Miracle-dz/UniFAR-FTUs huggingface dataset:
SOLAR-WIND ION-DRIVEN X-RAY EMISSION FROM COMETARY AND PLANETARY ATMOSPHERES: MEASUREMENTS AND THEORETICAL PREDICTIONS OF CHARGE-EXCHANGE CROSS-SECTIONS AND EMISSION SPECTRA FOR O6+ + H2O, CO, CO2, CH4, N2, NO, N2O, AND Ar

Relevant to modeling and understanding X-ray emission from cometary and planetary atmospheres, total cross-sections for 1.17 and 2.33 keV/u O6+ colliding with H2O, CO, CO2, CH4, N2, NO, N2O, and Ar have been measured for the processes of single, double, and triple charge exchanges. Using these measurements as benchmarks, synthetic emission spectra spanning the X-ray, UV, and visible range have been calculated based on theoretical treatment of the transfer of between one and six electrons from the target neutrals to the projectile ion, followed by radiative and non-radiative decay of the highly excited states produced in these collisions. The results help add to the base of knowledge required to simulate ion-neutral processes in astrophysical environments; refine the present understanding of these fundamental atomic processes; and guide future observations, laboratory measurements, and theoretical predictions.
The Effects of Work Design Characteristics on Organizational Citizenship Behaviour: An Empirical Investigation

This study was aimed to examine the effect of work design characteristics on employee engagement in Organizational Citizenship Behaviour (OCB). Drawing upon the Expanded Work Design Model (Humphrey, Nahrgang, & Morgeson, 2007) and the Job Characteristics Theory (Hackman & Oldham 1975), this study specifically examined the direct effect of seven dimensions of work design characteristics on OCB. A total of 646 nursing and clinical employees holding non supervisory jobs in 3 public hospitals in Malaysia participated in this study. Hierarchical multiple regression results indicated a statistically significant positive relationship between work design characteristics (feedback, task significance, psychological demand, autonomy and social support) and OCB. Managerial implications, theoretical implications, limitations of the study and the directions for future research were discussed.
Crime Modeling with Truncated Levy Flights and Effects of Police Patrol

In this paper, we developed a truncated Levy flight model to study the crime dynamics. In the discrete case, our model allows criminals to perform long jumps in between committing crimes with a speed light. This is a more realistic extension of a pioneering random walk model by Short et. al and a Levy flight model thereafter in Chaturapruek, et al. We also derive a continuum limit and perform a stability analysis to study the formation of crime hotspots. Our model is more realistic than the Levy Flight Model, and provides an alternative to the Random Walk Model when the criminals can perform long jumps in between committing crimes. In the next step, we introduce patrolling police officers to our new model following that in. We examine the effects of police patrol when the police choose to adopt different strategies, including unbiased random walk, biased random walk, and truncated Levy flight. We evaluate the effectiveness of the police patrol with the number of crime events in a given time frame. With spatially non-uniform initial conditions, we find that the truncated Levy flight to be the best strategy in general.
Community structure and temporal dynamics of SARS-CoV-2 epistatic network allow for early detection of emerging variants with altered phenotypes

The emergence of viral variants with altered phenotypes is a public health challenge underscoring the need for advanced evolutionary forecasting methods. Given extensive epistatic interactions within viral genomes and known viral evolutionary history, efficient genomic surveillance necessitates early detection of emerging viral haplotypes rather than commonly targeted single mutations. Haplotype inference, however, is a significantly more challenging problem precluding the use of traditional approaches. Here, using SARS-CoV-2 evolutionary dynamics as a case study, we show that emerging haplotypes with altered transmissibility can be linked to dense communities in coordinated substitution networks, which become discernible significantly earlier than the haplotypes become prevalent. From these insights, we develop a computational framework for inference of viral variants and validate it by successful early detection of known SARS-CoV-2 strains. Our methodology offers greater scalability than phylogenetic lineage tracing and can be applied to any rapidly evolving pathogen with adequate genomic surveillance data.
Activation of a Vibrio cholerae CBASS anti-phage system by quorum sensing and folate depletion

