Miracle-dz/UniFAR-FTUs huggingface dataset:
Genetic Diversity of C4 Photosynthesis Pathway Genes in Sorghum bicolor (L.)

C4 photosynthesis has evolved in over 60 different plant taxa and is an excellent example of convergent evolution. Plants using the C4 photosynthetic pathway have an efficiency advantage, particularly in hot and dry environments. They account for 23% of global primary production and include some of our most productive cereals. While previous genetic studies comparing phylogenetically related C3 and C4 species have elucidated the genetic diversity underpinning the C4 photosynthetic pathway, no previous studies have described the genetic diversity of the genes involved in this pathway within a C4 crop species. Enhanced understanding of the allelic diversity and selection signatures of genes in this pathway may present opportunities to improve photosynthetic efficiency, and ultimately yield, by exploiting natural variation. Here, we present the first genetic diversity survey of 8 known C4 gene families in an important C4 crop, Sorghum bicolor (L.) Moench, using sequence data of 48 genotypes covering wild and domesticated sorghum accessions. Average nucleotide diversity of C4 gene families varied more than 20-fold from the NADP-malate dehydrogenase (MDH) gene family (θπ = 0.2 × 10−3) to the pyruvate orthophosphate dikinase (PPDK) gene family (θπ = 5.21 × 10−3). Genetic diversity of C4 genes was reduced by 22.43% in cultivated sorghum compared to wild and weedy sorghum, indicating that the group of wild and weedy sorghum may constitute an untapped reservoir for alleles related to the C4 photosynthetic pathway. A SNP-level analysis identified purifying selection signals on C4 PPDK and carbonic anhydrase (CA) genes, and balancing selection signals on C4 PPDK-regulatory protein (RP) and phosphoenolpyruvate carboxylase (PEPC) genes. Allelic distribution of these C4 genes was consistent with selection signals detected. A better understanding of the genetic diversity of C4 pathway in sorghum paves the way for mining the natural allelic variation for the improvement of photosynthesis.
Intrinsic Regulatory Role of RNA Structural Arrangement in Alternative Splicing Control

Alternative splicing is a highly sophisticated process, playing a significant role in posttranscriptional gene expression and underlying the diversity and complexity of organisms. Its regulation is multilayered, including an intrinsic role of RNA structural arrangement which undergoes time- and tissue-specific alterations. In this review, we describe the principles of RNA structural arrangement and briefly decipher its cis- and trans-acting cellular modulators which serve as crucial determinants of biological functionality of the RNA structure. Subsequently, we engage in a discussion about the RNA structure-mediated mechanisms of alternative splicing regulation. On one hand, the impairment of formation of optimal RNA structures may have critical consequences for the splicing outcome and further contribute to understanding the pathomechanism of severe disorders. On the other hand, the structural aspects of RNA became significant features taken into consideration in the endeavor of finding potential therapeutic treatments. Both aspects have been addressed by us emphasizing the importance of ongoing studies in both fields.
Fine Particulate Matter and Gaseous Compounds in Kitchens and Outdoor Air of Different Dwellings

Passive diffusion tubes for volatile organic compounds (VOCs) and carbonyls and low volume particulate matter (PM2.5) samplers were used simultaneously in kitchens and outdoor air of four dwellings. PM2.5 filters were analysed for their carbonaceous content (organic and elemental carbon, OC and EC) by a thermo-optical technique and for polycyclic aromatic hydrocarbon (PAHs) and plasticisers by GC-MS. The morphology and chemical composition of selected PM2.5 samples were characterised by SEM-EDS. The mean indoor PM2.5 concentrations ranged from 14 µg m−3 to 30 µg m−3, while the outdoor levels varied from 18 µg m−3 to 30 µg m−3. Total carbon represented up to 40% of the PM2.5 mass. In general, the indoor OC/EC ratios were higher than the outdoor values. Indoor-to-outdoor ratios higher than 1 were observed for VOCs, carbonyls and plasticisers. PAH levels were much higher in the outdoor air. The particulate material was mainly composed of soot aggregates, fly ashes and mineral particles. The hazard quotients associated with VOC inhalation suggested a low probability of non-cancer effects, while the cancer risk was found to be low, but not negligible. Residential exposure to PAHs was dominated by benzo[a]pyrene and has shown to pose an insignificant cancer risk.
Effect of dietary addition of pharmacological drugs on the production performance and plasma lipid profile and egg cholesterol content of laying hens

