Miracle-dz/UniFAR-FTUs huggingface dataset:
Emergence of Rice Blast AVR-Pi9 Resistance Breaking Haplotypes in Yunnan Province, China

The rice blast disease (caused by Magnaporthe oryzae) is a devastating disease in China. Understanding the molecular mechanisms of interaction for the cognate avirulence (AVR) gene with host resistance (R) genes, as well as their genetic evolution is essential for sustainable rice production. In the present study, we conducted a high-throughput nucleotide sequence polymorphism analysis of the AVR-Pi9 gene that was amplified from the rice-growing regions of the Yunnan Province in China. We detected the presence of seven novel haplotypes from 326 rice samples. In addition, the sequences of AVR-Pi9 were also obtained from two non-rice hosts, Eleusine coracana and Eleusine indica. The sequence analysis revealed the insertions and deletions in the coding and non-coding regions of the gene. The pathogenicity experiments of these haplotypes on previously characterized monogenic lines showed that the newly identified haplotypes are virulent in nature. The breakdown of resistance was attributed to the development of new haplotypes. Our results suggest that the mutation in the AVR-Pi9 gene is an alarming situation in the Yunnan province and thus needs attention.
Stability in Haptic Teleoperation Literature Review

Teleoperation is the indirect manipulation of an object using a robotic manipulator. The term haptic teleoperation is used to indicate the presence of force feedback. Haptic teleoperation can be very valuable, because it can help to perform a task more time effectively and more reliably. Stability is an important issue in haptic teleoperation, because the creating of a perfect transparent teleoperator leads to stability problems. This report discusses techniques to analyse the stability, the relationships between them, influences on stability and stabilising techniques. To analyse the stability, the teleoperator is modelled as a linear system consisting of a master device, a communication channel and a slave device. It is augmented with models of the human operator and the environment to yield the complete teleoperation system. If it is assumed that the operator and environment are passive then the stability of the teleoperation system can be analysed by looking at the teleoperator part only. One concept is the absolute stability criterion. The other one is the passivity criterion, which is also applicable to nonlinear systems and very easy to apply. Both concepts can be conservative, however. As an alternative, analysis tools based on the whole teleoperation system can be used. With Routh’s stability criterion the stability can be analysed without actually solving for the poles of the system. With the root-locus method the location of the poles can be plotted as a parameter varies. With the Nyquist stability concept the stability of a teleoperation system can be analysed using the open-loop transfer function. Lyapunov stability is also applicable to nonlinear systems and with the small gain theorem and μ-analysis the robust stability of a teleoperation system can be analysed. Based on the analysis techniques, influences on the stability can be investigated. Influences on stability can originate from any part in the system. Important influences on the stability are time delays, digital implementation of the controllers and a phase transition from free air to hard contact. Frequently used techniques to stabilise a teleoperation system are: H∞ control, adaptive control and addition of damping. Damping could be added by designing a passive communication channel or it could be added in an adaptive way, that is to say, by adding damping when the teleoperator becomes active.
Defining developmental trajectories of prosensory cells in human inner ear organoids at single-cell resolution

ABSTRACT The inner ear sensory epithelia contain mechanosensitive hair cells and supporting cells. Both cell types arise from SOX2-expressing prosensory cells, but the mechanisms underlying the diversification of these cell lineages remain unclear. To determine the transcriptional trajectory of prosensory cells, we established a SOX2-2A-ntdTomato human embryonic stem cell line using CRISPR/Cas9, and performed single-cell RNA-sequencing analyses with SOX2-positive cells isolated from inner ear organoids at various time points between differentiation days 20 and 60. Our pseudotime analysis suggests that vestibular type II hair cells arise primarily from supporting cells, rather than bi-fated prosensory cells in organoids. Moreover, ion channel- and ion-transporter-related gene sets were enriched in supporting cells versus prosensory cells, whereas Wnt signaling-related gene sets were enriched in hair cells versus supporting cells. These findings provide valuable insights into how prosensory cells give rise to hair cells and supporting cells during human inner ear development, and may provide a clue to promote hair cell regeneration from resident supporting cells in individuals with hearing loss or balance disorders.
Biomaterials as Implants in the Orthopedic Field for Regenerative Medicine: Metal versus Synthetic Polymers

