Miracle-dz/UniFAR-FTUs huggingface dataset:
Virtual stick balancing: sensorimotor uncertainties related to angular displacement and velocity

Sensory uncertainties and imperfections in motor control play important roles in neural control and Bayesian approaches to neural encoding. However, it is difficult to estimate these uncertainties experimentally. Here, we show that magnitude of the uncertainties during the generation of motor control force can be measured for a virtual stick balancing task by varying the feedback delay, τ. It is shown that the shortest stick length that human subjects are able to balance is proportional to τ 2. The proportionality constant can be related to a combined effect of the sensory uncertainties and the error in the realization of the control force, based on a delayed proportional-derivative (PD) feedback model of the balancing task. The neural reaction delay of the human subjects was measured by standard reaction time tests and by visual blank-out tests. Experimental observations provide an estimate for the upper boundary of the average sensorimotor uncertainty associated either with angular position or with angular velocity. Comparison of balancing trials with 27 human subjects to the delayed PD model suggests that the average uncertainty in the control force associated purely with the angular position is at most 14% while that associated purely with the angular velocity is at most 40%. In the general case when both uncertainties are present, the calculations suggest that the allowed uncertainty in angular velocity will always be greater than that in angular position.
What do we know about the fossil record of pinnipeds? A historiographical investigation

The fossil record of pinnipeds (seals, fur seals and walruses) is globally distributed, spanning from the late Oligocene to the Holocene. This record shows a complex evolutionary history that could not otherwise be inferred from their extant relatives, including multiple radiations and iterative ecomorphological specializations among different lineages, many of which are extinct. The fossil record of pinnipeds is not uniformly represented in space and time, however, leaving some gaps in our knowledge. We performed a historiographical investigation of the published fossil record of pinnipeds based on the information available in the Paleobiology Database, with the aim to broadly characterize and evaluate it from a taxonomic, geographical and temporal perspective. We identified major trends, strengths and weaknesses of the pinniped fossil record, including potential biases that may affect our interpretations. We found that 39% of the record corresponds to extant taxa, which are essentially from the Pleistocene and Holocene. There is a larger record from the Northern Hemisphere, suggesting biases in sampling and collection effort. The record is not strongly biased by sedimentary outcrop bias. Specifically, for extinct species, nearly half of them are represented by a single occurrence and a large proportion have type specimens consisting of single isolated postcranial elements. While the pinniped fossil record may have adequate temporal and taxonomic coverage, it has a strong geographical bias and its comparability is hindered by the incompleteness of type specimens. These results should be taken into account when addressing patterns of their past diversity, evolutionary history and paleoecology.
Altered Risk for Cardiovascular Events With Changes in the Metabolic Syndrome Status

Background Population-scale evidence for the association between dynamic changes in metabolic syndrome (MetS) status and alterations in the risk for major adverse cardiovascular events (MACE) is lacking. Objective To investigate whether recovery from or development of MetS in a population is associated with an altered risk for MACE. Design Nationwide cohort study. Setting An analysis based on the National Health Insurance Database of Korea. Participants A total of 27 161 051 persons who received national health screenings from 2009 to 2014 were screened. Those with a history of MACE were excluded. We determined the MetS status of 9 553 042 persons using the following harmonizing criteria: MetS-chronic (n = 1 486 485), MetS-developed (n = 587 088), MetS-recovery (n = 538 806), and MetS-free (n = 6 940 663). Measurements The outcome was the occurrence of MACE, including acute myocardial infarction, revascularization, and acute ischemic stroke, identified from the claims database. The incidence rate ratios (IRRs) were calculated with adjustments for body mass index, comorbidity scores, previous metabolic variables, and other clinical or demographic variables. Results At a median follow-up of 3.54 years, the MetS-recovery group (incidence rate, 4.55 per 1000 person-years) had a significantly lower MACE risk (adjusted IRR, 0.85 [95% CI, 0.83 to 0.87]) than that of the MetS-chronic group (incidence rate, 8.52 per 1000 person-years). The MetS-developed group (incidence rate, 6.05 per 1000 person-years) had a significantly higher MACE risk (adjusted IRR, 1.36 [CI, 1.33 to 1.39]) than that of the MetS-free group (incidence rate, 1.92 per 1000 person-years). Among the MetS components, change in hypertension was associated with the largest difference in MACE risk. Limitation Limited assessment of mortality and short follow-up. Conclusion Recovery from MetS was significantly associated with decreased risk for MACE, whereas development of MetS was associated with increased risk. Primary Funding Source Korea Healthcare Technology R&D Project, Ministry of Health and Welfare, Republic of Korea.
Preventive Effects of Duloxetine Against Methamphetamine Induced Neurodegeneration and Motor Activity Disorder in Rat: Possible Role of CREB/BDNF Signaling Pathway