Eighty, White Leghorn (WL) hens of 45 wks of age were fed with atorvastatin at 0.03%, niacin at 375 ppm and EDTA at 0.5% singly or in combination in this CRD experiment for 42 days. The body weight, egg production, egg weight, shell weight and shell thickness was not affected by drugs supplementation either singly or in combination. Feed intake was increased significantly (P<0.05) in atorvastatin, niacin and atorvastatin+niacin+EDTA supplemented groups (9.91, 9.21 and 9.41%, respectively) than control and atorvastatin + EDTA supplemented groups. But feed conversion ratio was significantly (56.68%) increased only in niacin supplemented group than the basal group.
Mycobacterium tuberculosis whole genome sequence data support repurposing antileprosy antibiotic as antituberculosis

Background We implanted WGS as the routine method to profile the antibiotic susceptibility of M. tuberculosis isolates focusing on in silico resistance to antileprosy drugs that we recently proposed to reposition for the treatment of pulmonary tuberculosis. Methods We prospectively performed WGS of 112 M. tuberculosis isolates recovered from respiratory tract samples of 106 patients diagnosed with pulmonary tuberculosis between 2017 and 2019 and defined their antibiotic susceptibility profile to 17 antibiotics including antileprotics drugs. Results We incidentally observed 08 sequence variations in 07 genes, specific to seven sublineages. Altogether, we observed 09 (8%) rifampicin-resistant, 05 (4.4%) multidrug-resistant and 02 (1.7%) extensively-drug resistant isolates; whereas only one isolate exhibited in silico resistance to clofazimine. Conclusion These results support repurposing of antileprosis antibiotics as antituberculosis; and offer new targets for genotyping M. tuberculosis.
The Microstructural and Ultrastruc-tural Study on Microsporogenesis of Cytoplasmic Male-sterile Cotton Line Jin A

This study was conducted on the male sterile cotton line Jin A in mo rphological characters.The results showed that: (1) The auxocyte abortion of Ji n A took place at the stage of sporogenous cell division. In most cases,the spor ogenous tissues collapsed and coalesced during the premiotic stage of developmen t,while occasionally a few microspore mother cells formed and meiosis progressed in some locules. However, these cells degenerated during the early stages of pr ophase Ⅰ. The collapse of the tapetum was responsible for the abortion of micros por mother cells. (2) The abnormal mitochondrium in microspore mother cells and tapetume cells had directly effects on abortion of MMCs.The abnormal characteris tics of mitochondrium are inflation and splitting of mitochondrium, melt and dis appearance of cristae.
How could the basal ganglia control sleep?

Disorders affecting basal ganglia function, such as Parkinson disease, are commonly associated with sleep disturbances, including insomnia. However, the involvement of the basal ganglia in sleep regulation and dysregulation has been largely unexplored. Components of the basal ganglia circuits, including the globus pallidus pars externa (GPe), may have a major role in sleep regulation. This has translational implications as these structures are potential targets of deep brain stimulation (DBS).
Self-management interventions to reduce healthcare use and improve quality of life among patients with asthma: systematic review and network meta-analysis

