Miracle-dz/UniFAR-FTUs huggingface dataset:
Peptide Nanocarriers for the Detection of Heavy Metal Ions Using Resistive Pulse Sensing.

The use of nanocarriers within resistive pulse sensing facilitates the detection and quantification of analytes. To date the field has been dominated by polyionic carriers or nanomaterials. Together they combine the recognition elements of a ligand with a stable support facilitating the sample handling, analysis times and multiplex detection. Here we develop the use of peptide functionalised superparamagnetic nanocarriers to extract and quantify metal ions in solution. The interaction between Nickel and the peptide ligand is measured as a change in translocation velocity of the carrier. The magnitude of change is proportional to the concentration of the metal ions in solution. Unlike DNA aptamers where a change in the tertiary structure and the folding of the polyanionic back bone influences the carrier velocity, the peptides here had a lower net charge under the assay conditions. To try and enhanced the signal, we engineered charged groups within the peptide to explore the effects on the signal. In all cases the metal ion binding dominated the velocity of the carrier. The assay was shown to work across three orders of magnitude and can detect Ni2+ in the presence of some other heavy metal ions. We demonstrate this by quantifying Ni2+ in both tap and pond water. The work allows for future multiplexed sensing strategies using both peptides and DNA aptamers in resistive pulse sensors.
scRNABatchQC: multi-samples quality control for single cell RNA-seq data

Abstract Summary Single cell RNA sequencing is a revolutionary technique to characterize inter-cellular transcriptomics heterogeneity. However, the data are noise-prone because gene expression is often driven by both technical artifacts and genuine biological variations. Proper disentanglement of these two effects is critical to prevent spurious results. While several tools exist to detect and remove low-quality cells in one single cell RNA-seq dataset, there is lack of approach to examining consistency between sample sets and detecting systematic biases, batch effects and outliers. We present scRNABatchQC, an R package to compare multiple sample sets simultaneously over numerous technical and biological features, which gives valuable hints to distinguish technical artifact from biological variations. scRNABatchQC helps identify and systematically characterize sources of variability in single cell transcriptome data. The examination of consistency across datasets allows visual detection of biases and outliers. Availability and implementation scRNABatchQC is freely available at https://github.com/liuqivandy/scRNABatchQC as an R package. Supplementary information Supplementary data are available at Bioinformatics online.
Antioxidant and Hepatoprotective Effects of Croton hypoleucus Extract in an Induced-Necrosis Model in Rats

The aim of this study was to evaluate the antioxidant and hepatoprotective activity of Croton hypoleucus (EC). The present work reports the first pharmacological, toxicological, and antioxidant studies of EC extract on liver injury. Liver necrosis was induced by thioacetamide (TAA). Five groups were established: Croton Extract (EC), thioacetamide (TAA), Croton extract with thioacetamide (EC + TAA), vitamin E with thioacetamide (VE + TAA) and the positive control and vehicle (CT). For EC and EC + TAA, Wistar rats (n = 8) were intragastrically pre-administered for 4 days with EC (300 mg/kg.day) and on the last day, EC + TAA received a single dose of TAA (400 mg/kg). At 24 h after damage induction, animals were sacrificed. In vitro activity and gene expression of superoxide dismutase (SOD), catalase (Cat), and Nrf2 nuclear factor were measured. The results show that EC has medium antioxidant properties, with an IC50 of 0.63 mg/mL and a ferric-reducing power of 279.8 µM/mg. Additionally, EC reduced hepatic damage markers at 24 h after TAA intoxication; also, it increased SOD and Cat gene expression against TAA by controlling antioxidant defense levels. Our findings demonstrated the hepatoprotective effect of EC by reducing hepatic damage markers and controlling antioxidant defense levels. Further studies are necessary to identify the mechanism of this protection.
A meta-analysis of memory ability in synaesthesia

