Miracle-dz/UniFAR-FTUs huggingface dataset:
Cryptic Species Exist in Vietnamella sinensis Hsu, 1936 (Insecta: Ephemeroptera) from Studies of Complete Mitochondrial Genomes

Simple Summary The family Vietnamellidae (Ephemeroptera) is one of the oldest insect families in the world. However, there are still controversies about the phylogenetic relationships among Vietnamellidae, Ephemerellidae, and Teloganodidae. The mitochondrial (mt) genome can be used to discuss phylogenetic relationships and cryptic species. We sequenced and annotated three complete mt genomes of Vietnamella sinensis from three different populations, identifying a cryptic species of V. sinensis and discuss the phylogenetic relationships of Vietnamellidae. Based on the genetic distance of the whole mt genomes, the phylogenetic relationship of three populations was uncovered and the divergence time of V. sinensis QY indicated that it was a cryptic species of V. sinensis. Abstract Ephemeroptera (Insecta: Pterygota) are widely distributed all over the world with more than 3500 species. During the last decade, the phylogenetic relationships within Ephemeroptera have been a hot topic of research, especially regarding the phylogenetic relationships among Vietnamellidae. In this study, three mitochondrial genomes from three populations of Vienamella sinensis collected from Tonglu (V. sinensis TL), Chun’an (V. sinensis CN), and Qingyuan (V. sinensis QY) in Zhejiang Province, China were compared to discuss the potential existence of cryptic species. We also established their phylogenetic relationship by combining the mt genomes of 69 Ephemeroptera downloaded from NCBI. The mt genomes of V. sinensis TL, V. sinensis CN, and V. sinensis QY showed the same gene arrangement with lengths of 15,674 bp, 15,674 bp, and 15,610 bp, respectively. Comprehensive analyses of these three mt genomes revealed significant differences in mt genome organization, genetic distance, and divergence time. Our results showed that the specimens collected from Chun’an and Tonglu in Zhejiang Province, China belonged to V. sinensis, and the specimens collected from Qingyuan, Zhejiang Province, China were a cryptic species of V. sinensis. In maximum likelihood (ML) and Bayesian inference (BI) phylogenetic trees, the monophyly of the family Vietnamellidae was supported and Vietnamellidae has a close relationship with Ephemerellidae.
Diffusion-Weighted Imaging to Assess HPV-Positive versus HPV-Negative Oropharyngeal Squamous Cell Carcinoma: The Importance of b-Values

BACKGROUND AND PURPOSE: Controversy exists as to whether ADC histograms are capable to distinguish human papillomavirus–positive (HPV+) from human papillomavirus–negative (HPV–) oropharyngeal squamous cell carcinoma. We investigated how the choice of b-values influences the capability of ADC histograms to distinguish between the two tumor types. MATERIALS AND METHODS: Thirty-four consecutive patients with histologically proved primary oropharyngeal squamous cell carcinoma (11 HPV+ and 23 HPV–) underwent 3T MR imaging with a single-shot EPI DWI sequence with 6 b-values (0, 50, 100, 500, 750, 1000 s/mm2). Monoexponentially calculated perfusion-sensitive (including b=0 s/mm2) and perfusion-insensitive/true diffusion ADC maps (with b ≥ 100 s/mm2 as the lowest b-value) were generated using Matlab. The choice of b-values included 2 b-values (ADCb0–1000, ADCb100–1000, ADCb500–1000, ADCb750–1000) and 3–6 b-values (ADCb0–750–1000, ADCb0–500–750–1000, ADCb0–50–100–1000, ADCb0–50–100–750–1000, ADCb0–50–100–500–750–1000). Readers blinded to the HPV– status contoured all tumors. ROIs were then copied onto ADC maps, and their histograms were compared. RESULTS: ADC histogram metrics in HPV+ and HPV– oropharyngeal squamous cell carcinoma changed significantly depending on the b-values. The mean ADC was lower, and skewness was higher in HPV+ than in HPV– oropharyngeal squamous cell carcinoma only for ADCb0–1000, ADCb0–750–1000, and ADCb0–500–750–1000 (P < .05), allowing distinction between the 2 tumor types. Kurtosis was significantly higher in HPV+ versus HPV– oropharyngeal squamous cell carcinoma for all b-value combinations except 2 perfusion-insensitive maps (ADCb500–1000 and ADCb750–1000). Among all b-value combinations, kurtosis on ADCb0–1000 had the highest diagnostic performance to distinguish HPV+ from HPV– oropharyngeal squamous cell carcinoma (area under the curve = 0.893; sensitivity = 100%, specificity = 82.6%). Acquiring multiple b-values for ADC calculation did not improve the distinction between HPV+ and HPV– oropharyngeal squamous cell carcinoma. CONCLUSIONS: The choice of b-values significantly affects ADC histogram metrics in oropharyngeal squamous cell carcinoma. Distinguishing HPV+ from HPV– oropharyngeal squamous cell carcinoma is best possible on the ADCb0–1000 map.
Smokeless tobacco use and public health nutrition: a global systematic review