Abstract Objective To compare the different self-management models (multidisciplinary case management, regularly supported self-management, and minimally supported self-management) and self-monitoring models against usual care and education to determine which are most effective at reducing healthcare use and improving quality of life in asthma. Design Systematic review and network meta-analysis. Data sources Medline, the Cochrane Library, CINAHL, EconLit, Embase, Health Economics Evaluations Database, NHS Economic Evaluation Database, PsycINFO, and ClinicalTrials.gov from January 2000 to April 2019. Review methods Randomised controlled trials involving the different self-management models for asthma were included. The primary outcomes were healthcare use (hospital admission or emergency visit) and quality of life. Summary standardised mean differences (SMDs) and 95% credible intervals were estimated using bayesian network meta-analysis with random effects. Heterogeneity and publication bias were assessed. Results From 1178 citations, 105 trials comprising 27 767 participants were included. In terms of healthcare use, both multidisciplinary case management (SMD –0.18, 95% credible interval −0.32 to −0.05) and regularly supported self-management (–0.30, −0.46 to −0.15) were significantly better than usual care. For quality of life, only regularly supported self-management (SMD 0.54, 0.11 to 0.96) showed a statistically significant benefit compared with usual care. For trials including adolescents/children (age 5-18 years), only regularly supported self-management showed statistically significant benefits (healthcare use: SMD –0.21, −0.40 to −0.03; quality of life: 0.23, 0.03 to 0.48). Multidisciplinary case management (SMD –0.32, −0.50 to −0.16) and regularly supported self-management (–0.32, −0.53 to −0.11) were most effective at reducing healthcare use in patients with symptoms of severe asthma at baseline. Conclusions This network meta-analysis indicates that regularly supported self-management reduces the use of healthcare resources and improves quality of life across all levels of asthma severity. Future healthcare investments should provide support that offer reviews totalling at least two hours to establish self-management skills, reserving multidisciplinary case management for patients with complex disease. Systematic review registration PROSPERO number CRD42019121350.
Exploiting Dynamism in HPC Applications to Optimize Energy-Efficiency

The growing need for computational performance is resulting in an increase in the energy consumption of HPC systems, which is a major challenge to reach Exascale computing. To overcome this challenge, we developed a tuning plugin that targets applications that exhibit dynamically changing characteristics between iterations of the time loop as well as change in the control flow within the time loop itself. To analyze the inter-loop dynamism, we propose features to characterize the behaviour of loops for clustering via DBSCAN and spectral clustering. To save tuning time and costs, we implemented a random search strategy with a Gaussian probability distribution model to test a large number of system configurations in a single application run. The goal is to select the best configurations of the CPU and uncore frequencies for groups of similarly behaving loops, as well as individual instances of regions called within these loops based on their unique computational characteristics. During production runs, the configurations are dynamically switched for different code regions. The results of our experiments for two highly dynamic real-world applications highlight the effectiveness of our methodology in optimizing energy-efficiency.
Scheduling Task-parallel Applications in Dynamically Asymmetric Environments

Shared resource interference is observed by applications as dynamic performance asymmetry. Prior art has developed approaches to reduce the impact of performance asymmetry mainly at the operating system and architectural levels. In this work, we study how application-level scheduling techniques can leverage moldability (i.e. flexibility to work as either single-threaded or multithreaded task) and explicit knowledge on task criticality to handle scenarios in which system performance is not only unknown but also changing over time. Our proposed task scheduler dynamically learns the performance characteristics of the underlying platform and uses this knowledge to devise better schedules aware of dynamic performance asymmetry, hence reducing the impact of interference. Our evaluation shows that both criticality-aware scheduling and parallelism tuning are effective schemes to address interference in both shared and distributed memory applications.
Liquid Biopsy of Extracellular Vesicle-Derived miR-193a-5p in Colorectal Cancer and Discovery of Its Tumor-Suppressor Functions