ABSTRACT People with synaesthesia (e.g., experiencing colours for letters and numbers) have been reported to possess enhanced memory relative to the general population. However, there are also inconsistencies in this literature and it is unclear whether this reflects sampling error (exacerbated by low Ns) or more meaningful differences that arise because synaesthesia relates to some aspects of memory more than others. To this end, a multi-level meta-analysis was conducted. Synaesthetes have enhanced long-term (episodic) memory with a medium population effect size ( = 0.61), whereas the effects on working memory (short-term memory) were significantly smaller ( = 0.36) but still exceeded that of controls. Moderation analyses suggested that, aside from the division between long-term vs. working memory, the effects of synaesthesia are pervasive, i.e., they extend to all kinds of stimuli, and extend to all kinds of test formats. This pattern is hard to reconcile with the view that synaesthetic experiences directly support memory ability: for instance, digit span (where synaesthesia could be helpful) showed a small effect whereas episodic memory for abstract images (where synaesthesia is irrelevant) yielded larger effects. Synaesthesia occupies a unique position of being the only known neurodevelopmental condition linked to a pervasive enhancement of long-term memory.
The Global Prevalence of Anxiety Among Medical Students: A Meta-Analysis

Anxiety, although as common and arguably as debilitating as depression, has garnered less attention, and is often undetected and undertreated in the general population. Similarly, anxiety among medical students warrants greater attention due to its significant implications. We aimed to study the global prevalence of anxiety among medical students and the associated factors predisposing medical students to anxiety. In February 2019, we carried out a systematic search for cross-sectional studies that examined the prevalence of anxiety among medical students. We computed the aggregate prevalence and pooled odds ratio (OR) using the random-effects model and used meta-regression analyses to explore the sources of heterogeneity. We pooled and analyzed data from sixty-nine studies comprising 40,348 medical students. The global prevalence rate of anxiety among medical students was 33.8% (95% Confidence Interval: 29.2–38.7%). Anxiety was most prevalent among medical students from the Middle East and Asia. Subgroup analyses by gender and year of study found no statistically significant differences in the prevalence of anxiety. About one in three medical students globally have anxiety—a prevalence rate which is substantially higher than the general population. Administrators and leaders of medical schools should take the lead in destigmatizing mental illnesses and promoting help-seeking behaviors when students are stressed and anxious. Further research is needed to identify risk factors of anxiety unique to medical students.
Alcohol-induced microtubule acetylation leads to the accumulation of large, immobile lipid droplets.

Although steatosis (fatty liver) is a clinically well-described early stage of alcoholic liver disease, surprisingly little is known about how it promotes hepatotoxicity. We have shown that ethanol consumption leads to microtubule hyperacetylation that can explain ethanol-induced defects in protein trafficking. Because almost all steps of the lipid droplet life cycle are microtubule dependent and because microtubule acetylation promotes adipogenesis, we examined droplet dynamics in ethanol-treated cells. In WIF-B cells treated with ethanol and/or oleic acid (a fatty acid associated with the "Western" diet), we found that ethanol dramatically increased lipid droplet numbers and led to the formation of large, peripherally-located droplets. Enhanced droplet formation required alcohol dehydrogenase-mediated ethanol metabolism and peripheral droplet distributions required intact microtubules. We also determined that ethanol-induced microtubule acetylation led to impaired droplet degradation. Live cell imaging revealed that droplet motility was microtubule dependent and that droplets were virtually stationary in ethanol-treated cells. To determine more directly whether microtubule hyperacetylation can explain impaired droplet motility, we overexpressed the tubulin-specific acetyltransferase, aTAT1, to promote microtubule acetylation in the absence of alcohol. Droplet motility was impaired in aTAT1 expressing cells, but to a lesser extent than in ethanol-treated cells. However, in both cases, the large immotile droplets (but not small motile ones) colocalized with dynein and dynactin (but not kinesin) implying that altered droplet-motor-microtubule interactions may explain altered dynamics. These studies further suggest that modulating cellular acetylation is a potential strategy for treating alcoholic liver disease.
Serotonin receptor oligomerization regulates cAMP-based signaling

