Miracle-dz/UniFAR-FTUs huggingface dataset:
PERFORMANCE AND BREEDING PARAMETERS FOR YIELD AND ITS ATTRIBUTES IN M 2 GENERATION OF THREE BREAD WHEAT CULTIVARS AS INFLUENCED BY GAMMA AND LASER RAY

: The present investigation was carried out at the Experimental Farm, Plant Research Department, Nuclear Research Center, Atomic Energy Authority, Inchas, Egypt during 2011/2012 and 2012/2013 seasons. Preliminary experiment was investigated to identify the proper dose radiation, seeds of the three cultivars (Sids 12, Sakha 94 and Gemmeiza 9) had been exposed to gamma irradiation doses of 0.0, 150, 200, 250, 300, 350, 400, 450 and 500 gray. Based on mean value of epicotyl length (cm), three gamma ray doses were selected i.e. , 250 (Gy 1 ), 300 (Gy 2 ) and 350 Gy (Gy 3 ) for both Sids 12 and Gemmeiza 9 cultivars as well as 350 (Gy 1 ), 400 (Gy 2 ) and 450 Gy (Gy 3 ) for Sakha 94 cultivar. LASER treatments were 1, 1.5 and 2 hr. , in addition to the control. The maximum values for both spike length and No. of fertile spikelets/spike were observed by Gemmeiza 9 which attained the lowest No. of sterile spikelets/spike (2.44). Furthermore, wheat cv. Sids 12 was the shortest height (75.19 cm) and gave the greatest No. of grains/spike (71.66) and the highest 1000-grain weight (41.27 g), while Gemmeiza 9 was the tallest (82.20 cm) and produced the greatest No. of spikes/plant (9.05) and grain yield/plant (14.79 g). Gamma irradiation dose (Gy 1 ) resulted in a decrease in plant height (79.75 cm) and No. of sterile spikelets/spike (2.40) rather than the control. Grain yield/plant, No. of spikes/plant and spike length recorded significant increase due to gamma ray treatments at the lowest dose (Gy 1 ) valued 14.42 g, 8.46 and 13.88 cm, respectively but both characters decreased with the highest dose (Gy 3 ). LASER exposure periods at 1 hr. , resulted in a significant increase in plant height and No. of fertile spikelets/spike, but significantly reduced No. of sterile spikelets/spike rather than 1.5 and 2 hr. Both 1.5 hr. , and 2 hr. , LASER exhibited significant increase in grain yield/plant valued 15.78 g and 15.57 g, respectively, rather than the control (13.67 g). Interaction of cultivar × mutagen treatments was significant for all studied wheat characters, except No. of fertile spikelets/ spike. Under gamma ray, GCV and PCV estimates were high for No. of spikes/plant only, with higher estimates of ECV for that character and grain yield/ plant. Whereas, it was relatively low for plant height, spike length, No. of fertile spikelets/spike and No. of sterile spikelets/spike. Heritability in broad sense was high (≥75%) for plant height, spike length, No. of sterile spikelets/spike, No. of spikes/plant, No. of grains/spike, and 1000-grain weight. Estimates of broad sense heritability coupled with genetic advance and were low for No. of fertile spikelets/spike and grain yield/plant. Estimates of GCV and PCV under LAZER ray were high for No. of grains/ spike, 1000-grain weight and grain yield/plant, whereas, it was low for plant height, spike length and No. of spikes/plant. These findings indicate the importance of previous results in wheat breeding programs for improving yield.
University of Birmingham Central 5-HT receptors and their function ; present and future

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GROWTH STIMULATION

The nucleoprotein fraction (NPF) from chick embryos that stimulates growth in tis sue culture has been fractionated by ultracentrifugation and electro convection. Various subfractions were obtained that were rich in nucleic acids or ri~h in lipids. When tested in tissue culturEl the various subfractions ex hibited essentially specific activities the same as or lower than the parent NPF. These data indicate that. the presence in the subfractions of nucleic. acid and lipid has no correlation with growth-stimulating activity, and consequently these substances are probably inert. The data indicate that the major con stituent of NPF- -namely, protein- -is probably the seat of biological activity of the NPF.
MafB Maintains β-Cell Identity under MafA-Deficient Conditions