ABSTRACT A major challenge faced by bacteria is infection by bacteriophage (phage). Abortive infection is one strategy for combating phage in which an infected cell kills itself to limit phage replication, thus protecting neighboring kin. One class of abortive infection systems is the cyclic oligonucleotide based anti-phage signaling system (CBASS) which relies on two core enzymatic activities; an oligo-nucleotide cyclase that is activated following phage infection and a cyclic-oligo-nucleotide sensitive effector whose activity kills the infected cell. However, the mechanisms behind the deployment and activation of these lethal CBASS systems prior to and following infection have largely remained a mystery. While exploring unique genomic features of the current pandemic Vibrio cholerae biotype El Tor for clues underlying its pandemic success we found its CBASS was spuriously activated by the folate biosynthesis inhibitor sulfamethoxazole, but only after the population had reached a high-cell density. This population density-dependent activity revealed that transcription of both the oligo-nucleotide cyclase, dncV, and the CBASS phospholipase effector, capV, is enhanced at high-cell density by quorum sensing. Taken together, these results demonstrate that the V. cholerae CBASS is deployed when the environment is densely populated and activated in response to a perturbation in folate biosynthesis. IMPORTANCE To counteract infection with phage, bacteria have evolved a myriad of molecular defense systems. Some of these systems initiate a process called abortive infection, in which the infected cell kills itself to prevent phage propagation. However, such systems must be inhibited in the absence of phage infection to prevent spurious death of the host. Here, we show that the cyclic oligonucleotide based anti-phage signaling system (CBASS) accomplishes this by sensing intracellular folate molecules and only expressing this system in a group. These results enhance our understanding of the evolution of the seventh Vibrio cholerae pandemic and more broadly how bacteria defend themselves against phage infection. To counteract infection with phage, bacteria have evolved a myriad of molecular defense systems. Some of these systems initiate a process called abortive infection, in which the infected cell kills itself to prevent phage propagation. However, such systems must be inhibited in the absence of phage infection to prevent spurious death of the host. Here, we show that the cyclic oligonucleotide based anti-phage signaling system (CBASS) accomplishes this by sensing intracellular folate molecules and only expressing this system in a group. These results enhance our understanding of the evolution of the seventh Vibrio cholerae pandemic and more broadly how bacteria defend themselves against phage infection.
In silico predictions of the hepatic metabolic clearance in humans for 10 drugs with highly variable in vitro pharmacokinetics

Challenges/problems for in vitro methodologies for prediction of human clinical pharmacokinetics include inter- and intra-laboratory variability, and common occurance of high limits of quantification, low recovery, low parameter validity and low reproducibility. In this study, 10 drugs with substantial differences in human hepatocyte intrinsic metabolic clearance (CLint) and fraction unbound in plasma (fu) between laboratories were selected. The average and maximum ratios between highest and lowest reported predicted in vivo hepatic metabolic clearance (CLH) for the drugs were 529- and 2436-fold, respectively. The in vivo CLH was predicted using in vitro CLint and fu data from the various highly sources and using our in silico methodology. The main aim was to compare the predictive accuracies for the in vitro and in silico methodologies. Prediction errors for in vitro methodology ranged from 1.1-to 578-fold, with an average of 150-fold for lowest predicted estimates and 16-fold for highest predicted estimates. The in vitro based predictions produced 36-to 38-fold higher average and maximum prediction errors than the in silico methodology, respectively. Mean and maximum in silico prediction errors were 4.2- and 15-fold, respectively, which is consistent with earlier results. In contrast to the in vitro methodology the in silico models did not predict high hepatic extraction ratio for drugs with low CLH. Overall, the in silico method clearly outperformed in vitro data for prediction of CLH in man for 10 drugs with large interlaboratory variability.
Sensitivity analysis-guided Bayesian Parameter Estimation for Neural Mass Models: Applications in Epilepsy