Background: The neuroprotective effects of duloxetine and neurodegenerative effects of methamphetamine have been shown in previous studies, but their exact mechanism remain unclear. In the current study it involved molecular mechanisms of neuroprotective effects of duloxetine against methamphetamine induced neurodegeneration were clarified. Methods: About 40 adult male rats randomly were divided to 5 groups. Group 1 and 2, as control and methamphetamine treated, received normal saline and methamphetamine (10 mg/kg) respectively. Groups 3, 4 and 5 concurrently treated with methamphetamine and duloxetine at doses of 10, 20 and 30 mg/kg respectively. All treatments were undertaken for 21 days. On day 22 Open Field Test (OFT) were used to examine the level of motor activity disturbance and anxiety in animals. After that hippocampus was isolated from each rat and oxidative, antioxidant, inflammatory factors and also level or expression of total and phosphorylated forms of CREB and P-CREB and BDNF proteins were measured. Results: Duloxetine in all mentioned doses could inhibit the effects of methamphetamine induced motor activity disturbance in MWM. Chronic abuse of methamphetamine could increase malondialdehyde (MDA), tumor necrosis factor-Alpha (TNF-α) and interleukine-1beta (IL-1β) while caused decreases in superoxide dismutase (SOD), glutathione peroxidase (GPx) and glutathione reductase (GR) activities and decreased CREB (both forms) and BDNF proteins, while duloxetine could prevent these malicious effects of methamphetamine. Conclusions: We conclude that P-CREB/BDNF signaling pathways might have critical role in duloxetine neuroprotective effects against methamphetamine induced neurodegeneration.
Can High Average Oxygen Saturation be a Risk Factor for Necrotizing Enterocolitis in VLBW Infants?

Background: Avoiding hyperoxia with oxygen saturation monitoring is important in the follow-up of very low birth weight (VLBW) infants. Role of oxygen-derived free radicals in the pathogenesis of necrotizing enterocolitis (NEC) has been well defined. However, a great majority of the evidence supporting the role of hyperoxia in NEC development are data from experimental studies and there are very few clinical studies. In this study, the association between NEC and average oxygen saturation (SpO2) levels in VLBW infants was researched. Methods: Average SpO2 values of VLBW infants in the last 24 h were recorded prospectively with pulse oximeter. Average SpO2 records were continued at least for 10 days starting from the first day after birth. In the follow-up, the average SpO2 values of the patients who developed NEC and those who did not were compared. Results: A total of 127 VLBW infants were followed up. Thirteen patients developed NEC (Bell's classification ≥ stage II). No differences were found between the average SpO2 levels (94.9 and 94.8%) of the patients who developed NEC and those who did not. It was found that average SpO2 value higher than 93 or 95 was not a risk for NEC development (P = 0.693 and P = 0.771). Conclusions: In this study, no association was found between average SpO2 values recorded in the first weeks of VLBW infants and NEC.
Subnational smoke-free laws in China