The transcription factor MafB plays an essential role in β-cell differentiation during the embryonic stage in rodents. Although MafB disappears from β-cells after birth, it has been reported that MafB can be evoked in β-cells and is involved in insulin+ β-cell number and islet architecture maintenance in adult mice under diabetic conditions. ABSTRACT The transcription factor MafB plays an essential role in β-cell differentiation during the embryonic stage in rodents. Although MafB disappears from β-cells after birth, it has been reported that MafB can be evoked in β-cells and is involved in insulin+ β-cell number and islet architecture maintenance in adult mice under diabetic conditions. However, the underlying mechanism by which MafB protects β-cells remains unknown. To elucidate this, we performed RNA sequencing using an inducible diabetes model (A0BΔpanc mice) that we previously generated. We found that the deletion of Mafb can induce β-cell dedifferentiation, characterized by the upregulation of dedifferentiation markers, Slc5a10 and Cck, as well as several β-cell-disallowed genes, and by the downregulation of mature β-cell markers, Slc2a2 and Ucn3. However, there is no re-expression of well-known progenitor cell markers, Foxo1 and Neurog3. Further, the appearance of ALDH1A3+ cells and the disappearance of UCN3+ cells also verify the β-cell dedifferentiation state. Collectively, our results suggest that MafB can maintain β-cell identity under certain pathological conditions in adult mice, providing novel insight into the role of MafB in β-cell identity maintenance.
Subtyping Evaluation of Salmonella Enteritidis Using Single Nucleotide Polymorphism and Core Genome Multilocus Sequence Typing with Nanopore Reads

Evaluation, standardization, and implementation of the ONT approach to WGS-based, strain-level subtyping is challenging, in part due to its relatively high base-calling error rates and frequent iterations of sequencing chemistry and bioinformatic analytics. Our study established a baseline for the continuously evolving nanopore technology as a viable solution to high-quality subtyping of Salmonella, delivering comparable subtyping performance when used standalone or together with short-read platforms. ABSTRACT Whole-genome sequencing (WGS) for public health surveillance and epidemiological investigation of foodborne pathogens predominantly relies on sequencing platforms that generate short reads. Continuous improvement of long-read nanopore sequencing, such as Oxford nanopore technologies (ONT), presents a potential for leveraging multiple advantages of the technology in public health and food industry settings, including rapid turnaround and onsite applicability in addition to superior read length. Using an established cohort of Salmonella Enteritidis isolates for subtyping evaluation, we assessed the technical readiness of nanopore long read sequencing for single nucleotide polymorphism (SNP) analysis and core-genome multilocus sequence typing (cgMLST) of a major foodborne pathogen. By multiplexing three isolates per flow cell, we generated sufficient sequencing depths in <7 h of sequencing for robust subtyping. SNP calls by ONT and Illumina reads were highly concordant despite homopolymer errors in ONT reads (R9.4.1 chemistry). In silico correction of such errors allowed accurate allelic calling for cgMLST and allelic difference measurements to facilitate heuristic detection of outbreak isolates. IMPORTANCE Evaluation, standardization, and implementation of the ONT approach to WGS-based, strain-level subtyping is challenging, in part due to its relatively high base-calling error rates and frequent iterations of sequencing chemistry and bioinformatic analytics. Our study established a baseline for the continuously evolving nanopore technology as a viable solution to high-quality subtyping of Salmonella, delivering comparable subtyping performance when used standalone or together with short-read platforms. This study paves the way for evaluating and optimizing the logistics of implementing the ONT approach for foodborne pathogen surveillance in specific settings.
Burkholderia pseudomallei JW270 Is Lethal in the Madagascar Hissing Cockroach Infection Model and Can Be Utilized at Biosafety Level 2 to Identify Putative Virulence Factors

