Miracle-dz/UniFAR-FTUs huggingface dataset:
Control of awn length in rice breeding programs in Hokkaido

Understanding genetic diversity among local populations may facilitate the development of new crop varieties and is a primary goal of the molecular evolution of genes. Awn length is a well-documented phenotype among domestication traits in rice ( Oryza sativa L.), from long to short awns. Short awned or awnless varieties have been selected in rice breeding programs. Awnlessness is favored by rice farmers in the current agriculture system. Here, we identified the genetic basis of awn length during rice breeding programs in Hokkaido, Japan. We found variation in awn length ranging from 0.0 to 37.6 mm among a local population consisted of breeding lines. Genetic analysis of awn length identified that RAE1 and RAE2 on chromosomes 4 and 8, respectively, accounted for awn presence. These genes are well known to be significant during Asian rice domestication. Sequence variations in these genes may clarify the molecular evolution of the genes for awn length in rice breeding programs. Firstly, a loss-of-function allele in RAE1 , rae1 , was selected for short awn length. Then, alleles of RAE2, RAE2-H01 to RAE2-H04, were targeted for the selection of short awns or awnlessness. The selections of an awnlessness phenotype can diversify these alleles in the genes RAE1 and RAE2 exhibiting variation in awn length.
Computational Analysis of Mutations in the Receptor-Binding Domain of SARS-CoV-2 Spike and Their Effects on Antibody Binding

Currently, SARS-CoV-2 causing coronavirus disease 2019 (COVID-19) is responsible for one of the most deleterious pandemics of our time. The interaction between the ACE2 receptors at the surface of human cells and the viral Spike (S) protein triggers the infection, making the receptor-binding domain (RBD) of the SARS-CoV-2 S-protein a focal target for the neutralizing antibodies (Abs). Despite the recent progress in the development and deployment of vaccines, the emergence of novel variants of SARS-CoV-2 insensitive to Abs produced in response to the vaccine administration and/or monoclonal ones represent a potential danger. Here, we analyzed the diversity of neutralizing Ab epitopes and assessed the possible effects of single and multiple mutations in the RBD of SARS-CoV-2 S-protein on its binding affinity to various antibodies and the human ACE2 receptor using bioinformatics approaches. The RBD-Ab complexes with experimentally resolved structures were grouped into four clusters with distinct features at sequence and structure level. The performed computational analysis indicates that while single amino acid replacements in RBD may only cause partial impairment of the Abs binding, moreover, limited to specific epitopes, the variants of SARS-CoV-2 with multiple mutations, including some which were already detected in the population, may potentially result in a much broader antigenic escape. Further analysis of the existing RBD variants pointed to the trade-off between ACE2 binding and antigenic escape as a key limiting factor for the emergence of novel SAR-CoV-2 strains, as the naturally occurring mutations in RBD tend to reduce its binding affinity to Abs but not to ACE2. The results provide guidelines for further experimental studies aiming to identify high-risk RBD mutations that allow for an antigenic escape.
Some anaerobic performance variations from morning to evening: massage affects performance and diurnal variation

This study was conducted to determine the effects of massage on some anaerobic performance and diurnal variation. Twelve male athletes between the ages of 18-25, who exercised regularly for three days a week (age, 18.00± 2.17 years; height, 168.± 3.15 cm; 65± 2.63 kg; BMI 22.49±.44 years) participated in the study. While the non-massage protocol consisted of only 15 minutes of jogging (NM), the protocol with sports massage consisted of 5 minutes of jogging and 10 minutes of sports massage (SM). The protocols were applied in two time periods of the day (morning: 09.00-11.00, evening: 16.00-18.00). It has been reported that SM positively affects peak power and mean power due to vertical jump performance compared to the NM protocol. In addition, it was determined that the SM protocol applied in the evening was more effective than SM protocol applied in the morning.
Information Asymmetry Between Physicians and Patients Undergoing Laparoscopic Cholecystectomy: Analysis of Patients' Awareness Level.