INTRODUCTION Implementing comprehensive smoke-free laws is an important part of tobacco control and has been promoted since China ratified the WHO Framework Convention on Tobacco Control (WHO FCTC) in 2005. This study shows the predictors of adopting subnational smoke-free laws and their alignment with Article 8 of WHO FCTC. METHODS The legislations of 125 cities from China’s top three city grades were assessed, covering the cities that have smoke-free laws. Logistic regression is applied to evaluate the characteristics of cities that adopted a smoke-free law. We also compare each smoke-free law with the WHO FCTC Article 8 requirements. RESULTS Provincial capital cities were more likely to adopt smoke-free laws compared with other cities. Smoke-free laws vary from comprehensive to partial bans with major exemptions. Among the 21 cities that have enacted smoke-free laws, 9 cities prohibited smoking in all indoor workplaces, indoor public places (restaurants, bars, health facilities, government buildings and schools) and public transportation. More than half of the smoke-free laws still allow designated indoor smoking rooms. Smoke-free laws that clearly ban e-cigarettes in smoke-free areas have been implemented in only two cities (Nanning and Hangzhou). CONCLUSIONS This study shows that a number of Chinese cities have taken legislative measures to protect people from exposure to tobacco smoke. It identifies signs of progress but also areas for improvement, such as the scope of smoke-free laws, imperfect implementation of such laws, and the potential omission of e-cigarettes from the legislation.
Epidemiologic Characteristics and Postoperative Complications following Augmentation Mammaplasty: Comparison of Transgender and Cisgender Females

Background: Breast augmentation in transgender women can be an important first step in addressing gender incongruence and improving psychosocial functioning. The aim of this study was to compare postoperative outcomes of augmentation mammoplasty in transgender and cisgender females. Methods: We queried the American College of Surgeons National Surgical Quality Improvement Program database from 2006 to 2017 to establish 2 cohorts: (1) transgender females undergoing gender-affirming breast augmentation (“top surgery”) and (2) cisgender females seeking cosmetic breast augmentation (CBA). Demographic characteristics and postoperative outcomes were compared between the 2 cohorts. Multivariable regression analysis was used to control for confounders. Results: A total of 1,360 cases were identified, of which 280 (21%) were feminizing top surgeries and 1,080 (79%) were CBA cases. The transfeminine cohort was significantly older, had a higher average body mass index, and was more racially diverse than the CBA cohort. Transfeminine patients also had higher rates of smoking, diabetes, and hypertension. The rates of all-cause complications were low in both cohorts, and differences were not significant (1.6% transfeminine versus 1.8% CBA, P = 0.890) for the first 30-days after operation. After controlling for confounding variables, transfeminine patients had postoperative complication profiles similar to their cisgender counterparts. Multivariable regression analysis revealed no statistically significant predictors for all-cause complications. Conclusions: Transfeminine breast augmentation is a safe procedure that has a similar 30-day complication profile to its cisgender counterpart. The results of this study should reassure and encourage surgeons who are considering performing this procedure.
Effect of microRNA-133a-3p/matrix metalloproteinase-9 axis on the growth of atherosclerotic vascular smooth muscle cells

Atherosclerosis (AS) is the leading cause of cardiovascular disease and poses a threat to human health. MicroRNAs (miRNAs/miRs) are a group of endogenous small non-coding RNAs that have been identified to serve important roles in AS. However, the expression and role of miR-133a-3p in AS remains unclear. The aim of the present study was to investigate miR-133a-3p in AS and to determine its underlying mechanism. The level of miR-133a-3p expression in the blood and vascular plaque tissue of patients with AS was detected via reverse transcription-quantitative PCR (RT-qPCR). The role of miR-133a-3p in human vascular smooth muscle cells (hVSMCs) was investigated, following upregulation and downregulation of this miR in hVSMCs. Cell proliferation and apoptosis were determined using a Cell Counting kit-8 assay and flow cytometry, respectively. The results demonstrated the downregulation of miR-133a-3p in the blood and vascular plaque tissue of patients with AS. Matrix metallopeptidase-9 (MMP-9) was revealed to be a direct target gene of miR-133a-3p, which was upregulated in the blood and vascular plaque tissue of patients with AS. Furthermore, MMP-9 was determined to be negatively regulated by miR-133a-3p in hVSMCs. In addition, significant inhibition of hVSMC proliferation and induction of cell apoptosis were observed following MMP-9 downregulation and following transfection with the miR-133a-3p mimic. The effects of the miR-133a-3p mimic on hVSMC proliferation and apoptosis were reversed by MMP-9 over-expression. Overall, the results indicated that miR-133a-3p was downregulated in AS, which results in the inhibition of hVSMC proliferation and the induction of cell apoptosis via MMP-9. miR-133a-3p may therefore be a promising therapeutic target for the treatment of AS.
Experimental evidence of chemical attraction in the mutualistic zebra mussel-killer shrimp system