Burkholderia pseudomallei, the causative agent of melioidosis, is classified by the CDC as a tier 1 select agent, and work involving it must be performed in a biosafety level 3 (BSL-3) laboratory. Three BSL-2 surrogate strains derived from B. pseudomallei 1026b, a virulent clinical isolate, have been removed from the CDC select agent list. ABSTRACT Burkholderia pseudomallei, the causative agent of melioidosis, is classified by the CDC as a tier 1 select agent, and work involving it must be performed in a biosafety level 3 (BSL-3) laboratory. Three BSL-2 surrogate strains derived from B. pseudomallei 1026b, a virulent clinical isolate, have been removed from the CDC select agent list. These strains, Bp82, B0011, and JW270, are highly attenuated in rodent models of melioidosis and cannot be utilized to identify virulence determinants because of their high 50% lethal dose (LD50). We previously demonstrated that the Madagascar hissing cockroach (MHC) is a tractable surrogate host to study the innate immune response against Burkholderia. In this study, we found that JW270 maintains its virulence in MHCs. This surprising result indicates that it may be possible to identify potential virulence genes in JW270 by using MHCs at BSL-2. We tested this hypothesis by constructing JW270 mutations in genes that are required (hcp1) or dispensable (hcp2) for B. pseudomallei virulence in rodents. JW270 Δhcp1 was avirulent in MHCs and JW270 Δhcp2 was virulent, suggesting that MHCs can be used at BSL-2 for the discovery of important virulence factors. JW270 ΔBPSS2185, a strain harboring a mutation in a type IV pilin locus (TFP8) required for full virulence in BALB/c mice, was also found to be attenuated in MHCs. Finally, we demonstrate that the hmqA-G locus, which encodes the production of a family of secondary metabolites called 4-hydroxy-3-methyl-2-alkylquinolines, is important for JW270 virulence in MHCs and may represent a novel virulence determinant.
Mycoplasma pneumoniae Compared to Streptococcus pneumoniae Avoids Induction of Proinflammatory Epithelial Cell Responses despite Robustly Inducing TLR2 Signaling

Mycoplasma pneumoniae and Streptococcus pneumoniae are the most common bacterial causes of pneumonia in children. The clinical characteristics of pneumonia differ significantly between the two bacteria. We aimed to elucidate the differences in pathogenesis between M. pneumoniae and S. pneumoniae by characterizing the respiratory epithelial cell immune response to both pathogens. ABSTRACT Mycoplasma pneumoniae and Streptococcus pneumoniae are the most common bacterial causes of pneumonia in children. The clinical characteristics of pneumonia differ significantly between the two bacteria. We aimed to elucidate the differences in pathogenesis between M. pneumoniae and S. pneumoniae by characterizing the respiratory epithelial cell immune response to both pathogens. Using primary human bronchial epithelial cells in air-liquid interface cultures, we observed lower production of the proinflammatory cytokines interleukin-6 (IL-6) and IL-8 in response to M. pneumoniae than to S. pneumoniae. In contrast to the differences in proinflammatory cytokine production, Toll-like receptor 2 (TLR2)-mediated signaling in response to M. pneumoniae was stronger than to S. pneumoniae. This difference largely depended on TLR1 and not TLR6. We found that M. pneumoniae, but not S. pneumoniae, also induced signaling of TLR10, a coreceptor of TLR2 that has inhibitory properties. M. pneumoniae-induced TLR10 signaling on airway epithelial cells was partially responsible for low IL-8 production, as blocking TLR10 by specific antibodies increased cytokine production. M. pneumoniae maintained Th2-associated cytokine production by epithelial cells, which concurs with the known association of M. pneumoniae infection with asthma. M. pneumoniae left IL-33 levels unchanged, whereas S. pneumoniae downregulated IL-33 production both under homeostatic and Th2-promoting conditions. By directly comparing M. pneumoniae and S. pneumoniae, we demonstrate that M. pneumoniae avoids induction of proinflammatory cytokine response despite its ability to induce robust TLR2 signaling. Our new findings suggest that this apparent paradox may be partially explained by M. pneumoniae-induced signaling of TLR2/TLR10.
Estimation of Affective States in Virtual Reality Environments using EEG

Recent developments in accessible virtual reality (VR) technologies have inspired research into increasing the user’s sense of immersion via monitoring and feedback of physiological and cognitive states. This work presents a pilot study that models the user’s affective state from electroencephalographic (EEG) measurements during observation of immersive VR videos. Participants passively viewed a series of short VR video clips and subjectively rated the level of valence, arousal, liking, and dominance. Separate regression and classification models were developed to estimate the subjective ratings for each category using EEG spectral features. The results indicate that both models are capable of capturing relevant EEG features for estimating the user’s affective state ratings.
ENORASI Assistive Computer Vision-based System for the Visually Impaired: A User Evaluation Study