ABSTRACT Protein–protein interaction is often investigated using quantitative molecular microscopy with Förster resonant energy transfer (FRET). Here, we combined ‘linear unmixing FRET’ (lux-FRET) with the simultaneous application of a FRET-based biosensor for cAMP to investigate the oligomerization between the 5-HT7 receptor (5-HT7R, also known as HTR7) and the 5-HT1A receptor (5-HT1AR, also known as HTR1A) and its importance for cAMP signaling. We found that the 5-HT7R not only stimulates cAMP production, but also forms hetero-oligomers with 5-HT1AR, which blocks the inhibitory effect of the latter. 5-HT7R signaling, however, is not affected by this hetero-oligomerization. By modeling the kinetics of intracellular cAMP level changes in relation to the 5-HT7R:5-HT1AR stoichiometry, we were able to decipher the complex signaling characteristics of endogenous serotonin receptors in cultured hippocampal neurons. Our findings indicate that serotonergic signaling is not only modulated by the concentration of an individual receptor but also by its specific interaction with other receptors in endogenous systems. We conclude that the regulated ratio of serotonin receptors in immature and mature neurons may be critically involved in both the onset and response to treatments of psychiatric diseases, such as anxiety and depression. Highlighted Article: A FRET-based method is used to assess the impact of GPCR hetero-oligomerization on downstream signaling and contributes to the identification of the stoichiometry of endogenously expressed GPCRs under physiological conditions.
Complete Genome Sequence of Halophilic Deep-Sea Bacterium Halomonas axialensis Strain Althf1

Halomonas axialensis is a halophilic bacterial species discovered near a deep-sea hydrothermal vent. Here, we report the first single closed genome sequence of the original strain, Halomonas axialensis strain Althf1. The genome was assembled by Nanopore sequencing and consisted of a single chromosome of 3.6 Mbp with 56.8% G+C content. ABSTRACT Halomonas axialensis is a halophilic bacterial species discovered near a deep-sea hydrothermal vent. Here, we report the first single closed genome sequence of the original strain, Halomonas axialensis strain Althf1. The genome was assembled by Nanopore sequencing and consisted of a single chromosome of 3.6 Mbp with 56.8% G+C content.
DetNet Configuration YANG Model

This document defines a YANG data model for Deterministic Networking (DetNet), which includes the DetNet topology YANG module, DetNet flow configuration YANG module and DetNet Transport QoS YANG Module. The YANG modules in this document conform to the Network Management Datastore Architecture (NMDA).
Deficiency in SIRP‐α cytoplasmic recruitment confers protection from acute kidney injury

Acute kidney injury (AKI) remains an important source of progressive chronic kidney injury. Loss of renal blood flow with subsequent restoration, termed ischemia reperfusion (IR), is a common cause of AKI. The cell surface receptor signal regulatory protein α (SIRP‐α) is expressed on macrophages and limits inflammation and phagocytosis. SIRP‐α has recently been found to have wider cell‐based expression and play a role in renal IR. We have explored this in a genetic model of deficient SIRP‐α signaling. Mice lacking SIRP‐α cytoplasmic signaling (SIRP‐αmut) and wild‐type (WT) littermate controls underwent renal ischemia and reperfusion. Chimeric mice transplanted with WT or SIRP‐αmut bone marrow were similarly challenged following engraftment. Molecular and immunohistochemical analysis of renal function, tissue damage, and key molecular targets was performed. SIRP‐αmut mice were protected from renal IR compared with WT animals, demonstrating improved serum creatinine, less histologic damage, reduced proinflammatory cytokine production, and diminished production of reactive oxygen species (ROS). Resistance to renal IR in SIRP‐αmut occurred alongside down‐regulation of CD47 and thrombospondin‐1, which are known to exert SIRP‐α crosstalk and also promote IR. In chimeric mice, lack of SIRP‐α signaling conferred protection to IR regardless of the genotype of circulating cells. Renal tubular epithelial cells from SIRP‐αmut mice produced fewer ROS and proinflammatory cytokines in vitro. These results identify parenchymal SIRP‐α as an independent driver of IR‐mediated AKI and a potential therapeutic target. —Ghimire, K. , Chiba, T. , Minhas, N. , Meijles, D. N. , Lu, B. , O'Connell, P., Rogers, N. M. Deficiency in SIRP‐a cytoplasmic recruitment confers protection from acute kidney injury. FASEB J. 33, 11528–11540 (2019). www.fasebj. org
Design, modeling and optimization of hybridized automated manual transmission for electrified vehicles