Invasion facilitation, whereby one species has a positive effect on the establishment of another species, could help explain the rapid colonisation shown by some freshwater invasive species, but the underlying mechanisms remain unclear. We employed two-choice test arenas to test whether the presence of zebra mussel (Dreissena polymorpha) could facilitate the establishment of the killer shrimp (Dikerogammarus villosus). Killer shrimp preferred to settle on mats of zebra mussel, but this was unrelated to mat size, and was not different from attraction shown to artificial grass, suggesting that zebra mussel primarily provides substrate and refuge to the killer shrimp. Killer shrimp were strongly attracted to water scented by zebra mussel, but not to water scented by fish. Chemical attraction to the zebra mussel’s scent did not differ between sympatric and allopatric populations of killer shrimp, suggesting that chemical attraction is not an acquired or learned trait. Our study shows, for the first time, chemical attraction between two highly invasive freshwater species, thereby providing a plausible mechanism for invasion facilitation. This has implications for managing the spread of killer shrimp, and perhaps other freshwater invasive species, because chemical attraction could significantly increase establishment success in mutualistic systems. Failure to consider invasion facilitation may underestimate the risk of establishment, and likely also the impact of some aquatic invaders.
LD-annot: A Bioinformatics Tool to Automatically Provide Candidate SNPs With Annotations for Genetically Linked Genes

A multitude of model and non-model species studies have now taken full advantage of powerful high-throughput genotyping advances such as SNP arrays and genotyping-by-sequencing (GBS) technology to investigate the genetic basis of trait variation. However, due to incomplete genome coverage by these technologies, the identified SNPs are likely in linkage disequilibrium (LD) with the causal polymorphisms, rather than be causal themselves. In addition, researchers could benefit from annotations for the identified candidate SNPs and, simultaneously, for all neighboring genes in genetic linkage. In such case, LD extent estimation surrounding the candidate SNPs is required to determine the regions encompassing genes of interest. We describe here an automated pipeline, “LD-annot,” designed to delineate specific regions of interest for a given experiment and candidate polymorphisms on the basis of LD extent, and furthermore, provide annotations for all genes within such regions. LD-annot uses standard file formats, bioinformatics tools, and languages to provide identifiers, coordinates, and annotations for genes in genetic linkage with each candidate polymorphism. Although the focus lies upon SNP arrays and GBS data as they are being routinely deployed, this pipeline can be applied to a variety of datasets as long as genotypic data are available for a high number of polymorphisms and formatted into a vcf file. A checkpoint procedure in the pipeline allows to test several threshold values for linkage without having to rerun the entire pipeline, thus saving the user computational time and resources. We applied this new pipeline to four different sample sets: two breeding populations GBS datasets, one within-pedigree SNP set coming from whole genome sequencing (WGS), and a very large multi-varieties SNP dataset obtained from WGS, representing variable sample sizes, and numbers of polymorphisms. LD-annot performed within minutes, even when very high numbers of polymorphisms are investigated and thus will efficiently assist research efforts aimed at identifying biologically meaningful genetic polymorphisms underlying phenotypic variation. LD-annot tool is available under a GPL license from https://github.com/ArnaudDroitLab/LD-annot.
QTL and Transcriptomic Analyses Implicate Cuticle Transcription Factor SHINE as a Source of Natural Variation for Epidermal Traits in Cucumber Fruit