Background: Obtaining informed consent is essential before conducting a healthcare intervention. Primary reason for obtaining informed consent is to eliminate asymmetry information between the physicians and patients. The aim of this study was to determine the significance of information symmetry between physicians and patients undergoing laparoscopic cholecystectomy.Methods: An analytical study was carried out in 2019. Moreover, the research population consisted of patients undergoing laparoscopic cholecystectomy. As for the data collection tool, a researcher-made questionnaire was introduced. The validity and reliability of this questionnaire was confirmed. Questionnaire had five sections and Cronbach's alpha of 0.85 was achieved. The data were then analyzed by SPSS Version: 18.0. Results: A total of 96 patients participated in the study, where around 30% of them were male. Only 20.3% of patients specified that they were aware of possible complications of their treatment, of which 62% cited their physician as the main source of this information. On the other hand, 80% of patients were fully aware of the benefits of their treatment.Conclusions: The information asymmetry between physicians and patients about the benefits and complications of treatments should be somehow eliminated and the crucial information about the chosen treatment plan or alternative courses of action should be fully provided to the patient by the attending physician or nurse.
Direction-sweep Markov chains

We discuss a non-reversible, lifted Markov-chain Monte Carlo (MCMC) algorithm for particle systems in which the direction of proposed displacements is changed deterministically. This algorithm sweeps through directions analogously to the popular MCMC sweep methods for particle or spin indices. Direction-sweep MCMC can be applied to a wide range of reversible or non-reversible Markov chains, such as the Metropolis algorithm or the event-chain Monte Carlo algorithm. For a single two-dimensional tethered hard-disk dipole, we consider direction-sweep MCMC in the limit where restricted equilibrium is reached among the accessible configurations for a fixed direction before incrementing it. We show rigorously that direction-sweep MCMC leaves the stationary probability distribution unchanged and that it profoundly modifies the Markov-chain trajectory. Long excursions, with persistent rotation in one direction, alternate with long sequences of rapid zigzags resulting in persistent rotation in the opposite direction in the limit of small direction increments. The mapping to a Langevin equation then yields the exact scaling of excursions while the zigzags are described through a non-linear differential equation that is solved exactly. We show that the direction-sweep algorithm can have shorter mixing times than the algorithms with random updates of directions. We point out possible applications of direction-sweep MCMC in polymer physics and in molecular simulation.
Structural Changes in Resin-Based Composites in Saliva of Patients with Leukemia before Starting Chemotherapeutic Regimen

Abstract Background: The aim of this in vitro study was to assess the morphological characteristics and stability of dental composites immersed in saliva collected from patients with leukemia. Material and Methods: A total number of five patients without systemic disease and 20 patients with leukemia (acute lymphoblastic leukemia (ALL), acute myeloid leukemia (AML), chronic lymphocytic leukemia (CLL), and chronic myeloid leukemia (CML)) were included for saliva sampling. Composite disks were immersed in the leukemia, control, and artificial environments for 7 days. At the end of the experiment, atomic force microscopy (AFM), color stability (ΔE), and saliva elements analysis were performed. Statistical significance was considered for a p-value under 0.05. Results: The most changed surface resulted for ALL with a roughness that was almost double that of the untreated sample and was significantly increased compared to the healthy saliva. The effect of CLL was not as intense as observed for acute leukemia, but was significantly over the control. ALL seemed to modify structural components of the saliva, which were able to deteriorate the surface of the composite. ALL saliva promoted a significant dissolution of the initial feature of the samples and promoted nano-particle clusterization. All dental composites showed clinically acceptable color change values (ΔE < 3.3) in all four-leukemia salivas; CLL and CML showed large color differences for all composites. The total concentrations of P, Na, and K showed wide ranges of variations, while the coefficient of variation in Fe, Cu, and Mg showed narrow variations between the salvias’ investigated. The salivary concentration of zinc decreased considerably in the CLL and CML environments compared to the ALL and AML environments. Fe and Cu were significantly increased in the CML environment. Conclusions: Control and artificial salivas have a mild erosive effect on the surface of dental composites. The acute stage of the disease seems to deteriorate the surface roughness rather than its morphology, however, in the chronic stage, it is the surface morphology that mostly deteriorates.
Influence of Heat Input on Cold Metal Transfer Welded Joints

