Miracle-dz/UniFAR-FTUs huggingface dataset:
Endophytic bacterial strain, Brevibacillus brevis-mediated green synthesis of copper oxide nanoparticles, characterization, antifungal, in vitro cytotoxicity, and larvicidal activity

Abstract The biomass filtrate containing various metabolites of endophytic bacterial strain, Brevibacillus brevis PI-5 was used as a biocatalyst for reducing and stabilizing copper oxide nanoparticles (CuO-NPs). UV-Vis spectroscopy, Fourier transform infrared, transmission electron microscopy, scanning electron microscopy with energy-dispersive X-ray (SEM-EDX), X-ray diffraction, and X-ray photoelectron spectroscopy were used for CuO-NPs characterization. A spherical, well-dispersed, and crystallographic structure with sizes of 2–28 nm was formed. The SEM-EDX confirmed the presence of Cu and O with weight percentages of 27.62% and 48.88%, respectively. The biological activities including antifungal, anticancer, and larvicidal of synthesized CuO-NPs were assessed using the fungal radial growth inhibition, MTT assay method, and mortality percentages, respectively. The obtained data showed that the CuO-NPs exhibit high activity in a dose-dependent manner. The growth of three phytopathogenic fungi, Fusarium oxysporum, Alternaria alternata, and Aspergillus niger was decreased by percentages of 64.5% ± 4.1%, 62.9% ± 0.3%, and 70.2% ± 2.3%, respectively at 300 µg·mL–1. Also, various clinical Candida spp. were successfully inhibited with varied zones of inhibition and minimum inhibitory concentration values in ranges of 6.25–50 µg·mL–1. The in vitro cytotoxicity exhibits target-orientation to breast cancer cells (T47D) at low concentration compared to normal cells (HFB4) with IC50 values of 122.3 ± 5.4 and 229.9 ± 5.7 μg·mL–1, respectively. The mortality percentages of I, II, III, and IV instar larvae of Culex antennatus were 60% ± 1.4%, 43.1% ± 1.1%, 36.2% ± 1%, and 32.1% ± 0.9%, at 10 mg·L–1 and increased to 86.9% ± 2.1%, 68.1% ± 1.7%, 64.4% ± 1.9%, and 53.1% ± 1.4% at 50 mg·L–1, respectively.
Meshed tree routing in folded-clos topologies

Data Center Networks (DCNs) are the backbone of data centers. Folded-Clos topologies are used in data centers networks due to the high redundancy and scalability they offer. Capacity challenges and advanced applications are placing increased demands on DCNs. While there have been a number of major studies focused on improving hardware and topology design for DCNs, fewer efforts have been directed towards investigating new algorithms and protocols to work efficiently on the highly connected and symmetrical topologies adopted in DCNs. Instead, we notice the integration of off-the-shelf protocols that are then retrofitted to the DCN communication needs. This increases the operational complexity in DCNs. In this article, we investigate a new Meshed Tree protocol (MTP) based off a novel Meshed Tree algorithm (MTA) to perform control and data plane operations in folded-Clos DCNs. We present implementation details of MTP, tested using the Global Environment for Network Innovation (GENI) testbed, and highlight features such as redundant route establishment and load balancing.
Research on simulation test method of CAN bus direct connection

The test method of CAN bus is studied systematically, and the test problem of CAN bus in vehicle electronic system is solved. Aiming at the problem that there is no comprehensive test method for bus performance at present, the advantages and disadvantages of the existing three methods are compared and analyzed, and a direct connection simulation test method is proposed to comprehensively test CAN bus network performance and single ECU performance. The analysis results show that this method CAN not only test the network performance of CAN bus, but also test and analyze the performance of a single ECU node, which solves the test problem of CAN bus in vehicle electronic system.
Development of TRL5 firmware for tuning, biasing, and readout of kilopixel TES bolometer arrays