Patients suffering bone fractures in different parts of the body require implants that will enable similar function to that of the natural bone that they are replacing. Joint diseases (rheumatoid arthritis and osteoarthritis) also require surgical intervention with implants such as hip and knee joint replacement. Biomaterial implants are utilized to fix fractures or replace parts of the body. For the majority of these implant cases, either metal or polymer biomaterials are chosen in order to have a similar functional capacity to the original bone material. The biomaterials that are employed most often for implants of bone fracture are metals such as stainless steel and titanium, and polymers such as polyethene and polyetheretherketone (PEEK). This review compared metallic and synthetic polymer implant biomaterials that can be employed to secure load-bearing bone fractures due to their ability to withstand the mechanical stresses and strains of the body, with a focus on their classification, properties, and application.
Gender, Obesity, Fat Distribution and 25-Hydroxyvitamin D

Background and Objectives: Obesity is a worldwide disease associated with systemic complications. In recent years, there has been growing interest in studying vitamin D but data related to obese subjects are still poor. AIM: The aim of this study was to evaluate the relationship between obesity degree and 25-hydroxyvitamin D [25(OH)D] levels. Materials and Methods: We recruited 147 Caucasian adult obese patients (BMI > 30 Kg/m2; 49 male; median age 53 years), and 20 overweight subjects as control group (median age 57 years), who had been referred to our Obesity Center of Chieti (Italy) between May 2020 and September 2021. Results: The median BMI was 38 (33–42) kg/m2 for obese patients and 27 (26–28) kg/m2 for overweight patients. 25(OH)D concentrations were lower in the obese population compared to the overweight population (19 ng/mL vs. 36 ng/mL; p < 0.001). Considering all obese subjects, a negative correlation was observed between 25(OH)D concentrations and obesity-related parameters (weight, BMI, waist circumference, fat mass, visceral fat, total cholesterol, LDL cholesterol) and glucose metabolism-related parameters. 25(OH)D was also negatively correlated with blood pressure. Conclusions: Our data confirmed the inverse relationship between obesity and blood concentration of 25(OH)D and highlighted how 25(OH)D levels decrease in the presence of glucose and lipid metabolism alterations.
Agro-Industrial Plant Proteins in Electrospun Materials for Biomedical Application

Plant proteins are receiving a lot of attention due to their abundance in nature, customizable properties, biodegradability, biocompatibility, and bioactivity. As a result of global sustainability concerns, the availability of novel plant protein sources is rapidly growing, while the extensively studied ones are derived from byproducts of major agro-industrial crops. Owing to their beneficial properties, a significant effort is being made to investigate plant proteins’ application in biomedicine, such as making fibrous materials for wound healing, controlled drug release, and tissue regeneration. Electrospinning technology is a versatile platform for creating nanofibrous materials fabricated from biopolymers that can be modified and functionalized for various purposes. This review focuses on recent advancements and promising directions for further research of an electrospun plant protein-based system. The article highlights examples of zein, soy, and wheat proteins to illustrate their electrospinning feasibility and biomedical potential. Similar assessments with proteins from less-represented plant sources, such as canola, pea, taro, and amaranth, are also described.
HIV RNA/DNA Levels at Diagnosis Can Predict Immune Reconstitution: A Longitudinal Analysis

Background: HIV DNA mirrors the number of infected cells and the size of the HIV viral reservoir. The aim of this study was to evaluate the effect of pre-cART HIV DNA levels as a predictive marker of immune reconstitution and on the post-cART CD4 counts trends. Methods: HIV DNA was isolated from PBMCs and quantified by real-time PCR. Immune reconstitution was assessed up to four years. Piecewise-linear mixed models were used to describe CD4 count changes. Results: 148 people living with HIV (PLWH) were included. The highest rate of immune reconstitution was observed during the first trimester. There was a trend showing that high HIV RNA level resulted in greater increase in CD4 count, especially during the first trimester of cART (difference above vs. below median 15.1 cells/μL/month; 95% CI −1.4–31.5; p = 0.073). Likewise, higher HIV DNA level would predict greater CD4 increases, especially after the first trimester (difference above vs. below median 1.2 cells/μL/month; 95% CI −0.1–2.6; p = 0.071). Higher DNA and RNA levels combined were significantly associated with greater CD4 increase past the first trimester (difference high/high vs. low/low 2.1 cells/μL/month; 95% CI 0.3–4.0; p = 0.024). In multivariable analysis, lower baseline CD4 counts predicted a greater CD4 rise. Conclusions: In successfully treated PLWH, pre-cART HIV DNA and HIV RNA levels are predictors of immune reconstitution.
Association between childhood maltreatment and cortical folding in women with eating disorders