It is well established that neural mass models (NMMs) can effectively simulate the mesoscopic and macroscopic dynamics of electroencephalography (EEG), including epileptic EEG. However NMMs are characterized by a high-dimensional parameter space and a lack of knowledge on what NMM parameters can be reliably estimated, thus limiting their application to clinical EEG data. In this article, we analyze the parameter sensitivity of Jansen and Rit NMM (JR NMM) in order to identify the most sensitive NMM parameters for reliable parameter estimation from EEG data. We also propose a joint estimation method for NMM states and parameters based on expectation–maximization combined with unscented Kalman smoother (UKS-EM). Global sensitivity analysis methods including Morris method and Sobol method are used to perform sensitivity analysis. Results from both the Morris and Sobol method show that the average inhibitory synaptic gain, B and the time constant of the average inhibitory post-synaptic potentials (PSPs), b−1 have significant impact on the JR NMM output along with having the least interaction with other model parameters. The UKS-EM method for estimating the parameters B and b is validated using simulations under varying levels of measurement noise. Finally we apply the UKS-EM algorithm to intracranial EEG data from 16 epileptic patients. Our results, both at individual and group-level show that the parameters B and b change significantly between the pre-seizure and seizure period, and between the seizure and post-seizure period, with transition to seizure characterized by decrease in average B and high frequency activity in seizure characterized by an increase in b. These results establish sensitivity analysis guided Bayesian parameter estimation as a powerful tool for reducing the parameter space of high dimensional NMMs enabling reliable and efficient estimation of the most sensitive NMM parameters, with the potential for online and fast tracking of NMM parameters in applications such as seizure tracking and control.
Behavior-relevant top-down cross-modal predictions in mouse neocortex

Han and Helmchen demonstrate that the dynamic interactions between a higher association area and a primary sensory area in the neocortex can shape sensory representation and govern behavioral choices. Animals adapt to a constantly changing world by predicting their environment and the consequences of their actions. The predictive coding hypothesis proposes that the brain generates predictions and continuously compares them with sensory inputs to guide behavior. However, how the brain reconciles conflicting top-down predictions and bottom-up sensory information remains unclear. To address this question, we simultaneously imaged neuronal populations in the mouse somatosensory barrel cortex and posterior parietal cortex during an auditory-cued texture discrimination task. In mice that had learned the task with fixed tone–texture matching, the presentation of mismatched pairing induced conflicts between tone-based texture predictions and actual texture inputs. When decisions were based on the predicted rather than the actual texture, top-down information flow was dominant and texture representations in both areas were modified, whereas dominant bottom-up information flow led to correct representations and behavioral choice. Our findings provide evidence for hierarchical predictive coding in the mouse neocortex.
Systems analysis of miR-199a/b-5p and multiple miR-199a/b-5p targets during chondrogenesis

Changes in chondrocyte gene expression can contribute to the development of osteoarthritis (OA), and so recognition of the regulative processes during chondrogenesis can lead to a better understanding of OA. microRNAs (miRNAs) are key regulators of gene expression in chondrocytes/OA and we have used a combined experimental, bioinformatic, and systems biology approach to explore the multiple miRNA-mRNA interactions that regulate chondrogenesis. A longitudinal chondrogenesis bioinformatic analysis identified paralogues miR-199a-5p and miR-199b-5p as pro-chondrogenic regulators. Experimental work demonstrated alteration of miR-199a-5p or miR-199b-5p expression led to significant inverse modulation of key chondrogenic genes and extracellular matrix production. miR-199a/b-5p targets FZD6, ITGA3 and CAV1 were identified by inhibition experiments and verified as direct targets by luciferase assay. The experimental work was used to generate and parameterize a multi-miRNA 14-day chondrogenesis kinetic model to be used as a repository for the experimental work and as a resource for further investigation of this system. This is the first multi-miRNA model of a chondrogenesis-based system, and highlights the complex relationships between regulatory miRNAs, and their target mRNAs.
Seed endophytic bacterial profiling from wheat varieties of contrasting heat sensitivity