ABSTRACT During welding, the heat input is a critical parameter in determining the quality of the joints welded by any welding process. In the case of dissimilar welding, as dissimilar metals have significant differences in melting point, it is challenging to achieve an adequate joint. The emerging cold metal transfer welding process can resolve it effectively by controlling the heat while joining dissimilar metals. Therefore, in this research work, Aluminum-galvanized steel dissimilar joints were fabricated using varying heat inputs and their mechanical, metallurgical, and corrosion properties were evaluated. Furthermore, the second-phase formation at the weld interface has been investigated, and corrosion behavior is analyzed using electrochemical techniques in a 0.1% sodium chloride environment. The Tafel polarization and electrochemical impedance spectroscopy studies reveal it improved corrosion resistance due to an increase in heat input. The reduced solidification defects and the establishment of an appropriate intermetallic layer thickness with a suitable microstructure at the interface are the reasons for the improved corrosion resistance and strength of the dissimilar joints.
Oral Vancomycin Prophylaxis for Primary and Secondary Prevention of Clostridioides difficile Infection in Patients Treated with Systemic Antibiotic Therapy: A Systematic Review, Meta-Analysis and Trial Sequential Analysis

Background: Clostridioides difficile infection (CDI) is associated with substantial morbidity and mortality as well as high propensity of recurrence. Systemic antibiotic therapy (SAT) represents the top inciting factor of CDI, both primary and recurrent (rCDI). Among the many strategies aimed to prevent CDI in high-risk subjects undergoing SAT, oral vancomycin prophylaxis (OVP) appears promising under a cost-effectiveness perspective. Methods: A systematic review with meta-analysis and trial sequential analysis (TSA) of studies assessing the efficacy and the safety of OVP to prevent primary CDI and rCDI in persons undergoing SAT was carried out. PubMed and EMBASE were searched until 30 September 2021. The protocol was pre-registered on PROSPERO (CRD42019145543). Results: Eleven studies met the inclusion criteria, only one being a randomized controlled trial (RCT). Overall, 929 subjects received OVP and 2011 represented the comparator group (no active prophylaxis). OVP exerted a strong protective effect for CDI occurrence: odds ratio 0.14, 95% confidence interval 0.04–0.38. Moderate heterogeneity was observed: I2 54%. This effect was confirmed throughout several subgroup analyses, including prevention of primary CDI versus rCDI. TSA results pointed at the conclusive nature of the evidence. Results were robust to a variety of sensitivity and quantitative bias analyses, although the underlying evidence was deemed as low quality. No differences between the two groups were highlighted regarding the onset of vancomycin-resistant Enterococcus infections. Conclusions: OVP appears to be an efficacious option for prevention of CDI in high-risk subjects undergoing SAT. Nevertheless, additional data from RCTs are needed to establish OVP as good clinical practice and define optimal dosage and duration.
Improving Knowledge of Chicken Nugget Processing Using Animated Videos for Junior High School Students

The purpose of this study was to increase the knowledge of junior high school students regarding the processing of chicken nuggets in terms of knowledge of materials, equipment and stages of manufacture. The method used in this research is video animation. This method uses audio-visual so that it can increase students' interest in learning the processing of chicken nuggets. The approach used in this research is quantitative. The results showed that the students' knowledge about processing chicken nuggets increased. This can be seen from the students' post-test results increased by 31.25%. The animated video method given to students provides an explanation of the pictures of tools and materials as well as an explanation of the manufacturing process optimally. Therefore, students can understand the material well.
Adaptable buildings for sustainable built environment

