regulatory information. We believe that researchers can go further in studying PS proteins with the updated PhaSepDB (http://db.phasep.pro/).
Hepatitis E virus is effectively inactivated by methylene blue plus light treatment

Photodynamic treatment with methylene blue (MB) and visible light is a well‐established pathogen inactivation system for human plasma. This technique is routinely used in different countries. MB/light treatment was shown to inactivate several transfusion‐transmittable viruses, but its efficiency for the inactivation of the quasi‐enveloped hepatitis E virus (HEV) has not yet been investigated.
The abundance, biomass, and distribution of ants on Earth

Significance The astounding ubiquity of ants has prompted many naturalists to contemplate their exact number on Earth, but systematic and empirically derived estimates are lacking. Integrating data from all continents and major biomes, we conservatively estimate 20 × 1015 (20 quadrillion) ants on Earth, with a total biomass of 12 megatons of dry carbon. This exceeds the combined biomass of wild birds and mammals and equals 20% of human biomass. Ant abundance is distributed unevenly on Earth, peaking in the tropics and varying sixfold among habitats. Our global map of ant abundance expands our understanding of the geography of ant diversity and provides a baseline for predicting ants’ responses to worrying environmental changes that currently impact insect biomass.
Fatty liver disease reverses the obesity paradox in chronic kidney disease stages 3–5: A follow‐up study of NHANES III

High body mass index (BMI) has been associated with better survival in patients with end‐stage kidney disease. Individuals with fatty liver disease (FLD) have a higher risk of chronic kidney disease. It remains unclear whether the survival benefit of high BMI in patients with chronic kidney disease is present when there is concomitant FLD. This study used the data set from the Third American National Health and Nutrition Examination Survey and the corresponding survival data. The Cox proportional hazards model was used to evaluate the effect of BMI on mortality. A total of 12,445 participants were included. The prevalence of FLD was 39.8%. The median follow‐up time (with interquartile range) was 22.8 (20.8–24.8) years. During this period, 3749 (30.1%, 14.4 of 1000 person‐year) deaths were observed. Among these, 1169 (31.2%) died within the first 10 years. The Cox regression analysis showed that the BMI level was not associated with 25‐year mortality in patients with decreased glomerular filtration rate (GFR < 60 ml/min/1.73 m2), but 10‐year mortality was significantly lower in patients with BMI ≥ 25 kg/m2 than in those with BMI < 25 kg/m2 (p = 0.049). Multivariate analysis showed BMI ≥ 25 kg/m2 was an independent protective factor for 10‐year mortality (hazard ratio [HR] 0.691, 95% confidence interval [CI] 0.559–0.856; p = 0.001). This protective effect of higher BMI was lost in patients with FLD (HR 0.884, 95% CI 0.585–1.335; p = 0.557) but persisted in the non‐FLD group (HR 0.625, 95% CI 0.479–0.816; p = 0.001). The survival benefit of overweight/obesity for patients with decreased GFR, which was attenuated by the presence of FLD, only existed in the first decade.
Continent‐wide patterns of song variation predicted by classical rules of biogeography

Abstract Physiological constraints related to atmospheric temperature pose a limit to body and appendage size in endothermic animals. This relationship has been summarised by two classical principles of biogeography: Bergmann's and Allen's rules. Body size may also constrain other phenotypic traits important in ecology, evolution and behaviour, and such effects have seldom been investigated at a continental scale. Through a multilevel‐modelling approach, we demonstrate that continent‐wide morphology of related African barbets follows predictions of Bergmann's rule, and that body size mirrors variation in song pitch, an acoustic trait important in species recognition and sexual selection. Specifically, effects on song frequency in accordance with Bergmann's rule dwarf those of acoustic adaptation at a continental scale. Our findings suggest that macroecological patterns of body size can influence phenotypic traits important in ecology and evolution, and provide a baseline for further studies on the effects of environmental change on bird song.
Anomalous water transport in narrow-diameter carbon nanotubes

Significance Typically, as the channel length increases, the flow rate decreases due to the increase in flow resistance. Based on molecular dynamics simulations, we show that the pressure-driven flow rate of water through narrow-diameter carbon nanotubes (CNTs) exhibits anomalous transport behavior, whereby the flow rate increases markedly first and then either slowly decreases or changes slightly as the CNT length increases. This anomalous transport behavior of water cannot be simply explained by the tube-length dependence of the free energy barrier for a single water molecule passing through the CNTs; rather, it can be attributed to the tube-length–dependent stability of the cross–CNT orifice hydrogen bonds that formed between water molecules inside and outside the CNT.
Effect of 6-week curcumin supplementation on aerobic capacity, antioxidant status and sirtuin 3 level in middle-aged amateur long-distance runners

ABSTRACT Background The study was undertaken to evaluate the effect of 6-week supplementation with a daily dose of 2g of curcumin on VO2max and prooxidant/antioxidant homeostasis in middle-aged amateur long-distance runners during the preparatory period of the macrocycle. Methods Thirty runners were randomly assigned to a placebo group (PL) and a curcumin-supplemented group (CU). Their VO2max was assessed before supplementation and after 6 weeks of supplementation. Venous blood samples were collected from the participants at rest, immediately after exercise, and after 1h of recovery to evaluate the activity of antioxidant enzymes (SOD, CAT, GPx), non-enzymatic antioxidants (GSH, UA) and sirtuin 3 level (SIRT 3), as well as the levels of oxidative stress markers (TOS/TOC, MDA, and 8-OHdG) and muscle damage markers (CK, LDH, and Mb). Results VO2max, the activity of enzymatic antioxidants, the concentrations of non-enzymatic antioxidants, the levels of oxidative stress markers, and the levels of muscle damage markers did not change significantly in the CU group over 6 weeks of supplementation with curcumin. However, the resting concentration of SIRT 3 was found to be significantly higher (p ≤ 0.05) compared with pre-supplementation. Conclusion Curcumin supplementation does not have a significant effect on VO2max and prooxidant/antioxidant homeostasis in runners.
Draft Genome Sequence of Glutamicibacter sp. Strain JC586, Isolated from Soil Sediment of the Floating Islands of Loktak Lake, India

The 3.52-Mbp whole-genome sequence of a Glutamicibacter sp. strain isolated from soil sediment of the floating islands of Loktak Lake is reported. The genomic information here gives insight into the presence of genes linked to oxidative stress, osmo-protection, and cold shock proteins which helps in the survival of the organism under extreme environmental conditions. ABSTRACT The 3.52-Mbp whole-genome sequence of a Glutamicibacter sp. strain isolated from soil sediment of the floating islands of Loktak Lake is reported. The genomic information here gives insight into the presence of genes linked to oxidative stress, osmo-protection, and cold shock proteins which helps in the survival of the organism under extreme environmental conditions.