Miracle-dz/UniFAR-FTUs huggingface dataset:
Sortase A: A chemoenzymatic approach for the labeling of cell surfaces

Sortase A, a transpeptidase enzyme is present in many Gram‐positive bacteria and helps in the recruitment of the cell surface proteins. Over the last two decades, Sortase A has become an attractive tool for performing in vivo and in vitro ligations. Sortase A‐mediated ligation has continuously been used for its specificity, robustness, and highly efficient nature. These properties make it a popular choice among protein engineers as well as researchers from different fields. In this review, we give an overview of Sortase A‐mediated ligation of various molecules on the cell surfaces, which can have diverse applications in interdisciplinary fields.
Entropy drives protein conformational distributions in native globular proteins

Protein conformational transitions, which are essential for function, may be driven either by entropy or enthalpy when molecular systems comprising solute and solvent molecules are the focus[1, 2]. Revealing thermodynamic origin of a given molecular process is an important but difficult task, and general principles governing protein conformational distributions remain elusive. Here we demonstrate that when protein molecules are taken as thermodynamic systems and solvents being treated as the environment, conformational entropy is an excellent proxy for free energy and is sufficient to explain protein conformational distributions. Specifically, by defining each unique combination of side chain torsional state as a conformer, the population distribution (or free energy) on an arbitrarily given order parameter is approximately a linear function of conformational entropy. Additionally, span of various microscopic potential energy terms is observed to be highly correlated with both conformational entropy and free energy. Presently widely utilized free energy proxies, including minimum potential energy[3, 4, 5], average potential energy terms by themselves[6] or in combination with vibrational entropy[7], are found to correlate with free energy rather poorly. Therefore, our findings provide a fundamentally new theoretical base for development of significantly more reliable and efficient next generation computational tools, where the number of available conformers, rather than poential energy of microscopic configurations, is the central focus. We anticipate that many related research fields, including structure based drug design and discovery, protein design, docking and prediction of general intermolecular interactions involving proteins, are expected to benefit greatly.
IN SILICO ANALYSIS OF THE LETTUCE (Lactuca sativa L.) MADS-BOX GENE FAMILY ANÁLISE IN SILICO DOS GENES DA FAMÍLIA MADS-BOX EM ALFACE (Lactuca sativa L.) ANÁLISIS IN SILICO DE LOS GENES DE LA FAMILIA MADS-BOX EN LECHUGA (Lactuca sativa L.)

High temperatures can negatively affect lettuce production by promoting early bolting, which leads to increased levels of latex accumulation in the leaves, causing them to become bitter. The lack of adaptation of this culture to such conditions made it an object of study for plant breeding programs, resulting in well succeeded studies. However, little is known about the genes that regulate lettuce flowering. A better understanding of the complex genic interactions involved in the process of lettuce floral initiation is of great importance, since it can enable the development of late-bolting cultivars through plant genetic transformation. MADS-box transcriptional factors are key flowering regulators and have been extensively studied during the flowering process in several species. Thus, this study aimed to identify and characterize the Lettuce MADS-box gene family through the use of bioinformatics tools. The computational analysis consisted in gene prediction, alignment, and phylogenetic analysis. 91 sequences of putative MADS-box genes were identified and characterized by a phylogenetic study of 20 MADS-box genes. Future studies comprising mutants for these genes in plant model species and in lettuce will enable a better understanding of the functions performed by these genes during lettuce flowering, as well as, a better comprehension of this process.
Use of Functional Response Modeling to Evaluate the Effect of Temperature on Predation of Amblyseius swirskii (Acari: Phytoseiidae) Adults Preying on Tetranychus urticae (Acari: Tetranychidae) Nymphs

Abstract In this research, functional responses of Amblyseius swirskii Athias-Henriot preying on different Tetranychus urticae Koch nymphal densities (2, 4, 8, 16, 32, 64, and 128) were studied at eight constant temperatures (15, 20, 25, 27.5, 30, 32.5, 35 and 37.5°C) in a circular Petri dish (3-cm diameter × 1-cm height) under lab conditions. At all temperatures, the logistic regression showed a type II functional response. A nonlinear relationship was found between temperature and attack rate and the reciprocal of handling time. The reciprocal of handling time decreased exponentially with increasing temperature. In contrast, the attack rate grew rapidly with increasing temperatures up to an optimum, showing a decreasing trend at higher temperatures. In order to quantify the functional response of A. swirskii over a broad range of temperatures and to gain a better estimation of attack rate and handling time, a temperature-settled functional response equation was suited to our data. Our model showed that the number of prey consumed increased with rising prey density. Also, the predation rates increased with increasing temperatures but decreased at extremely high temperatures. Based on our model, the predation rate begins at the lower temperature threshold (11.73°C) and reaches its peak at upper temperature threshold (29.43°C). The coefficient of determination (R2) of the random predator model was 0.99 for all temperatures. The capability of A. swirskii to search and consume T. urticae over a wide range of temperatures makes it a good agent for natural control of T. urticae in greenhouses.
Color values models for determination of citric acid in pineapple