The next generation of space-based mm-wave telescopes, such as JAXA’s LiteBIRD mission, require focal planes with thousands of detectors in order to achieve their science goals. Digital frequency-domain multiplexing (dfmux) techniques allow detector counts to scale without a linear growth in wire harnessing, sub-Kelvin refrigerator loads, and other scaling problems. In this paper, we describe the Digital Signal Processing (DSP) firmware executed in the design’s Field-Programmable Gate Arrays (FPGAs). This firmware is responsible for synthesizing bias tones, performing dynamic feedback control of the bolometer voltage bias and/or Superconducting Quantum Interference Device (SQUID) nuller currents, demodulating and decimating bolometer channels into science data, and streaming the results for storage and eventual downlink. We describe how this firmware has been tailored for LiteBIRD, including the control path, improvements to power- and resource-efficiency, the addition of radiation-mitigation functions, and the integration of new bolometer biasing schemes that may help mitigate mission-specific design challenges. This paper is a companion piece to the description of the electronics platform in which the firmware operates.
Multi-objective optimization of underwater towed system during course-keeping motion

In this paper, the underwater towed system during the course-keeping motion was taken as the research object, in addition, the governing equation of motion was given as well. By the means of the experimental data obtained by the design of experiment, the second-order polynomial response surface models reflecting the steady-state motion characteristics of the towrope were established. Apart from mentioned above, the tail drag depth and the head tension were taken as objective functions, and the optimal solution set of Pareto was obtained by using the multi-objective optimization algorithm. The results shown that the approximate models were used to optimize the towrope when the parameters of the towrope were within a certain range, which can quickly and accurately analyzed the influences of each parameter on the steady-state motion characteristics of the towrope.
Research on the emissions of China Ⅵ light-duty vehicle under different altitude

In order to study the effect of different altitudes on vehicle emissions, two China Ⅵ light-duty gasoline and diesel vehicles are selected to carry out pollution emission tests at different altitudes in the altitude environment simulation chamber. The result show that with the increase of altitude, CO, HC and PM emissions show an upward trend, and NOx emissions show a fluctuating downward trend.
A hierarchy of cell death pathways confers layered resistance to shigellosis in mice

Bacteria of the genus Shigella cause shigellosis, a severe gastrointestinal disease driven by bacterial colonization of colonic intestinal epithelial cells. Vertebrates have evolved programmed cell death pathways that sense invasive enteric pathogens and eliminate their intracellular niche. Previously we reported that genetic removal of one such pathway, the NAIP–NLRC4 inflammasome, is sufficient to convert mice from resistant to susceptible to oral Shigella flexneri challenge (Mitchell, Roncaioli et al., 2020). Here, we investigate the protective role of additional cell death pathways during oral mouse Shigella infection. We find that the Caspase-11 inflammasome, which senses Shigella LPS, restricts Shigella colonization of the intestinal epithelium in the absence of NAIP–NLRC4. However, this protection is limited when Shigella expresses OspC3, an effector that antagonizes Caspase-11 activity. TNFα, a cytokine that activates Caspase-8-dependent apoptosis, also provides protection from Shigella colonization of the intestinal epithelium, but only in the absence of both NAIP– NLRC4 and Caspase-11. The combined genetic removal of Caspases-1,-11, and -8 renders mice hyper-susceptible to oral Shigella infection. Our findings uncover a layered hierarchy of cell death pathways that limit the ability of an invasive gastrointestinal pathogen to cause disease.
Cis-regulatory variation in relation to sex and sexual dimorphism in Drosophila melanogaster

Much of sexual dimorphism is likely due to sex-biased gene expression, which results from differential regulation of a genome that is largely shared between males and females. Here we use allele-specific expression to explore cis-regulatory variation in Drosophila melanogaster in relation to sex. We develop a Bayesian framework to infer the transcriptome-wide joint distribution of cis-regulatory effects across the sexes. We use this approach to quantify transcriptome-wide sex differences in cis-regulatory effects as well as examine patterns of cis-regulatory variation with respect to two other levels of variation in sexual dimorphism: (i) across genes varying in their degree of sex-biased expression, and (ii) among tissues that vary in their degree of dimorphism (e.g., relatively low dimorphism in heads vs high dimorphism in gonads). We uncover evidence of widespread cis-regulatory variation in all tissues examined, with female-biased genes being especially enriched for this variation. A sizeable proportion of cis-regulatory variation is inferred to have sex-specific effects, with sex-dependent cis effects being much more frequent in gonads than in heads. Finally, we detect some genes with reversed allelic imbalance between the sexes. Such variants could provide a mechanism for sex-specific dominance reversals, a phenomenon important for sexually antagonistic balancing selection.
Metamorphic proteins at the basis of human autophagy initiation and lipid transfer