Wheat yield can be limited by many biotic and abiotic factors. Heat stress at the grain filling stage is a factor that reduces wheat production tremendously. The potential role of endophytic microorganisms in mitigating plant stress through various biomolecules like enzymes and growth hormones and also by improving plant nutrition has led to a more in-depth exploration of the plant microbiome for such functions. Hence, we devised this study to investigate the abundance and diversity of wheat seed endophytic bacteria (WSEB) from heatS (heat susceptible, GW322) and heatT (heat tolerant, HD3298 and HD3271) varieties by culturable and unculturable approaches. The results evidenced that the culturable diversity was higher in the heatS variety than in the heatT variety and Bacillus was found to be dominant among the 10 different bacterial genera identified. Though the WSEB population was higher in the heatS variety, a greater number of isolates from the heatT variety showed tolerance to higher temperatures (up to 55°C) along with PGP activities such as indole acetic acid (IAA) production and nutrient acquisition. Additionally, the metagenomic analysis of seed microbiota unveiled higher bacterial diversity, with a predominance of the phyla Proteobacteria covering >50% of OTUs, followed by Firmicutes and Actinobacteria. There were considerable variations in the abundance and diversity between heat sensitivity contrasting varieties, where notably more thermophilic bacterial OTUs were observed in the heatT samples, which could be attributed to conferring tolerance against heat stress. Furthermore, exploring the functional characteristics of culturable and unculturable microbiomes would provide more comprehensive information on improving plant growth and productivity for sustainable agriculture.
Neuroprotective effects of resistance physical exercise on the APP/PS1 mouse model of Alzheimer’s disease

Introduction Physical exercise has beneficial effects by providing neuroprotective and anti-inflammatory responses to AD. Most studies, however, have been conducted with aerobic exercises, and few have investigated the effects of other modalities that also show positive effects on AD, such as resistance exercise (RE). In addition to its benefits in developing muscle strength, balance and muscular endurance favoring improvements in the quality of life of the elderly, RE reduces amyloid load and local inflammation, promotes memory and cognitive improvements, and protects the cortex and hippocampus from the degeneration that occurs in AD. Similar to AD patients, double-transgenic APPswe/PS1dE9 (APP/PS1) mice exhibit Αβ plaques in the cortex and hippocampus, hyperlocomotion, memory deficits, and exacerbated inflammatory response. Therefore, the aim of this study was to investigate the effects of 4 weeks of RE intermittent training on the prevention and recovery from these AD-related neuropathological conditions in APP/PS1 mice. Methods For this purpose, 6-7-month-old male APP/PS1 transgenic mice and their littermates, negative for the mutations (CTRL), were distributed into three groups: CTRL, APP/PS1, APP/PS1+RE. RE training lasted four weeks and, at the end of the program, the animals were tested in the open field test for locomotor activity and in the object recognition test for recognition memory evaluation. The brains were collected for immunohistochemical analysis of Aβ plaques and microglia, and blood was collected for plasma corticosterone by ELISA assay. Results APP/PS1 transgenic sedentary mice showed increased hippocampal Aβ plaques and higher plasma corticosterone levels, as well as hyperlocomotion and reduced central crossings in the open field test, compared to APP/PS1 exercised and control animals. The intermittent program of RE was able to recover the behavioral, corticosterone and Aβ alterations to the CTRL levels. In addition, the RE protocol increased the number of microglial cells in the hippocampus of APP/PS1 mice. Despite these alterations, no memory impairment was observed in APP/PS1 mice in the novel object recognition test. Discussion Altogether, the present results suggest that RE plays a role in alleviating AD symptoms, and highlight the beneficial effects of RE training as a complementary treatment for AD.
PREDICTION OF SHOCK STRUCTURE BY BIMODAL DISTRIBUTION FUNCTION METHOD

A system of fluid dynamic equations is derived by using Mott-Smith distribution function to study the structure of shock wave in a neutral, monatomic gas of Maxwell molecules. The predicted shock solutions using the newly proposed formalism are presented and compared with the experimental data, direct-simulation Monte Carlo (DSMC) solution and the solutions predicted by other existing theories for Mach numbers M<10. The density, temperature, heat flux profiles and shock thickness calculated at different Mach numbers have been shown to have good agreement with the experimental and DSMC solutions. In addition, the predicted shock thickness is in good agreement with the DSMC simulation result at low Mach numbers.
Analysis of independent risk factors for progression of different degrees of diabetic retinopathy as well as non-diabetic retinopathy among type 2 diabetic patients