The fruit surface is a unique tissue with multiple roles influencing fruit development, post-harvest storage and quality, and consumer acceptability. Serving as the first line of protection against herbivores, pathogens, and abiotic stress, the surface can vary markedly among species, cultivars within species, and developmental stage. In this study we explore developmental changes and natural variation of cucumber (Cucumis sativus L.) fruit surface properties using two cucumber lines which vary greatly for these traits and for which draft genomes and a single nucleotide polymorphism (SNP) array are available: Chinese fresh market type, Chinese Long ‘9930’ (CL9930), and pickling type, ‘Gy14’. Thin-section samples were prepared from the mid-region of fruit harvested at 0, 4, 8, 12, 16, 20, 24 and 30 days post pollination (dpp), stained with Sudan IV and evaluated for cuticle thickness, depth of wax intercalation between epidermal cells, epidermal cell size and shape, and number and size of lipid droplets. ‘Gy14’ is characterized by columnar shaped epidermal cells, a 2–3 fold thicker cuticular layer than CL9930, increased cuticular intercalations between cells and a larger number and larger sized lipid droplets. In both lines maximal deposition of cuticle and increase in epidermal size coincided with exponential fruit growth and was largely completed by approximately 16 dpp. Phenotyping and quantitative trait locus mapping (QTL) of fruit sampled from an F7:F8 Gy14 × CL9930 recombinant inbred line (RIL) population identified QTL regions on chromosomes 1, 4 and 5. Strong QTL for epidermal cell height, cuticle thickness, intercalation depth, and diameter of lipid droplets co-localized on chromosome 1. SSR markers on chromosome 1 were used to screen for recombinants in an extended RIL population to refine the QTL region. Further fine mapping by KASP assay combined with gene expression profiling suggested a small number of candidate genes. Tissue specificity, developmental analysis of expression, allelic diversity and gene function implicate the regulatory factor CsSHINE1/WIN1 as a source of natural variation for cucumber fruit epidermal traits.
The Cholesterol-Lowering Effect of Oats and Oat Beta Glucan: Modes of Action and Potential Role of Bile Acids and the Microbiome

Consumption of sufficient quantities of oat products has been shown to reduce host cholesterol and thereby modulate cardiovascular disease risk. The effects are proposed to be mediated by the gel-forming properties of oat β-glucan which modulates host bile acid and cholesterol metabolism and potentially removes intestinal cholesterol for excretion. However, the gut microbiota has emerged as a major factor regulating cholesterol metabolism in the host. Oat β-glucan has been shown to modulate the gut microbiota, particularly those bacterial species that influence host bile acid metabolism and production of short chain fatty acids, factors which are regulators of host cholesterol homeostasis. Given a significant role for the gut microbiota in cholesterol metabolism it is likely that the effects of oat β-glucan on the host are multifaceted and involve regulation of microbe-host interactions at the gut interface. Here we consider the potential for oat β-glucan to influence microbial populations in the gut with potential consequences for bile acid metabolism, reverse cholesterol transport (RCT), short-chain fatty acid (SCFA) production, bacterial metabolism of cholesterol and microbe-host signaling.
Channel-Unet: A Spatial Channel-Wise Convolutional Neural Network for Liver and Tumors Segmentation

It is a challenge to automatically and accurately segment the liver and tumors in computed tomography (CT) images, as the problem of over-segmentation or under-segmentation often appears when the Hounsfield unit (Hu) of liver and tumors is close to the Hu of other tissues or background. In this paper, we propose the spatial channel-wise convolution, a convolutional operation along the direction of the channel of feature maps, to extract mapping relationship of spatial information between pixels, which facilitates learning the mapping relationship between pixels in the feature maps and distinguishing the tumors from the liver tissue. In addition, we put forward an iterative extending learning strategy, which optimizes the mapping relationship of spatial information between pixels at different scales and enables spatial channel-wise convolution to map the spatial information between pixels in high-level feature maps. Finally, we propose an end-to-end convolutional neural network called Channel-UNet, which takes UNet as the main structure of the network and adds spatial channel-wise convolution in each up-sampling and down-sampling module. The network can converge the optimized mapping relationship of spatial information between pixels extracted by spatial channel-wise convolution and information extracted by feature maps and realizes multi-scale information fusion. The proposed ChannelUNet is validated by the segmentation task on the 3Dircadb dataset. The Dice values of liver and tumors segmentation were 0.984 and 0.940, which is slightly superior to current best performance. Besides, compared with the current best method, the number of parameters of our method reduces by 25.7%, and the training time of our method reduces by 33.3%. The experimental results demonstrate the efficiency and high accuracy of Channel-UNet in liver and tumors segmentation in CT images.