This research systematically compares various electrified vehicles based upon electrification levels and powertrain configurations. A series of novel hybrid electric powertrain systems based on the newly proposed Hybridized Automated Manual Transmission (HAMT) concept are introduced. One representative hybrid powertrain system is selected to illustrate their operation principle. The new HAMT-based hybrid powertrain system overcomes the bottleneck problem of mainstream power-split hybrid systems with relatively low torque capacity and the constraint for utility vehicle electrification, and presents advantages over other hybrid powertrain systems in efficiency and costs. In addition, the new hybrid powertrain system can deliver continuous output torque by filling torque hole during gearshift, through coordinated control of engine, motor, and transmission, improving the driveability of regular Automated Manual Transmission (AMT), whose applications have been hampered by torque hole over the past years. The proposed HAMT-based hybrid systems with improved torque capacity, efficiency, costs, and driveability come with a compact design and more flexible operation through the amount of gearwheels equivalent to a 5-speed AMT to achieve 8 variable gear ratios for the Hybrid Electric Vehicle (HEV) mode and Electric Vehicle (EV) mode operations of a Plug-in Hybrid Electric Vehicle (PHEV). Model-based optimization, dynamics analysis, and powertrain control strategies have been introduced for a PHEV with a representative 8-speed HAMT. Vehicle simulations have been made to study and verify the capability and advantages of the new electrified powertrain system. Firstly, the operation principles of various HAMTs are discussed through detailed power flows at each gear. The fundamental principles of typical HAMT variations are explained using a new power-flow triangle with three ports. Based on the concept of Torque Gap Filler (TGF), a set of HAMT system designs have been introduced and closely studied to provide continuous and stable output torque. The selected hybrid powertrain system equipped with a representative HAMT system supports both HEV mode and EV mode with eight variable gear ratios for each mode. Among the eight forward gear ratios, six are independent and two are dependent on the
Identification of Prognostic Biomarkers and Drugs Targeting Them in Colon Adenocarcinoma: A Bioinformatic Analysis

Objective: To identify prognostic biomarkers and drugs that target them in colon adenocarcinoma (COAD) based on the Cancer Genome Atlas (TCGA) and Gene Expression Omnibus databases. Methods: The TCGA dataset was used to identify the top 50 upregulated differentially expressed genes (DEGs), and Gene Expression Omnibus profiles were used for validation. Survival analyses were conducted with the TCGA dataset using the RTCGAToolbox package in the R software environment. Drugs targeting the candidate prognostic biomarkers were searched in the DrugBank and herbal databases. Results: Among the top 50 upregulated DEGs in patients with COAD in the TCGA dataset, the Wnt signaling pathway and cytokine-cytokine receptor interactions and pathways in cancer Kyoto Encyclopedia of Genes and Genomes pathway analysis were enriched in DEGs. Tissue development and regulation of cell proliferation were the main Gene Ontology biological processes associated with upregulated DEGs. MYC and KLK6 were overexpressed in tumors validated in the TCGA, GSE41328, and GSE113513 databases (all P < .001) and were significantly associated with overall survival in patients with COAD (P = .021 and P = .047). Nadroparin and benzamidine were identified as inhibitors of MYC and KLK6 in DrugBank, and 8 herbs targeting MYC, including Da Huang (Radix Rhei Et Rhizome), Hu Zhang (Polygoni Cuspidati Rhizoma Et Radix), Huang Lian (Coptidis Rhizoma), Ban Xia (Arum Ternatum Thunb), Tu Fu Ling (Smilacis Glabrae Rhixoma), Lei Gong Teng (Tripterygii Radix), Er Cha (Catechu), and Guang Zao (Choerospondiatis Fructus), were identified. Conclusion: MYC and KLK6 may serve as candidate prognostic predictors and therapeutic targets in patients with COAD.
Automated Vulnerability Discovery and Exploitation in the Internet of Things †