Autophagy is a conserved intracellular degradation pathway that uses de novo doublemembrane vesicle (autophagosome) formation to target a wide range of cytoplasmic material for lysosomal degradation. In multicellular organisms, autophagy initiation requires the timely assembly of a contact site between the ER and the nascent autophagosome. Here, we report the in vitro reconstitution of a full-length sevensubunit human autophagy initiation supercomplex and found at its core ATG13-101 and transmembrane protein ATG9. Assembly of this core complex requires the rare ability of ATG13 and ATG101 to adopt topologically distinct folds. The slow spontaneous conversion between folds creates a rate-limiting step to regulate selfassembly of the super-complex. The interaction of the core complex with ATG2-WIPI4 enhances tethering of membrane vesicles and accelerates lipid transfer of ATG2 by both ATG9 and ATG13-101. Our work uncovers the molecular basis of the contact site and its assembly mechanisms imposed by the metamorphosis of ATG13-101 to regulate autophagosome biogenesis in space and time.
Self-organized Critical Model Based on Complex Brain Networks with Hierarchical Organization

The dynamical behavior in the cortical brain network of macaque is studied by modelling each cortical area with a subnetwork of interacting excitable neurons. We find that the avalanche of our model on different levels exhibits power-law. Furthermore the power-law exponent of the distribution and the average avalanche size are affected by the topology of the network.
Structural characterization of human tryptophan hydroxylase 2 reveals L-Phe as the superior regulatory domain ligand relevant for serotonin biosynthesis

Tryptophan hydroxylase 2 (TPH2) catalyzes the rate-limiting step in the biosynthesis of serotonin in the brain. Consequently, regulation of TPH2 is relevant for serotonin related diseases, yet, the regulatory mechanism of TPH2 is poorly understood and structural as well as dynamical insights are missing. Here, we use NMR spectroscopy to determine the structure of a 47 N-terminally truncated variant of the regulatory domain (RD) dimer of human TPH2 in complex with L-Phe, and show that L-Phe is the superior RD ligand compared to the natural substrate, L-Trp. Using cryo-EM we obtain a low-resolution structure of a similarly truncated variant of the complete tetrameric enzyme with dimerized RDs. The cryo-EM 2D class averages additionally indicate that the RDs are dynamic in the tetramer and likely exist in a monomer-dimer equilibrium. Our results provide structural information on the RD both as an isolated domain and in the TPH2 tetramer, which will facilitate future elucidation of TPH2’s regulatory mechanism affecting serotonin regulation.
Functionally conserved Pkd2, mutated in autosomal dominant polycystic kidney disease, localizes to the endoplasmic reticulum and regulates cytoplasmic calcium homeostasis in fission yeast

Mutations in PKD1 or PKD2 genes lead to autosomal dominant polycystic kidney disease (ADPKD) that is the most frequent family inherited renal disorder. These genes encode polycystin-1/PC-1 and polycycstin-2/PC-2, respectively. Although the genetic basis of ADPKD is well established, the crucial functions of polycystins underlying onset and development of cyst formation remain elusive. Fission yeast Schizosaccharomyces pombe has a single polycystin homolog, Pkd2, which is essential for cell growth. In this study, the truncation analyses of Pkd2 reveal that Pkd2 localizes to not only the plasma membrane but also the endoplasmic reticulum (ER) and regulates cytoplasmic calcium signaling in fission yeast. Internal transmembrane domains within Pkd2 are sufficient for these processes. Surprisingly, more than half of Pkd2 is not required for cell viability. Cytoplasmic calcium levels are mainly regulated through C-terminus of Pkd2. Importantly, human Pkd2 also localizes to the ER and furthermore, fully complements the loss of fission yeast Pkd2. As the functions of polycystin-2 are conserved, fission yeast provides a suitable model to study the mechanism of ADPKD as well as polycystins.
Transcriptomic profiling revealed the role of 24-epibrassinolide in alleviating salt stress damage in tall fescue (Festuca arundinacea)