Visual impairment affects a significantly large number of individuals and in many cases it may disturb their daily life. This study presents a novel prototype wearable device which aims to assist them in tasks such as navigation within outdoor sites of cultural interest, while it may be used to enhance their experience. It presents an overview of the system architecture, which includes a wearable component, a cloud infrastructure, and a remote assistant service. The wearable components is a set of smart glasses, equipped with a stereoscopic camera, serving as a link between the cloud infrastructure and the remote assisting service of the system. User evaluation trials of the system have been performed, focusing on the obstacle detection capabilities of the system, and preliminary results are reported. The results provide initial evidence about the usability of the system, and indicate its potential as a future assistive technology for people with impairments.
In silico investigation of oxindole alkaloids from Uncaria perrottetii and Uncaria lanosa f. philippinensis for COVID-19 therapy: binding site prediction and molecular docking

On January 31, 2020, WHO declared the global outbreak of novel Coronavirus as a public health emergency of international concern. The biological origin of COVID-19 is caused by three primary pathophysiological conditions: immunosuppression, viral infection, and inflammation. In the Philippines, nine alkaloids with potential antiviral and anti-inflammatory effects have been isolated from two plants, Uncaria perrottetii and Uncaria lanosa f. philippinensis. The binding site of A2AR was proven to be pocket 0, which is similar to the literature. Two drug candidates showed the best result for molecular docking: mitraphylline and rauniticine-allo-oxindole A for A2AR and 3CLpro receptors. Mitraphylline candidate showed the lowest free energy scores and RMSD scores. This study is extended to other in silico tests to prove the impact of the alkaloid against COVID-19.
Identification of patients at risk of cardiac conduction diseases requiring a permanent pacemaker following TAVI procedure: a deep-learning approach on ECG signals

This research aims to investigate the feasibility in predicting, at several stages of the transcatheter aortic valve implantation (TAVI) procedure, the risk to develop cardiac conduction defects (CCD) requiring a permanent pacemaker installation. Adopting deep-learning techniques specifically designed for time series signals, 2197 electrocardiograms for 631 TAVI patients have been analyzed. The most important leads for the perioperative stages have been identified. The experimental results have shown that more information is available during- and in the post-procedure stages. The highest AUC results have been obtained on the following leads and stages: 0.635 (lead V1) at pre-procedure stage, 0.711 (lead III) at during-procedure stage and 0.721 (lead aVF) at post-procedure stage. Overall, the highest AUC result has been obtained for the post-procedure stage reaching an AUC of 0.740 for the lead V1. This study confirms that it is possible to identify and stratify even further, the risk for patients that will develop CCD after TAVI, by using the information available in the ECG data immediately following the procedure.
Alzheimer’s disease risk gene BIN1 modulates neural network activity through the 1 regulation of L-type calcium channel expression in human induced neurons 2

Bridging Integrator 1 (BIN1) is the second most important Alzheimer’s disease (AD) risk 28 gene after APOE, but its physiological roles and contribution to brain pathology are largely 29 elusive. In this work, we tackled the short- and long-term effects of BIN1 deletion in human 30 induced neurons (hiNs) grown in bi-dimensional cultures and in cerebral organoids. We 31 show that BIN1 loss-of-function leads to specific transcriptional alterations in glutamatergic 32 neurons involving mainly genes associated with calcium homeostasis, ion transport and 33 synapse function. We also show that BIN1 regulates calcium transients and neuronal 34 electrical activity through interaction with the L-type voltage-gated calcium channel Cav 1.2 35 and regulation of activity-dependent internalization of this channel. Treatment with the 36 Cav 1.2 antagonist nifedipine partly rescues neuronal electrical alterations in BIN1 knockout 37 hiNs. Together, our results indicate that BIN1 misexpression impairs calcium homeostasis in 38 glutamatergic neurons, potentially contributing to the transcriptional changes and neural 39 network dysfunctions observed in AD. 40 41 Ca 2+ signaling cascades and protect cells against aberrant Ca 2+ influx. We show that BIN1 interacts with Cav 1.2 in hiNs, similar to previous findings in cardiac tubules 32 and in mouse hippocampal neurons and provide evidence supporting a novel role for BIN1 in the regulation of activity-dependent internalization of Cav 1.2 in human neurons, thus linking BIN1 to firing homeostasis in human neurons through that LTVGCC.
Deciphering of BTH-induced response of tomato (Solanum lycopersicum L.) and its effect on plant virus infection through the multi-omics approach