Childhood maltreatment (CM) is associated with distinct clinical and biological characteristics in people with eating disorders (EDs). The measurement of local gyrification index (lGI) may help to better characterize the impact of CM on cortical structure. Thus, the present study investigated the association of CM with lGI in women with EDs. Twenty‐six women with anorexia nervosa (AN) and 24 with bulimia nervosa (BN) underwent a 3T MRI scan. All participants filled in the Childhood Trauma Questionnaire. All neuroimaging data were processed by FreeSurfer. LGI maps underwent a general linear model to evaluate differences between groups with or without CM. People with AN and BN were merged together. Based on the Childhood Trauma Questionnaire cutoff scores, 24 participants were identified as maltreated and 26 as non‐maltreated. Maltreated people with EDs showed a significantly lower lGI in the left middle temporal gyrus compared with non‐maltreated people, whereas no differences emerged in the right hemisphere between groups. The present study showed that in people with EDs, CM is associated with reduced cortical folding in the left middle temporal gyrus, an area that could be involved in ED psychopathology. This finding corroborates the hypothesis of a ‘maltreated ecophenotype’, which argues that CM may allow to biologically, other than clinically, distinguish individuals with the same psychiatric disorder.
Effects of Oral Cannabidiol on Health and Fitness in Healthy Adults: An 8-Week Randomized Trial

Background: There is a lack of research on the effects of cannabidiol (CBD) on health-related fitness, physical activity, cognitive health, psychological wellbeing, and concentrations of C-reactive protein (CRP) in healthy individuals. CBD has potential anti-inflammatory and neuroprotective effects. Methods: This study aimed to investigate the effects of 8 weeks of CBD on the above-mentioned measures in healthy individuals. Forty-eight participants were randomized into two groups receiving either oral capsules of 50 mg of CBD or a calorie-matched placebo daily. Participants completed pre- and post-intervention assessments, including blood draws, body composition, fitness, physical activity, and self-reported surveys. Results: There were no significant differences between groups regarding body composition, aerobic fitness, muscular strength, physical activity, cognitive health, psychological wellbeing, and resting CRP concentrations. However, the placebo group experienced a decline in mean peak power and relative peak power compared to the CBD group. Conclusions: The results suggest that 8 weeks of CBD supplementation may prevent declines in anaerobic fitness over time. However, long-term CBD supplementation may not be beneficial for altering measures of health-related fitness, mental health, and inflammation in healthy individuals.
Hyperhalophilic Diatom Extract Protects against Lead-Induced Oxidative Stress in Rats and Human HepG2 and HEK293 Cells

This work investigated the protective effects of microalga Halamphora sp. extract (HExt), a nutraceutical and pharmacological natural product, on human lead-intoxicated liver and kidney cells in vitro and in vivo in Wistar rats. The human hepatocellular carcinoma cell line HepG2 and the human embryonic kidney cell line HEK293 were used for the in vitro study. The analysis of the fatty acid methyl esters in the extract was performed via GC/MS. The cells were pretreated with HExt at 100 µg mL−1, followed by treatment with different concentrations of lead acetate, ranging from 25 to 200 µM for 24 h. The cultures were incubated (5% CO, 37 °C) for 24 h. Four groups, each containing six rats, were used for the in vivo experiment. The rats were exposed to subchronic treatment with a low dose of lead acetate (5 mg kg−1 b.w. per day). Pretreating HepG2 and HEK293 cells with the extract (100 µg mL−1) significantly (p < 0.05) protected against the cytotoxicity induced by lead exposure. For the in vivo experiment, the biochemical parameters in serum—namely, the level of malondialdehyde (MDA), and the activities of superoxide dismutase (SOD), catalase (CAT), and glutathione peroxidase (GPx)—were measured in the organ homogenate supernatants. HExt was found to be rich in fatty acids, mainly palmitic and palmitoleic acids (29.464% and 42.066%, respectively). In both the in vitro and in vivo experiments, cotreatment with HExt protected the liver and kidney cell structures and significantly preserved the normal antioxidant and biochemical parameters in rats. This study discovered the possible protective effect of HExt, which could be beneficial for Pb-intoxicated cells.
Pangenome Reconstruction of Mycobacterium tuberculosis as a Guide to Reveal Genomic Features Associated with Strain Clinical Phenotype