Recently, automated software vulnerability detection and exploitation in Internet of Things (IoT) has attracted more and more attention, due to IoT’s fast adoption and high social impact. However, the task is challenging and the solutions are non-trivial: the existing methods have limited effectiveness at discovering vulnerabilities capable of compromising IoT systems. To address this, we propose an Automated Vulnerability Discovery and Exploitation framework with a Scheduling strategy, AutoDES that aims to improve the efficiency and effectiveness of vulnerability discovery and exploitation. In the vulnerability discovery stage, we use our Anti-Driller technique to mitigate the “path explosion” problem. This approach first generates a specific input proceeding from symbolic execution based on a Control Flow Graph (CFG). It then leverages a mutation-based fuzzer to find vulnerabilities while avoiding invalid mutations. In the vulnerability exploitation stage, we analyze the characteristics of vulnerabilities and then propose to generate exploits, via the use of several proposed attack techniques that can produce a shell based on the detected vulnerabilities. We also propose a genetic algorithm (GA)-based scheduling strategy (AutoS) that helps with assigning the computing resources dynamically and efficiently. The extensive experimental results on the RHG 2018 challenge dataset and the BCTF-RHG 2019 challenge dataset clearly demonstrate the effectiveness and efficiency of the proposed framework.
A lexical database for public textual cyberbullying detection

Public textual cyberbullying has become one of the most prevalent issues associated with online safety of young people, particularly on social networks. To address this issue, we argue that the boundaries of what constitutes public textual cyberbullying needs to be first identified and a corresponding linguistically motivated definition needs to be advanced. Thus, we propose a definition of public textual cyberbullying that contains three necessary and sufficient elements: the personal marker, the dysphemistic element and the cyberbullying link between the previous two elements. Subsequently, we argue that one of the cornerstones in the overall process of mitigating the effects of cyberbullying is the design of a cyberbullying lexical database that specifies what linguistic and cyberbullying specific information is relevant to the detection process. In this vein, we propose a novel cyberbullying lexical database based on the definition of public textual cyberbullying. The overall architecture of our cyberbullying lexical database is determined semantically, and, in order to facilitate cyberbullying detection, the lexical entry encapsulates two new semantic dimensions that are derived from our definition: cyberbullying function and cyberbullying referential domain. In addition, the lexical entry encapsulates other semantic and syntactic information, such as sense and syntactic category, information that, not only aids the process of detection, but also allows us to expand the cyberbullying database using WordNet (Miller, 1993).
Lymphovascular space invasion as a predictive factor for lymph node metastases and survival in endometrioid endometrial cancer – a Swedish Gynecologic Cancer Group (SweGCG) study

Abstract Background: The aim of this study is to evaluate the impact of lymphovascular space invasion (LVSI) on the risk of lymph node metastases and survival in endometrioid endometrial adenocarcinoma. Material and methods: As regard the study design, this is a cohort study based on prospectively recorded data. Patients with endometrioid endometrial adenocarcinoma registered in the Swedish Quality Registry for Gynecologic Cancer 2010–2017 with FIGO stages I–III and verified nodal status were identified (n = 1587). LVSI together with established risk factors, namely DNA ploidy, FIGO grade, myometrial invasion and age, were included in multivariable regression analyses with lymph node metastases as the dependent variable. Associations between the risk factors and overall and relative survival were included in multivariable models. Estimates of risk ratios (RR), hazard ratios (HR), excess mortality rate ratios (EMR), and 95% confidence intervals (95% CI) were calculated. Results: The presence of LVSI presented the strongest association with lymph node metastases (RR = 5.46, CI 3.69–8.07, p < .001) followed by deep myometrial invasion (RR = 1.64, CI 1.13–2.37). In the multivariable survival analyses, LVSI (EMR = 7.69, CI 2.03–29.10,) and non-diploidy (EMR = 3.23, CI 1.25–8.41) were associated with decreased relative survival. In sub-analyses including only patients with complete para-aortic and pelvic lymphadenectomy and negative lymph nodes (n = 404), only LVSI (HR = 2.50, CI 1.05–5.98) was associated with a worsened overall survival. Conclusion: This large nationwide study identified LVSI as the strongest independent risk factor for lymph node metastases and decreased survival in patients with endometrioid adenocarcinomas. Moreover, decreased overall survival was also seen in patients with LVSI-positive tumors and negative lymph nodes, indicating that hematogenous dissemination might also be important.