Abstract Objective: Tobacco consumption among low- and middle-income countries where food insecurity remains a challenge poses several concerns. This review examines the available global evidence linking smokeless tobacco (SLT) use with public health nutrition and its implications. Design: Systematic review of articles extracted from PubMed and Scopus from January 2000 to December 2020. Setting: Included studies that demonstrated the relationship between SLT and nutrition-related factors, that is, BMI, malnutrition, anaemia, poor birth outcomes and metabolic disorders. Preferred Reporting Items for Systematic Reviews and Meta-Analysis (PRISMA) guidelines have been followed to conduct the systematic evidence review. Participants: A total of thirty-four studies were finally used in the systematic review, which included cross-sectional (thirty-one) and cohort (three). Results: SLT use has a huge impact on body weight, alteration in taste, poor oral health, and consumption of fruits and vegetables leading to malnutrition. Maternal use of SLT not only leads to anaemia but also hampers birth outcomes. Increased risk of metabolic syndrome and gallstone disease among SLT users are also well documented in the studies. Conclusion: The review highlights the linkages between SLT usage and poor nutritional outcomes. Tobacco control efforts should be convergent with public health nutrition to achieve overall health benefits. Attention is also required to explore suitable mechanisms for SLT cessation combined with enhancing food and nutrition security at the community level in sync with investments in public health nutrition intervention.
Nucleophosmin 1: from its pathogenic role to a tantalizing therapeutic target in acute myeloid leukemia

ABSTRACT Nucleophosmin 1 (NPM1, also known as B23) is a multifunctional protein involved in a variety of cellular processes, including ribosomal maturation, centrosome replication, maintenance of genomic stability, cell cycle control, and apoptosis. NPM1 is the most commonly mutated gene in adult acute myeloid leukemia (AML) and is present in approximately 40% of all AML cases. The underlying mechanisms of mutant NPM1 (NPM1mut) in leukemogenesis remain unclear. This review summarizes the structure and physiological function of NPM1, mechanisms underlying the pathogenesis of NPM1-mutated AML, and the potential role of NPM1 as a therapeutic target. It is reported that dysfunctional NPM1 might cause AML pathogenesis via its role as a protein chaperone, inhibiting differentiation of leukemia stem cells and regulation of non-coding RNAs. Besides conventional chemotherapies, NPM1 is a promising therapeutic target against AML that warrants further investigation. NPM1-based therapeutic strategies include inducing nucleolar relocalisation of NPM1 mutants, interfering with NPM1 oligomerization, and NPM1 as an immune response target.
Isoquercetin alleviates sleep deprivation dependent hippocampal neurons damage by suppressing NLRP3-induced pyroptosis

Abstract Purpose: Sleep deprivation (SD) leads to memory and cognitive impairment due to damage to the hippocampus. Isoquercetin possesses neuron-protective properties. Our study aimed to investigate the effects of isoquercetin on SD-induced hippocampal neurons damage and the underlying mechanism. Materials and methods: Herein, the cognitive competence was evaluated by Morris water maze test after SD. The morphology of the hippocampus was observed after Nissl staining. Moreover, the level of NLRP3 was detected by Immunofluorescent staining and western blot. In vitro study, pyroptosis was tested by TUNEL assay and flow cytometry. The levels of pyroptosis-related factors were measured by western blot. Results: The results indicated that isoquercetin improved spatial memory and prevented change of hippocampal neurons of SD mice. Moreover, SD upregulated NLRP3 level, which was downregulated by isoquercetin. Additionally, isoquercetin rescued the increase of pyroptosis and the upregulation of NLRP3, caspase-1, ASC, IL-1β, IL-18, and GSDMD levels induced by LPS. Conclusions: In conclusion, isoquercetin improved learning and cognitive capability of SD mice via suppressing NLRP3-induced pyroptosis of hippocampal neurons cells, suggesting that isoquercetin might be an efficacious drug for memory disorders caused by SD.
Minimalist running: evolution of spatiotemporal parameters and plantar pressure following a training of specific running technique in novice subjects