Tuberculosis (TB) is one of the leading causes of human deaths worldwide caused by infectious diseases. TB infection by Mycobacterium tuberculosis can occur in the lungs, causing pulmonary tuberculosis (PTB), or in any other organ of the body, resulting in extrapulmonary tuberculosis (EPTB). There is no consensus on the genetic determinants of this pathogen that may contribute to EPTB. In this study, we constructed the M. tuberculosis pangenome and used it as a tool to seek genomic signatures associated with the clinical presentation of TB based on its accessory genome differences. The analysis carried out in the present study includes the raw reads of 490 M. tuberculosis genomes (PTB n = 245, EPTB n = 245) retrieved from public databases that were assembled, as well as ten genomes from Mexican strains (PTB n = 5, EPTB n = 5) that were sequenced and assembled. All genomes were annotated and then used to construct the pangenome with Roary and Panaroo. The pangenome obtained using Roary consisted of 2231 core genes and 3729 accessory genes. On the other hand, the pangenome resulting from Panaroo consisted of 2130 core genes and 5598 accessory genes. Associations between the distribution of accessory genes and the PTB/EPTB phenotypes were examined using the Scoary and Pyseer tools. Both tools found a significant association between the hspR, plcD, Rv2550c, pe_pgrs5, pe_pgrs25, and pe_pgrs57 genes and the PTB genotype. In contrast, the deletion of the aceA, esxR, plcA, and ppe50 genes was significantly associated with the EPTB phenotype. Rv1759c and Rv3740 were found to be associated with the PTB phenotype according to Scoary; however, these associations were not observed when using Pyseer. The robustness of the constructed pangenome and the gene–phenotype associations is supported by several factors, including the analysis of a large number of genomes, the inclusion of the same number of PTB/EPTB genomes, and the reproducibility of results thanks to the different bioinformatic tools used. Such characteristics surpass most of previous M. tuberculosis pangenomes. Thus, it can be inferred that the deletion of these genes can lead to changes in the processes involved in stress response and fatty acid metabolism, conferring phenotypic advantages associated with pulmonary or extrapulmonary presentation of TB. This study represents the first attempt to use the pangenome to seek gene–phenotype associations in M. tuberculosis.
Eradication of Drug-Tolerant Mycobacterium tuberculosis 2022: Where We Stand

The lungs of tuberculosis (TB) patients contain a spectrum of granulomatous lesions, ranging from solid and well-vascularized cellular granulomas to avascular caseous granulomas. In solid granulomas, current therapy kills actively replicating (AR) intracellular bacilli, while in low-vascularized caseous granulomas the low-oxygen tension stimulates aerobic and microaerophilic AR bacilli to transit into non-replicating (NR), drug-tolerant and extracellular stages. These stages, which do not have genetic mutations and are often referred to as persisters, are difficult to eradicate due to low drug penetration inside the caseum and mycobacterial cell walls. The sputum of TB patients also contains viable bacilli called differentially detectable (DD) cells that, unlike persisters, grow in liquid, but not in solid media. This review provides a comprehensive update on drug combinations killing in vitro AR and drug-tolerant bacilli (persisters and DD cells), and sterilizing Mycobacterium tuberculosis-infected BALB/c and caseum-forming C3HeB/FeJ mice. These observations have been important for testing new drug combinations in noninferiority clinical trials, in order to shorten the duration of current regimens against TB. In 2022, the World Health Organization, following the results of one of these trials, supported the use of a 4-month regimen for the treatment of drug-susceptible TB as a possible alternative to the current 6-month regimen.
Effects of Prolonged Fasting during Inpatient Multimodal Treatment on Pain and Functional Parameters in Knee and Hip Osteoarthritis: A Prospective Exploratory Observational Study