One of the preventive methods used to limit the losses caused by viruses is the application of synthetic immunity inducers, such as benzo(1,2,3)-thiadiazole-7-carbothioic acid S-methyl ester (BTH). This study aimed to explain how the BTH treatment affects the defence and developmental processes in tomato plants (Solanum lycopersicum L.) as well as plant response to virus infection. The comparative multi-omics analyses of tomato plants treated with BTH were performed, including transcriptomics (RNA-seq), proteomics (Liquid Chromatography-Mass Spectrometry), and metabolomics (targeted hormonal analysis). To confirm the priming effect of BTH on tomato resistance, the plants were infected with tomato mosaic virus (ToMV) seven days post-BTH treatment. The combined functional analysis indicated the high impact of BTH on the plant’s developmental processes and activation of the immune response early after the treatment. In the presented experimental model, the increased level of WRKY TRANSCRIPTION FACTORS, ARGONAUTE 2A, thiamine and glutathione metabolism, cell wall reorganization, and detoxification processes, as well as accumulation of three phytohormones: abscisic acid, jasmonic-isoleucine (JA-Ile), and indole-3-carboxylic acid (I3CA), were observed upon BTH application. The immune response activated by BTH was related to increased expression of genes associated with the cellular detoxification process, systemic acquired resistance, and induced systemic resistance as well as post-transcriptional gene silencing. Increased levels of I3CA and JA-Ile might explain the BTH’s effectiveness in the induction of the plant defence against a broad spectrum of pathogens. For the first time, the BTH impact on the thiamine metabolism was revealed in tomatoes.
Development of genome-driven, lifestyle-informed primers for identification of the cereal-infecting pathogens Xanthomonas translucens pathovars undulosa and translucens

Bacterial leaf streak, blight and black chaff caused by Xanthomonas translucens pathovars are major diseases affecting small grains. Xanthomonas translucens pv. translucens and X. translucens pv. undulosa are seedborne pathogens that cause similar symptoms on barley, but only X. translucens pv. undulosa causes bacterial leaf streak of wheat. Recent outbreaks of X. translucens have been a concern for wheat and barley growers in the Northern Great Plains and Upper Midwest; however, there are limited diagnostic tools for pathovar differentiation. We developed a multiplex PCR based on whole-genome differences to distinguish X. translucens pv. translucens and X. translucens pv. undulosa. We validated the primers across different Xanthomonas and non-Xanthomonas strains. To our knowledge, these are the first multiplex PCR to distinguish X. translucens pv. translucens and X. translucens pv. undulosa. These molecular tools will support disease management strategies enabling detection and pathovar incidence analysis of X. translucens.
Transcriptional drifts associated with environmental changes in endothelial cells

Environmental cues, such as physical forces and heterotypic cell interactions play a critical role in cell function, yet their collective contributions to transcriptional changes are unclear. Focusing on human endothelial cells, we performed broad individual sample analysis to identify transcriptional drifts associated with environmental changes that were independent of genetic background. Global gene expression profiling by RNA-seq and protein expression by LC-MS directed proteomics distinguished endothelial cells in vivo from genetically matched culture (in vitro) samples. Over 43% of the transcriptome was significantly changed by the in vitro environment. Subjecting cultured cells to long-term shear stress significantly rescued the expression of approximately 17% of genes. Inclusion of heterotypic interations by co-culture of endothelial cells with smooth muscle cells normalized approximately 9% of the original in vivo signature. We identify novel flow depedent genes, as well as, genes that necessitate heterotypic cell interactions to mimic the in vivo transcriptome. Our findings highlight specific genes and pathways that rely on contextual information and physical forces.