Citric acid is important chemical properties of pineapple which is used for deciding quality in pineapple industry. Nowadays titratable acidity analysis is standard method for determination of citric acid. This method is difficultly, used long time and destectively. This research aims to study establishment of color value models for determination of citric acid in pineapple. The 225 samples of Smooth Cayenne (Pattavia) pineapple were collected from difference markets around Chonburi province (100 samples) and commercial orchard at 5 difference maturity (125 samples). Color values of pineapple flesh were recorded on CIE system (L*, a* and b* values). Citric acid was measured by AOAC titratable analysis. Multiple linear regressions (MLR) were used to establish color values models for determination of citric acid. The best prediction results showed that r val was 0.63; SEP was 0.11 and bias was -0.01. This finding indicates possibility of application of color of pineapple flash to evaluate citric acid of pineapple.
Characterization of volatile compounds in pickled and dried mustard (Brassica juncea, Coss.) using optimal HS-SPME-GC-MS

ABSTRACT Pickled and dried mustard (PDM; Brassica juncea, Coss) is a traditional fermented vegetable product that is widely consumed as a food ingredient with aromatic flavour in China. Here, we aimed to determine the volatile compounds in PDM by headspace solid-phase micro-extraction combined with gas chromatography-mass spectrometry (HS-SPME-GC-MS). The results showed that a total of 41 volatile compounds were identified and quantified in PDM by optimized HS-SPME-GC-MS. Approximately 15 compounds were considered to be the dominant volatile compounds in PDM with relatively high concentrations. These findings make the volatile composition characteristics in PDM clear for the first time.
Systematic review and meta-analysis on efficacy of traditional Chinese medicine for atrial fibrillation through cluster analysis.

BACKGROUND Traditional Chinese medicine (TCM) has shown excellent therapeutic effects in the treatment of heart diseases. This meta-analysis was to evaluate the therapeutic effects of TCM on patients with atrial fibrillation (AF). METHODS Four databases were searched from their establishment to 1 April 2021 for randomized controlled trials (RCTs) on the treatment of AF using TCM. The Cochrane Handbook 5.0. 2 was used to perform to bias risk assessment, and RevMan 5.3 was used for meta-analysis. RESULTS A total of 7 references were included. It was found that compared with conventional Western medicine, the effective rate of TCM or the combined therapy of TCM and Western medicine was higher [mean difference (MD) =1.85; 95% confidence interval (CI): 1.28 to 2.68; Z=3.26; P=0.001]; the success rate of conversion was increased (MD =1.58; 95% CI: 1.02 to 2.44; Z=2.06; P=0.04), the conversion time was shortened (MD =-224.82; 95% CI: -262.56 to -187.08; Z=11.68; P<0.00001), the incidence of adverse reactions was reduced (MD =0.62; 95% CI: 0.40 to 0.97; Z=2.11; P=0.03). DISCUSSION The use of TCM to treat AF can improve clinical treatment efficiency, increase the success rate of conversion, and shorten the conversion time. Compared with conventional Western medicine, the combined therapy demonstrated better therapeutic effects.
The clinical efficacy of Er:YAG lasers in the treatment of peri-implantitis: a systematic review and meta-analysis.

BACKGROUND Erbium-doped yttrium aluminum garnet (ER:YAG) lasers have been used to treat peri-implant, but there are some disputes. To dispel these negative views, our study aims to compare the efficacy and safety of Er:YAG lasers versus conventional mechanical debridement in the treatment of peri-implantitis. METHODS Seven databases were used to search for relevant studies and full-text articles which evaluate the comparisons of Er:YAG lasers and mechanical debridement for patients with peri-implantitis. Review Manager 5.4 was employed to assess the effects of the results among the selected studies. Forest plots, subgroup analyses, and on the included articles were also completed. Cochrane risk of bias assessment tool was used to assess the risk of bias. RESULTS Our study focused on 10 previously conducted studies which included 294 patients with peri-implantitis and a total of 461 implants. No significant differences in clinical attachment level (CAL) (MD =0.17, P=0.25, at 6 months; MD =0.23, P=0.15, at 12 months), reduction in bleeding on probing (BOP) (MD =9.54%, P=0.18, at 6 months; MD =11.28%, P=0.24, at 12 months), or plaque index (PI) (MD =-0.02, P=0.75, at 6 months; MD =-0.07, P=0.66, at 12 months) were observed between the Er:YAG laser group and the mechanical debridement group. However, in reducing probing depth (PD) (MD =0.28, P=0.03, at 6 months; MD =0.35, P=0.002, at 12 months) and gingival recession (GR) changes (MD =-0.12, P=0.04, at 6 months; MD =-0.16, P=0.03, at 12 months), the Er:YAG laser group showed some advantages at 6-month and 12-month intervals following treatment. No significant publication bias existed in our meta-analysis by using funnel plot and Egger's test (PD: P=0.65; CAL: P=0.73). DISCUSSION Our research supported the premise that Er:YAG lasers offer health benefits to patients with peri-implantitis and can effectively reduce PD and GR. Due to the limitations of the included studies, further studies should be carried out to validate our findings.
Thermal Profile of Pulse Precision Capsulotomy: In Vivo and In Vitro Infrared Thermography Study