Preliminary clinical data suggest that pain reduction through fasting may be effective for different diagnoses. This uncontrolled observational clinical study examined the effects of prolonged modified fasting on pain and functional parameters in hip and knee osteoarthritis. Patients admitted to the inpatient department of Internal Medicine and Nature-based Therapies of the Immanuel Hospital Berlin between February 2018 and December 2020 answered questionnaires at the beginning and end of inpatient treatment, as well as at 3, 6, and 12 months after discharge. Additionally, selected blood and anthropometric parameters, as well as subjective pain ratings, were routinely assessed during the inpatient stay. Fasting was the only common intervention for all patients, being performed as part of a multimodal integrative treatment program, with a daily caloric intake of <600 kcal for 7.7 ± 1.7 days. N = 125 consecutive patients were included. The results revealed an amelioration of overall symptomatology (WOMAC Index score: −14.8 ± 13.31; p < 0.001; d = 0.78) and pain alleviation (NRS Pain: −2.7 ± 1.98, p < 0.001, d = 1.48). Pain medication was reduced, stopped, or replaced by herbal remedies in 36% of patients. Improvements were also observed in secondary outcome parameters, including increased quality of life (WHO-5: +4.5 ± 4.94, p < 0.001, d = 0.94), reduced anxiety (HADS-A: −2.1 ± 2.91, p < 0001, d = 0.55) and depression (HADS-D: −2.3 ± 3.01, p < 0.001, d = 0.65), and decreases in body weight (−3.6 kg ± 1.65, p < 0.001, d = 0.21) and blood pressure (systolic: −6.2 ± 15.93, p < 0.001, d = 0.43; diastolic: −3.7 ± 10.55, p < 0.001, d = 0.43). The results suggest that patients with osteoarthritis of the lower extremities may benefit from prolonged fasting as part of a multimodal integrative treatment to improve quality of life, pain, and disease-specific functional parameters. Confirmatory randomized controlled trials are warranted to further investigate these hypotheses.
Optimal High-Dimensional Entanglement Concentration for Pure Bipartite Systems

Considering pure quantum states, entanglement concentration is the procedure where, from N copies of a partially entangled state, a single state with higher entanglement can be obtained. Obtaining a maximally entangled state is possible for N=1. However, the associated success probability can be extremely low when increasing the system’s dimensionality. In this work, we study two methods to achieve a probabilistic entanglement concentration for bipartite quantum systems with a large dimensionality for N=1, regarding a reasonably good probability of success at the expense of having a non-maximal entanglement. Firstly, we define an efficiency function Q considering a tradeoff between the amount of entanglement (quantified by the I-Concurrence) of the final state after the concentration procedure and its success probability, which leads to solving a quadratic optimization problem. We found an analytical solution, ensuring that an optimal scheme for entanglement concentration can always be found in terms of Q. Finally, a second method was explored, which is based on fixing the success probability and searching for the maximum amount of entanglement attainable. Both ways resemble the Procrustean method applied to a subset of the most significant Schmidt coefficients but obtaining non-maximally entangled states.
Physical and Thermal Characterizations of Newly Synthesized Liquid Crystals Based on Benzotrifluoride Moiety

The mesomorphic stability and optical activity of new group-based benzotrifluoride liquid crystals, (E)-4-(((4-(trifluoromethyl) phenyl) imino) methyl) phenyl 4-(alkyloxy)benzoate, or In, were investigated. The end of the molecules connected to the benzotrifluoride moiety and the end of the phenylazo benzoate moiety have terminal alkoxy groups which can range in chain length from 6 to 12 carbons. The synthesized compounds’ molecular structures were verified using FT-IR, 1H NMR, mass spectroscopy, and elemental analysis. Mesomorphic characteristics were verified using differential scanning calorimetry (DSC) and a polarized optical microscope (POM). All of the homologous series that have been developed display great thermal stability across a broad temperature range. Density functional theory (DFT) determined the examined compounds’ geometrical and thermal properties. The findings showed that every compound is entirely planar. Additionally, by using the DFT approach, it was possible to link the experimentally found values of the investigated compounds’ investigated compounds’ mesophase thermal stability, mesophase temperature ranges, and mesophase type to the predicted quantum chemical parameters.