Soil salinization is a major problem all over the world. The accumulation of salt in soil reduces the root water uptake and directly affects plant growth and metabolic activities. Brassinosteroid is a plant hormone that plays an important role in regulation of plant growth and physiological process, including promotion of cell expansion and elongation, signal transduction and stress response. Exogenous 24-epibrassinolide (EBL) has been proved to alleviate various environmental stress in plants. However, the role that EBL plays in salt stress response is still unknown in tall fescue (Festuca arundinacea). In this study, the physiology and molecular mechanisms regulated by exogenous EBL of salt stress response in tall fescue was investigated. Tall fescue plants were divided into four groups, including control (CK), NaCl solution (SALT), 24-epibrassinolide (EBL), NaCl solution + 24-epibrassinolide (SE). During the growth period of tall fescue, we found that electrolyte leakage (EL) and malondialdehyde (MDA) were decreased, chlorophyll (Chl) content and antioxidant enzyme activity were increased in leaves of tall fescue in SE group compared with SALT group, indicating that EBL improved the salt tolerance in grasses. Transcriptomic profiling analysis showed that after 12 h of treatments, 10,265, 13,830 and 10,537 differential genes were expressed in EBL, SALT, and SE groups compared with control, respectively. These differentially expressed genes (DEGs) mainly focused on binding, catalytic activity, cellular process, metabolic process, cellular anatomical entity. Moreover, most of the differential genes were expressed in the plant hormone signal transduction pathway. These results helped us to better understand the mechanism of exogenous 24-epibrassinolide to improve the salt tolerance of tall fescue.
The grand challenge of discovering new cardiovascular drugs

Heart disease is the #1 killer worldwide, greater than all cancers combined. This is despite the fact that, in the developed world, there has been a substantial decline in cardiovascular mortality since the mid-20th century (Centers for Disease Control and Prevention (CDC), 1999), driven largely by a reduction in ischemic heart disease (Mensah et al., 2017; Nowbar et al., 2019). This decline is multifactorial, involving a reduction in tobacco use, changes in diet, treatment of hypertension, advances in rapid coronary revascularization, and the advent of β-hydroxy β-methylglutaryl-CoA (HMG-CoA) reductase inhibitors, and P2Y12 ADP receptor antagonists (Arnett et al., 2019). However, with the adoption of the Western diet and lifestyle in the developing world, and the rise in prevalence of cardiometabolic diseases and obesity, there has been an increase in the global burden of cardiovascular diseases (CVD) (Roth et al., 2020) and a stalling of improvements in the United States (Sinatra and Huston, 2020).
Detection of pediatric drug-induced kidney injury signals using a hospital electronic medical record database

Background: Drug-induced kidney injury (DIKI) is one of the most common complications in clinical practice. Detection signals through post-marketing approaches are of great value in preventing DIKI in pediatric patients. This study aimed to propose a quantitative algorithm to detect DIKI signals in children using an electronic health record (EHR) database. Methods: In this study, 12 years of medical data collected from a constructed data warehouse were analyzed, which contained 575,965 records of inpatients from 1 January 2009 to 31 December 2020. Eligible participants included inpatients aged 28 days to 18 years old. A two-stage procedure was adopted to detect DIKI signals: 1) stage 1: the suspected drugs potentially associated with DIKI were screened by calculating the crude incidence of DIKI events; and 2) stage 2: the associations between suspected drugs and DIKI were identified in the propensity score-matched retrospective cohorts. Unconditional logistic regression was used to analyze the difference in the incidence of DIKI events and to estimate the odds ratio (OR) and 95% confidence interval (CI). Potentially new signals were distinguished from already known associations concerning DIKI by manually reviewing the published literature and drug instructions. Results: Nine suspected drugs were initially screened from a total of 652 drugs. Six drugs, including diazepam (OR = 1.61, 95%CI: 1.43–1.80), omeprazole (OR = 1.35, 95%CI: 1.17–1.54), ondansetron (OR = 1.49, 95%CI: 1.36–1.63), methotrexate (OR = 1.36, 95%CI: 1.25–1.47), creatine phosphate sodium (OR = 1.13, 95%CI: 1.05–1.22), and cytarabine (OR = 1.17, 95%CI: 1.06–1.28), were demonstrated to be associated with DIKI as positive signals. The remaining three drugs, including vitamin K1 (OR = 1.06, 95%CI: 0.89–1.27), cefamandole (OR = 1.07, 95%CI: 0.94–1.21), and ibuprofen (OR = 1.01, 95%CI: 0.94–1.09), were found not to be associated with DIKI. Of these, creatine phosphate sodium was considered to be a possible new DIKI signal as it had not been reported in both adults and children previously. Moreover, three other drugs, namely, diazepam, omeprazole, and ondansetron, were shown to be new potential signals in pediatrics. Conclusion: A two-step quantitative procedure to actively explore DIKI signals using real-world data (RWD) was developed. Our findings highlight the potential of EHRs to complement traditional spontaneous reporting systems (SRS) for drug safety signal detection in a pediatric setting.
Exosomes in the f ield of reproduction: A scientometric study and visualization analysis