Purpose – The purpose of this paper is to explore the ability of “adaptable buildings” to respond to future potential built environment changes in sustainable way. Design/methodology/approach – A detailed literature review and a case study were undertaken to identify the life cycle changes of typical buildings over a period of more than 100 years. In total, 12 semi-structured interviews were conducted among construction industry professionals to identify how adaptable buildings enhance sustainability within the built environment. Case study data were analysed through a Morphological Analysis, and the interview data were analysed through discourse analysis. Findings – Out of the many adaptable features, the results revealed “change of use” as the dominant trend within the buildings of the selected urban cluster. More than 60 per cent of buildings have changed their original use during their life cycle. Around 10 per cent of them have changed their use frequently (every six year) during the last 20 years th.
Docking and Molecular Dynamic of Microalgae Compounds as Potential Inhibitors of Beta-Lactamase

Bacterial resistance is responsible for a wide variety of health problems, both in children and adults. The persistence of symptoms and infections are mainly treated with β-lactam antibiotics. The increasing resistance to those antibiotics by bacterial pathogens generated the emergence of extended-spectrum β-lactamases (ESBLs), an actual public health problem. This is due to rapid mutations of bacteria when exposed to antibiotics. In this case, β-lactamases are enzymes used by bacteria to hydrolyze the beta-lactam rings present in the antibiotics. Therefore, it was necessary to explore novel molecules as potential β-lactamases inhibitors to find antibacterial compounds against infection caused by ESBLs. A computational methodology based on molecular docking and molecular dynamic simulations was used to find new microalgae metabolites inhibitors of β-lactamase. Six 3D β-lactamase proteins were selected, and the molecular docking revealed that the metabolites belonging to the same structural families, such as phenylacridine (4-Ph), quercetin (Qn), and cryptophycin (Cryp), exhibit a better binding score and binding energy than commercial clinical medicine β-lactamase inhibitors, such as clavulanic acid, sulbactam, and tazobactam. These results indicate that 4-Ph, Qn, and Cryp molecules, homologous from microalgae metabolites, could be used, likely as novel β-lactamase inhibitors or as structural templates for new in-silico pharmaceutical designs, with the possibility of combatting β-lactam resistance
Vehicle excess fuel consumption due to pavement deflection

The pavement structural rolling resistance (SRR) effect on vehicles' excess fuel consumption (EFC) was investigated. A practical approach was proposed to assess vehicle EFC due to pavement deflection based on the fundamental energy-deformation principles. The proposed model was formulated using a quadratic form of maximum pavement deflection, whose parameters are truck loading and speed and pavement temperature. The proposed model utilizes input used in the current AASHTOWare design methods. This allows the integration of the developed model in pavement design and performance prediction while used in pavement life cycle assessment (LCA). Sensitivity analysis showed the reasonableness of the model over a wide range of loading, temperature, and speed scenarios. The estimated EFC for a heavy truck ranged from 0.03% (half loaded, 0 °C, 115 km/h) and 6.5% (fully loaded, 40 °C, 8 km/h). The truck EFC is highly nonlinear and exponentially grows with decreasing speed and increasing temperature.
The importance of relational work design characteristics: A person-centred approach

Adopting a person-centred approach, we integrate the job demands-control-support model with relational work design theory to investigate employee work design profiles involving autonomy, workload, social support and prosocial characteristics (representing the combined influence of task significance and beneficiary contact). For a sample of Australian not-for-profit employees (N = 2421), we identified four work design profiles: ‘active connected’, ‘passive disconnected’, ‘high strain disconnected’ and ‘controlled disconnected’. The most favourable profile, active connected, demonstrated the highest vigour and social worth, and was predicted by people being in higher managerial positions and having permanent employment contracts. The high strain disconnected and controlled disconnected profiles were associated with greater psychological exhaustion. Longer working hours predicted membership of the high strain disconnected profile. JEL Classification: L31, L30, L20, L29
Effect of Biostimulants on the Yield and Quality of Selected Herbs