Purpose To study the independent risk factors for development of different degrees of diabetic retinopathy (DR) as well as non-DR (NDR) among type 2 diabetic patients. Methods This cross-sectional study included 218 patients with type 2 diabetes between January 2022 and June 2022. All the patients were divided into two groups: the DR group and the NDR group. The DR group was subdivided into the mild, moderate and severe non-proliferative DR (NPDR) group and the proliferative DR (PDR) group. Data recorded for all patients included age, gender, duration of diabetes, blood pressure, glycated hemoglobin (HbA1c), fasting blood glucose (FBG), blood lipids, best corrected visual acuity (BCVA), intraocular pressure (IOP), axial length (AL), anterior chamber depth (ACD), and renal function. Logistic regression methods were used to analyze the risk factors for DR. Results The prevalence of DR in type 2 diabetes was 28.44%. The duration of diabetes, age, mean arterial pressure (MAP), HbA1c, FBG, urinary albumin/creatinine ratio (UACR), BCVA, AL, and ACD were significantly different between the DR and the NDR groups (p < 0.05). Multivariate logistic regression analysis identified age, FBG, UACR, and AL as the independent risk factors for DR (OR = 0.843, 2.376, 1.049, 0.005; p = 0.034, 0.014, 0.016, p < 0.001). Conclusion Young age, short AL, higher levels of FBG and UACR were the independent risk factors for the progression of DR in type 2 diabetes.
The role of invasive and non-invasive imaging technologies and calcium modification therapies in the evaluation and management of coronary artery calcifications

The treatment of coronary artery disease (CAD) has advanced significantly in recent years due to improvements in medical therapy and percutaneous or surgical revascularization. However, a persistent obstacle in the percutaneous management of CAD is coronary artery calcification (CAC), which portends to higher rates of procedural challenges, post-intervention complications, and overall poor prognosis. With the advent of novel multimodality imaging technologies spanning from intravascular ultrasound to optical coherence tomography to coronary computed tomography angiography combined with advances in calcium debulking and modification techniques, CACs are now targets for intervention with growing success. This review will summarize the most recent developments in the diagnosis and characterization of CAC, offer a comparison of the aforementioned imaging technologies including which ones are most suitable for specific clinical presentations, and review the CAC modifying therapies currently available.
Transvaginal versus transabdominal specimen extraction surgery for right colon cancer: A propensity matching study

Background The transvaginal route for specimen extraction is considered ideal for colorectal surgery, but its safety is still questioned. There has been little research on transvaginal natural orifice specimen extraction surgery (NOSES) in the right hemicolectomy. As a result, we conducted a study comparing transvaginal NOSES to traditional transabdominal specimen extraction surgery. Patients and methods Data on female patients who underwent radical right hemicolectomy at the First Affiliated Hospital of Nanchang University between January 2015 and December 2020 were collected retrospectively. A total of 847 patients were compliant, with 51 undergoing the transvaginal specimen extraction surgery (NOSES) group and 796 undergoing the transabdominal specimen extraction surgery (TISES) group. A propensity score matching method (1:2) was used to balance the clinicopathological characteristics of the two groups. Results Finally, 138 patients were enrolled in our study, with 46 in the NOSES group and 92 in the TISES group. Compared to the TISES group, the NOSES group had less intraoperative blood loss (p = 0.036), shorter time to first flatus (p < 0.001), shorter time to first liquid diet (p < 0.001), lower postoperative white blood cell counts (p = 0.026), lower C-reactive protein levels (p = 0.027), and lower visual analog scale (VAS) scores (p < 0.001). Regarding the quality of life after surgery, the NOSES group had better role function (p < 0.01), emotional function (p < 0.001), and improved symptoms of postoperative pain (p < 0.001) and diarrhea (p = 0.024). The scar satisfaction was significantly higher in the NOSES group than in the TISES group. Overall survival and disease-free survival in two groups were similar. Conclusion The short-term results of transvaginal NOSES were superior to conventional transabdominal specimen extraction surgery. At the same time, transvaginal NOSES could improve the abdominal wall appearance and quality of life. The long-term survival was similar in the two surgical approaches. Therefore, transvaginal NOSES is worthy of our implementation and promotion.