Previously, abnormal extracellular vesicle (EV) sorting of miR-193a was identified in colorectal cancer (CRC) progression. Although a reduced level of miR-193a-5p in plasma/serum has been reported in many different types of cancer, the EV-derived miR-193a-5p level in CRC and its potential application as a minimally invasive biomarker are still unknown. Here, we evaluated the circulating EV-derived miR-193a-5p expression levels in a cohort of 101 participants by real-time quantitative polymerase chain reaction (RT-qPCR). We found that plasma EV-miR-193a-5p decreased significantly in CRC patients as compared with precancerous colorectal adenoma (CA) and non-cancerous control (NC) individuals. The circulating EV-miR-193a-5p showed an area under the receiver operating characteristic curve (AUC) of 0.740 in distinguishing CRC from CA and an AUC of 0.759 in distinguishing CRC from NC. Furthermore, the suppression on CRC cells of miR-193a-5p was verified by transwell, MTS (3-(4,5-dimethylthiazol-2-yl)-5-(3-carboxymethoxyphenyl)-2-(4-sulfophenyl)-2H-tetrazolium), EdU, RT-qPCR, and western blotting. Bioinformatic analysis predicted 32 genes, which were the most likely miR-193a-5p targeted and mainly focused on tumor progression. Among them, we revealed that miR-193a-5p could inhibit CRC migration and invasion via targeting tumor-associated genes like CUT-like homeobox 1 (CUX1) and intersectin 1 (ITSN1). In conclusion, miR-193a-5p could suppress CRC development, and decreased plasma EV-miR-193a-5p could be a promising biomarker for human CRC detection.
Comparison of Neck Injury Criteria Values Across Human Body Models of Varying Complexity

Due to the severity and frequency of cervical spine injuries, the neck injury criterion (Nij) was developed to provide a quantitative relationship between forces and moments of the upper neck with accompanied injury risk. The present study was undertaken to evaluate differences in calculated Nij for the Global Human Body Model Consortium’s detailed and simplified average 50th percentile male models. The simplified model is a computationally light version of the more detailed model and therefore it is of interest to achieve similar Nij values between the two models. These models were compared in 15 match paired conditions of rigid head impact and a mixture of seven full body rigid hub and sled pulses, for 44 total simulations. Collectively, Nij values of the simplified model were found to exhibit a second-degree polynomial fit, allowing for a conversion to the prediction of the detailed model. Correlates were also derived for impact and inertial loading cases individually, for which the latter may be the subject of future work. The differences in Nij may be attributed to a variety of modeling approach differences related to neck muscles (attachment location and morphometric implementation), localization of head mass within the M50-OS, head geometry, and intervertebral joint space properties. With a primary focus on configurations in the anterior-posterior direction, there is a potential limitation in extensibility to lateral loading cases. In response to the relatively low Nij values exhibited, future work should evaluate the appropriateness of the established critical intercepts of Nij for computational human body models.
Viral Transmission and Clinical Features in Asymptomatic Carriers of SARS-CoV-2 in Wuhan, China

We report the clinical characteristics, viral shedding duration, and contact tracing for asymptomatic carriers of SARS-CoV-2 in Wuhan, China. The asymptomatic carriers were relatively young (median age: 34.5 years). Chest computed tomography showed no abnormalities. The nasopharyngeal swab was an optimum specimen for RNA testing. The median viral shedding duration was 11.5 days. Notably, 2 months of viral shedding duration were reported in two nurses, which was much longer than previously reported or than usually thought. The transmissibility of SARS-CoV-2 by asymptomatic carriers during the studied period in Wuhan appeared to be weak. Only one patient (1/12) was found to have transmitted the virus to another person. Early asymptomatic carrier detection, isolation, and contact tracing could be useful to mitigate the spread of the disease.
Consequences of CRISPR-Cas9-Mediated CFTR Knockout in Human Macrophages

Macrophage dysfunction is fundamentally related to altered immunity in cystic fibrosis (CF). How genetic deficits in the cystic fibrosis transmembrane conductance regulator (CFTR) lead to these defects remains unknown. Rapid advances in genomic editing such as the clustered regularly interspaced short palindromic repeats associated protein 9 (CRISPR/Cas9) system provide new tools for scientific study. We aimed to create a stable CFTR knockout (KO) in human macrophages in order to study how CFTR regulates macrophage function. Peripheral blood monocytes were isolated from non-CF healthy volunteers and differentiated into monocyte-derived macrophages (MDMs). MDMs were transfected with a CRISPR Cas9 CFTR KO plasmid. CFTR KO efficiency was verified and macrophage halide efflux, phagocytosis, oxidative burst, apoptosis, and cytokine functional assays were performed. CFTR KO in human MDMs was efficient and stable after puromycin selection. CFTR KO was confirmed by CFTR mRNA and protein expression. CFTR function was abolished in CFTR KO MDMs. CFTR KO recapitulated known defects in human CF MDM (CFTR class I/II variants) dysfunction including (1) increased apoptosis, (2) decreased phagocytosis, (3) reduced oxidative burst, and (4) increased bacterial load. Activation of the oxidative burst via nicotinamide adenine dinucleotide phosphate (NADPH) oxidase assembly was diminished in CFTR KO MDMs (decreased phosphorylated p47phox). Cytokine production was unchanged or decreased in response to infection in CFTR KO MDMs. In conclusion, we developed a primary human macrophage CFTR KO system. CFTR KO mimics most pathology observed in macrophages obtained from persons with CF, which suggests that many aspects of CF macrophage dysfunction are CFTR-dependent and not just reflective of the CF inflammatory milieu.
Effect of Trichoderma reesei Degraded Date Pits on Antioxidant Enzyme Activities and Biochemical Responses of Broiler Chickens