Background: The diagnostic capabilities of exosomes in the field of reproductive biomedicine have attracted much attention. The aim of this scientometric study was to statistically and qualitatively assess the knowledge structure, hot issues, and research trends of papers about exosomes in the field of reproduction using visualization methods. Methods: The Web of Science Core Collection was searched for studies on exosomes in the field of reproduction. We performed bibliometric and visual analyses using VOSviewer, CiteSpace, and Microsoft Excel. Results: After database search, 1,011 articles were included, with number of studies being published every year continually increasing. These publications came from 61 nations or regions, with the US having the highest number. The University of Queensland was the main institution in which the research was conducted. The journal Placenta contained the highest number studies. There were 5,247 authors in total. Carlos Salomon had the highest number of papers with co-citations. Exosomes, extracellular vesicles, pregnancy, microRNAs, preeclampsia, placenta, microvesicles, gene expression, biomarkers, and first trimester were the most frequently used terms. Conclusion: Exosome research is booming in reproductive biomedicine. Future studies will likely focus on exosomes as biomarkers in gamete formation and fertilization, pregnancy, and cancers associated with reproduction. In addition to focusing on fundamental research, we should concentrate on the application of the results and the investigation of exosomes in infertile patients.
Assessment of Canadian perinatal mental health services from the provider perspective: Where can we improve?

Purpose Perinatal mental health disorders are common, and rates have increased during the COVID-19 pandemic. It is unclear where providers may improve perinatal mental health care, particularly in countries lacking national guidelines, such as Canada. Methods A cross-sectional survey of perinatal health providers was conducted to describe the landscape of perinatal mental health knowledge, screening, and treatment practices across Canada. Providers were recruited through listservs, social media, and snowball sampling. Participants completed an online survey that assessed their perinatal mental health training, service provision types, their patient wait times, and treatment barriers, and COVID-19 pandemic-related impacts. Results A total of 435 providers completed the survey, including physicians, midwives, psychologists, social workers, nurses, and allied non-mental health professionals. Most (87.0%) did not have workplace mandated screening for perinatal mental illness but a third (66%) use a validated screening tool. Many (42%) providers stated their patients needed to wait more than 2 months for services. More than half (57.3%) reported they did not receive or were unsure if they received specialized training in perinatal mental health. Most (87.0%) indicated there were cultural, linguistic, and financial barriers to accessing services. Over two-thirds (69.0%) reported the COVID-19 pandemic reduced access to services. Conclusion Survey findings reveal significant gaps in training, screening tool use, and timely and culturally safe treatment of perinatal mental health concerns. There is critical need for coordinated and nationally mandated perinatal mental health services in Canada to improve care for pregnant and postpartum people.
Functional characterization of a new ORF βV1 encoded by radish leaf curl betasatellite

Whitefly-transmitted begomoviruses infect and damage a wide range of food, feed, and fiber crops worldwide. Some of these viruses are associated with betasatellite molecules that are known to enhance viral pathogenesis. In this study, we investigated the function of a novel βV1 protein encoded by radish leaf curl betasatellite (RaLCB) by overexpressing the protein using potato virus X (PVX)-based virus vector in Nicotiana benthamiana. βV1 protein induced lesions on leaves, suggestive of hypersensitive response (HR), indicating cell death. The HR reaction induced by βV1 protein was accompanied by an increased accumulation of reactive oxygen species (ROS), free radicals, and HR-related transcripts. Subcellular localization through confocal microscopy revealed that βV1 protein localizes to the cellular periphery. βV1 was also found to interact with replication enhancer protein (AC3) of helper virus in the nucleus. The current findings suggest that βV1 functions as a protein elicitor and a pathogenicity determinant.