The aim of this study was to determine the effect of amino acid biopreparations on the yield of summer savory, marjoram, and lemon balm, and the concentrations of selected biochemical and mineral compounds in their herbage. The first experimental factor was plant species: summer savory (Satureja hortensis L.) var. Saturn, marjoram (Origanum majorana L.) var. Miraż, and lemon balm (Melissa officinalis L.). The second experimental factor was the effect exerted by two biopreparations, Calleaf Aminovital and Maximus Amino Protect, on herbage yield and quality. In the control treatment, plants were sprayed with water. The analyzed herb species differed considerably in yield and the concentrations of selected biochemical compounds and minerals. Lemon balm was characterized by the highest yield (1.73 kg m−2). Marjoram var. Miraż was characterized by the highest concentrations of reducing sugars (0.89 g 100 g−1 FM) and L-ascorbic acid (39.7 mg 100 g−1 FM). Summer savory was most abundant in total N, K, and Ca. The tested biostimulants contributed to a decrease in nitrate concentrations in the studied plants. The interaction between the experimental factors significantly affected the content of nitrates and mineral compounds and total N, P, K, and Ca in the herbage of the analyzed plant species.
A window of opportunity against diabetes: frequency of microvascular and macrovascular complications in prediabetes

Objectives: To determine the chronic complications of diabetes mellitus (DM) in patients with prediabetes, and to compare prediabetics with normoglycemic group participants in terms of the presence of the complications of DM. Methods: An observational study was conducted between December 2018 to April 2019. The patients aged 18-65 years were recruited from an internal medicine outpatient clinic of a tertiary care hospital. A total of 106 prediabetic patients and 54 normoglycemic subjects were included to the study. OGTT-0 th , OGTT-2 nd and HbA1c levels, lipid parameters, blood pressure, the homeostasis model assessment of insulin resistan (HOMA-IR), body mass index (BMI) were estimated. Nephropathy (urine protein/urine creatinine ratio, serum creatinine [sCre], Chronic Kidney Disease Epidemiology Collaboration [CKD-EPI] equation-- creatinine clearance), retinopathy by dilated fundus examination and neuropathy (10-g monofilament testing and electroneuromyography [ENMG]) were assessed. Results: Age, gender, BMI, HOMA-IR, smoking status, lipid parameters, systolic blood pressure were similar in both groups. The values of oral glucose tolerance test (OGTT)-0 th , OGTT-2 nd and glycated hemoglobin (HbA1c) were higher in prediabetics. Although not statistically significant, proteinuria was slightly more occurred in the prediabetics than the controls. sCre was significantly higher, and CKD-EPI equation was significantly lower in prediabetics than in controls ( p = 0.012, p = 0.001, respectively). We did not detected diabetic retinopathy in any participants. Neuropathy was slightly more occured in prediabetics, but it was not significantly different ( p = 0.309). There were no correlation between sCre, CKD-EPI, proteinuria and age, BMI, HOMA-IR, OGTT-0 th , OGTT-2 nd , and HbA1c. Conclusions: Managing the prediabetes by early diagnosis is very meaningful in terms of prevention from DM and its complications. So, prediabetes may be a window of opportunity for diabetes associated morbidity.
Specific of magneto-optical response of nanostructures with various shapes and sizes for magnetic memory elaboration

In this work it is established that for regularities of the magneto-optical response from curved magnetic nanosructures, a crossover occurs at certain scales. At scales less than characteristic length the normalized value of magneto-optical hysteresis loop for transverse magneto-optical Kerr effect does not depend on incident angle of electromagnetic radiation. For curved nanostructures at scales of the order or large than characteristic length and at certain incident angles, hysteresis loops were observed that are inherent in magnetic vortex structures. For systems based on nanometers thick cobalt films deposited on various nanostructured substrates the characteristic length is of about of 100 nm. On the basis of the experimental data the energy consumption for the formation of vortex structures is estimated.