The long-term use of antimicrobials as growth promoters in poultry feed leads to antimicrobial resistance in pathogens. Thus, alternatives to antibiotics are essential for reasons associated with both safety and cost-effectiveness. Underutilized plant sources need to be developed to replace antibiotics in broiler feed. Several feed resources have been introduced so far, but they have yet to be applied widely. Date pits are a major by-product of the date industry (6–8%) and have the potential antioxidant to replace antibiotics. In this study, fresh date pits were degraded using the mold Trichoderma reesei under solid-state degradation (SSD), resulting in degraded date pits (DDP). A total of 180 Brazilian “Cobb 500” broiler chicks were divided into six feed treatments in triplicate groups. The treatments were corn-soy basal diet (positive control; C+), corn-soy + 20% oxytetracycline at 0.05% (negative control; C–), corn-soy + 10% DDP, corn-soy + 0.2% mannan-oligosaccharides (MOS), corn-soy + 0.1% mannose, and corn-soy + 0.2% mannose. The antioxidant and biochemical effects of DDP, MOS, and mannose were determined in the blood serum, liver, and intestine of broilers at age 21 and 42 days. The results indicated that the contents of antioxidants such as flavonoids and phenolics, as well as the MOS content in DDP, were increased by the degradation process. Additionally, mannose, glucose, arabinose, rhamnose, and glucuronic acid were significantly increased in DDP after degradation. The activity of antioxidant enzymes (GPx—glutathione peroxidase, catalase, and SOD—superoxide dismutase) in the serum, liver, and intestine of broilers fed with diets containing 10% DDP and 0.2% MOS was increased significantly compared to the control group. Malondialdehyde activity was decreased, whereas the mean corpuscular hemoglobin level and the iron content were significantly upregulated in the broilers fed with 10% DDP, 0.1% mannose, and 0.2% MOS diets compared with the control. Thus, DDP can be used to improve the antioxidant status and has a prebiotic-like effect in broiler chicken performance.
Functional Electrical Stimulation and the Modulation of the Axon Regeneration Program

Neural injury in mammals often leads to persistent functional deficits as spontaneous repair in the peripheral nervous system (PNS) is often incomplete, while endogenous repair mechanisms in the central nervous system (CNS) are negligible. Peripheral axotomy elicits growth-associated gene programs in sensory and motor neurons that can support reinnervation of peripheral targets given sufficient levels of debris clearance and proximity to nerve targets. In contrast, while damaged CNS circuitry can undergo a limited amount of sprouting and reorganization, this innate plasticity does not re-establish the original connectivity. The utility of novel CNS circuitry will depend on effective connectivity and appropriate training to strengthen these circuits. One method of enhancing novel circuit connectivity is through the use of electrical stimulation, which supports axon growth in both central and peripheral neurons. This review will focus on the effects of CNS and PNS electrical stimulation in activating axon growth-associated gene programs and supporting the recovery of motor and sensory circuits. Electrical stimulation-mediated neuroplasticity represents a therapeutically viable approach to support neural repair and recovery. Development of appropriate clinical strategies employing electrical stimulation will depend upon determining the underlying mechanisms of activity-dependent axon regeneration and the heterogeneity of neuronal subtype responses to stimulation.