Running is a part of the most spread sports activities in our societies. It does not require much equipment and is not submitted to schedule constraints, for example. However, the risk of injuries is not negligible. Minimalist running is very fashionable and the object of numerous recent researches, because of its potential to reduce the risks of running-related injuries. It is also said to be more natural (Altman & Davis, 2012; Crowell & Davis, 2011, Giandolini, Horvais, Farges, Samozino, & Morin, 2013; Honeine, Schieppati, Gagey, & Do, 2014; Lieberman et al., 2010; Nunns, House, Fallowfield, Allsopp, & Dixon, 2013; Squadrone & Gallozzi, 2009). The approach chosen within the framework of this study (learning of the minimalist running technique by novices wearing conventional running shoes) is in line with recent training approaches (Giandolini et al., 2013; Warne et al., 2014) and could allow contributing to promote the inclusion of running technique exercises in jogging training programs.
Granule cell dispersion in two mouse models of temporal lobe epilepsy and reeler mice is associated with changes in dendritic orientation and spine distribution

Temporal lobe epilepsy is characterized by hippocampal neuronal death in CA1 and hilus. Dentate gyrus granule cells survive but show dispersion of the compact granule cell layer. This is associated with decrease of the glycoprotein Reelin, which regulates neuron migration and dendrite outgrow. Reelin‐deficient (reeler) mice show no layering, their granule cells are dispersed throughout the dentate gyrus. We studied granule cell dendritic orientation and distribution of postsynaptic spines in reeler mice and two mouse models of temporal lobe epilepsy, namely the p35 knockout mice, which show Reelin‐independent neuronal migration defects, and mice with unilateral intrahippocampal kainate injection. Granule cells were Golgi‐stained and analyzed, using a computerized camera lucida system. Granule cells in naive controls exhibited a vertically oriented dendritic arbor with a small bifurcation angle if positioned proximal to the hilus and a wider dendritic bifurcation angle, if positioned distally. P35 knockout‐ and kainate‐injected mice showed a dispersed granule cell layer, granule cells showed basal dendrites with wider bifurcation angles, which lost position‐specific differences. Reeler mice lacked dendritic orientation. P35 knockout‐ and kainate‐injected mice showed increased dendritic spine density in the granule cell layer. Molecular layer dendrites showed a reduced spine density in kainate‐injected mice only, whereas in p35 knockouts no reduced spine density was seen. Reeler mice showed a homogenous high spine density. We hypothesize that granule cells migrate in temporal lobe epilepsy, develop new dendrites which show a spread of the dendritic tree, create new spines in areas proximal to mossy fiber sprouting, which is present in p35 knockout‐ and kainate‐injected mice and loose spines on distal dendrites if mossy cell death is present, as it was in kainate‐injected mice only. These results are in accordance with findings in epilepsy patients.
Inhaled nitric oxide as temporary respiratory stabilization in patients with COVID-19 related respiratory failure (INOCOV): Study protocol for a randomized controlled trial

Background In March 2020, WHO announced the COVID-19 a pandemic and a major global public health emergency. Mortality from COVID-19 is rapidly increasing globally, with acute respiratory failure as the predominant cause of death. Many patients experience severe hypoxia and life-threatening respiratory failure often requiring mechanical ventilation. To increase safety margins during emergency anaesthesia and rapid sequence intubation (RSI), patients are preoxygenated with a closed facemask with high-flow oxygen and positive end-expiratory pressure (PEEP). Due to the high shunt fraction of deoxygenated blood through the lungs frequently described in COVID-19 however, these measures may be insufficient to avoid harmful hypoxemia. Preoxygenation with inhaled nitric oxide (iNO) potentially reduces the shunt fraction and may thus allow for the necessary margins of safety during RSI. Methods and design The INOCOV protocol describes a phase II pharmacological trial of inhaled nitric oxide (iNO) as an adjunct to standard of care with medical oxygen in initial airway and ventilation management of patients with known or suspected COVID-19 in acute respiratory failure. The trial is parallel two-arm, randomized, controlled, blinded trial. The primary outcome measure is the change in oxygen saturation (SpO2), and the null hypothesis is that there is no difference in the change in SpO2 following initiation of iNO. Trial registration EudraCT number 2020-001656-18; WHO UTN: U1111-1250-1698. Protocol version: 2.0 (June 25th, 2021).
Acute Toxicity of Major Geochemical Ions to Fathead Minnows (Pimephales Promelas): Part A—Observed Relationships for Individual Salts and Salt Mixtures

The results of a series of experiments on the acute toxicity of major geochemical ions (Na+, K+, Ca2+, Mg2+, Cl−, SO42−, HCO3−/CO32−) to fathead minnows (Pimephales promelas) are reported. Tests of individual major ion salts in various dilution waters demonstrated that the toxicities of Na, Mg, and K salts decrease as the overall ion content of the dilution water increases. For Na and Mg salts, this is attributable to Ca content as previously reported for Ceriodaphnia dubia. For K salts, the cause is unclear, but it is not due to Na as reported for C. dubia. In an unregulated test at high pH (9.3), NaHCO3 was also found to be twice as toxic compared to when the pH was reduced to 8.4. Experiments with binary salt mixtures indicated the existence of multiple independent mechanisms of action. These include K‐specific toxicity and Ca/Mg‐specific toxicity previously reported for C. dubia, but also apparent toxicities related to SO4 and to high pH/alkalinity in CO3/HCO3‐dominated exposures. Previous work with C. dubia also suggested a general ion toxicity involving all ions that was correlated with osmolarity. For fathead minnow, similar correlations were observed, but multiple mechanisms were indicated. At higher Ca, this general toxicity could be attributable to osmotic effects, but at lower Ca, osmolarity may be more a covariate than a cause, with this toxicity being related to a combined effect of ions other than via osmolarity. Environ Toxicol Chem 2022;41:2078–2094. © 2022 SETAC. This article has been contributed to by U.S. Government employees and their work is in the public domain in the USA.
The use of propensity score stratification and synthetic data to address allocation bias when assessing bicycle helmet effectiveness

Case‐control studies have found bicycle helmet use significantly mitigates the risk and severity of head injury in a motor vehicle collision. However, critics argue the decision to wear a helmet is confounded with other factors related to cycling safety such as cycling speed. If such an allocation bias exists, results from case‐ control studies may be invalid if confounding factors are ignored. Although allocation bias and bicycle helmet effectiveness is frequently mentioned in the literature, there is a paucity of research that has explored this relationship. This study aims to examine bicycle helmet effectiveness in a motor vehicle collision using the propensity score stratification method, which removes allocation bias from case (head injury) and control (no head injury) groups to allow for direct comparison of helmet effectiveness in reducing head injury. Due to privacy and data accessibility issues, synthetic data was created from a recently published Australian study of linked hospital and police data over a nine‐year period. In a motor vehicle collision, helmet use was associated with factors that have been argued to influence estimates of helmet effectiveness; however, using propensity score stratification, there is no evidence these confounding factors influence estimates of helmet effectiveness.
Smart wearables: utilizing persuasive devices to reduce sedentary time

This research studied the effectiveness of alerts from smart wearables on health. Topics include sedentary behavior, smart wearables, and behavior modification. Building on work that shows alerts to be effective in various health and medical circumstances, this study asked participants to wear a device, specifically an Apple Watch, to measure a renewed area of interest in health research effects of sedentary time on health. Metrics studied included a measure of sedentary time, calories, exercise, and steps, which were recorded first without and then with alerts prompting the wearer to break up long stretches of sedentary time. Both quantitative and qualitative findings are discussed, including the finding that an increase in the number of steps taken was correlated to the use of alerts reminding wearer to break up long stretches of sedentary time.
On the Reliability of Computing-in-Memory Accelerators for Deep Neural Networks

Computing-in-memory with emerging non-volatile memory (nvCiM) is shown to be a promising candidate for accelerating deep neural networks (DNNs) with high energy efficiency. However, most non-volatile memory (NVM) devices suffer from reliability issues, resulting in a difference between actual data involved in the nvCiM computation and the weight value trained in the data center. Thus, models actually deployed on nvCiM platforms achieve lower accuracy than their counterparts trained on the conventional hardware (e.g., GPUs). In this chapter, we first offer a brief introduction to the opportunities and challenges of nvCiM DNN accelerators and then show the properties of different types of NVM devices. We then introduce the general architecture of nvCiM DNN accelerators. After that, we discuss the source of unreliability and how to efficiently model their impact. Finally, we introduce representative works that mitigate the impact of device variations.
Subspace clustering in high-dimensions: Phase transitions \& Statistical-to-Computational gap

A simple model to study subspace clustering is the high-dimensional $k$-Gaussian mixture model where the cluster means are sparse vectors. Here we provide an exact asymptotic characterization of the statistically optimal reconstruction error in this model in the high-dimensional regime with extensive sparsity, i.e. when the fraction of non-zero components of the cluster means $\rho$, as well as the ratio $\alpha$ between the number of samples and the dimension are fixed, while the dimension diverges. We identify the information-theoretic threshold below which obtaining a positive correlation with the true cluster means is statistically impossible. Additionally, we investigate the performance of the approximate message passing (AMP) algorithm analyzed via its state evolution, which is conjectured to be optimal among polynomial algorithm for this task. We identify in particular the existence of a statistical-to-computational gap between the algorithm that require a signal-to-noise ratio $\lambda_{\text{alg}} \ge k / \sqrt{\alpha} $ to perform better than random, and the information theoretic threshold at $\lambda_{\text{it}} \approx \sqrt{-k \rho \log{\rho}} / \sqrt{\alpha}$. Finally, we discuss the case of sub-extensive sparsity $\rho$ by comparing the performance of the AMP with other sparsity-enhancing algorithms, such as sparse-PCA and diagonal thresholding.
On the Eigenvalues of Global Covariance Pooling for Fine-Grained Visual Recognition

The Fine-Grained Visual Categorization (FGVC) is challenging because the subtle inter-class variations are difficult to be captured. One notable research line uses the Global Covariance Pooling (GCP) layer to learn powerful representations with second-order statistics, which can effectively model inter-class differences. In our previous conference paper, we show that truncating small eigenvalues of the GCP covariance can attain smoother gradient and improve the performance on large-scale benchmarks. However, on fine-grained datasets, truncating the small eigenvalues would make the model fail to converge. This observation contradicts the common assumption that the small eigenvalues merely correspond to the noisy and unimportant information. Consequently, ignoring them should have little influence on the performance. To diagnose this peculiar behavior, we propose two attribution methods whose visualizations demonstrate that the seemingly unimportant small eigenvalues are crucial as they are in charge of extracting the discriminative class-specific features. Inspired by this observation, we propose a network branch dedicated to magnifying the importance of small eigenvalues. Without introducing any additional parameters, this branch simply amplifies the small eigenvalues and achieves state-of-the-art performances of GCP methods on three fine-grained benchmarks. Furthermore, the performance is also competitive against other FGVC approaches on larger datasets. Code is available at https://github.com/KingJamesSong/DifferentiableSVD.
Grasping as Inference: Reactive Grasping in Heavily Cluttered Environment

Although, in the task of grasping via a data-driven method, closed-loop feedback and predicting 6 degrees of freedom (DoF) grasp rather than conventionally used 4DoF top-down grasp are demonstrated to improve performance individually, few systems have both. Moreover, the sequential property of that task is hardly dealt with, while the approaching motion necessarily generates a series of observations. Therefore, this paper synthesizes three approaches and suggests a closed-loop framework that can predict the 6DoF grasp in a heavily cluttered environment from continuously received vision observations. This can be realized by formulating the grasping problem as Hidden Markov Model and applying a particle filter to infer grasp. Additionally, we introduce a novel lightweight Convolutional Neural Network (CNN) model that evaluates and initializes grasp samples in real-time, making the particle filter process possible. The experiments, which are conducted on a real robot with a heavily cluttered environment, show that our framework not only quantitatively improves the grasping success rate significantly compared to the baseline algorithms, but also qualitatively reacts to a dynamic change in the environment and cleans up the table.