Purpose This study aimed to elucidate the thermal safety of precision pulse capsulotomy (PPC) via in vivo and in vitro evaluation of the thermal profile using infrared thermography. Methods This prospective observational study enrolled 15 eyes from 15 participants who underwent cataract surgery using the Zepto PPC. All patients underwent temperature measurements of the incision site and the entire cornea using an infrared thermographer during the capsulotomy procedure. To accurately analyze the temperature change of the Zepto PPC, infrared thermography was performed with the Zepto handpiece while exposed to air and then in porcine eyes. Moreover, in each case, the difference in temperature change according to the use of an ophthalmic viscosurgical device (OVD) was also checked to determine the temperature buffering effect. Results In the clinical evaluations, the mean temperature elevation around the corneal incision and time duration from baseline to peak temperature during the Zepto capsulotomy were 4.0°C ± 1.9°C and 4.43 ± 1.26 seconds, respectively, with a mean peak temperature of 32.6°C ± 2.0°C. The mean peak temperature and rise time of the naïve Zepto nitinol ring, as measured from the bottom side, were 109.0°C ± 22.9°C and 43.40 ± 11.06 seconds in the experimental procedures, respectively. In the porcine eyes, the mean elevation of temperature and rise time of the Zepto nitinol ring were 6.2°C ± 1.6°C and 11.67 ± 2.08 seconds with the use of OVDs, and 10.5°C ± 3.3°C and 14.00 ± 3.61 seconds without OVDs, respectively. Conclusions Zepto PPC has the potential to generate extremely high thermal energy, according to an in vitro study. However, the temperature rise of the Zepto capsulotomy can be minimized by using OVDs.
Meta-Analysis of Human Molecular Responses to Staphylococcus aureus

including impetigo, folliculitis, cellulitis, infected ulcers, wounds, respiratory diseases and food poisoning. The severity of S. aureus infections can range from mild local to severe deeper soft tissue infections requiring hospitalization. Many antibiotics have been designed to target the bacterial wall synthesis. However, antibiotic-resistant forms of pathogenic S. aureus, e.g. methicillin-resistant S. aureus (MRSA), have become a widespread clinical problem. S. aureus produce enzymes that protect it from degradation and have acquired two types of strategies to avoid killing by host immune cells. S. aureus infection activates cell growth and metabolic pathways, which provides a rich growth environment. It activates anti-apoptotic protein transcription to decrease apoptosis of the infected 1 cells. S. aureus and associated toxins are recognized by a Introduction Staphylococcus aureus (S. aureus) is a gram-positive bacterium found as part of normal flora in 50% of population. It is a common cause of skin infections Meta-Analysis of Human Molecular Responses to Staphylococcus aureus
Factors predicting technical difficulties during endoscopic submucosal excavation for gastric submucosal tumor

Objective Endoscopic submucosal excavation (ESE) has been established as an effective method for removal of gastric submucosal tumors (SMTs). The aim of the present study was to explore risk factors for technical difficulties in ESE. Methods In this retrospective study, we collected clinical data from patients who underwent ESE for gastric SMTs. Difficult ESE was defined as a procedure time ≥90 minutes, piecemeal resection, and/or occurrence of major adverse events. Univariate and multivariate analyses were performed to explore the risk factors for a difficult ESE. Results ESE was successfully performed in 96.5% (195/202) of patients from April 2011 to December 2019. The average tumor size was 17.41 mm, and en bloc resection was achieved in 97.4% of patients (190/195). Five patients (2.56%, 5/195) had complications, including two with delayed bleeding, two with fever, and one with chest pain accompanying ST-T changes in an electrocardiogram. Twenty-four patients (11.88%, 24/202) had a difficult ESE. Logistic analysis showed that outgrowth behavior and an inexperienced surgeon were risk factors for a difficult ESE. Conclusion ESE may be safe and effective to treat patients with gastric SMTs. Outgrowth behavior and an inexperienced surgeon were risk factors for a difficult ESE.
Drug evaluation based on phosphomimetic PDHA1 reveals the complexity of activity-related cell death in A549 non-small cell lung cancer cells

Cancer cells predominantly generate energy via glycolysis, even in the presence of oxygen, to support abnormal cell proliferation. Suppression of PDHA1 by PDK1 prevents the conversion of cytoplasmic pyruvate into Acetyl-CoA. Several PDK inhibitors have been identified, but their clinical applications have not been successful for unclear reasons. In this study, endogenous PDHA1 in A549 cells was silenced by the CRISPR/Cas9 system, and PDHA1WT and PDHA13SD were transduced. Since PDHA13SD cannot be phosphorylated by PDKs, it was used to evaluate the specific activity of PDK inhibitors. This study highlights that PDHA1WT and PDHA13SD A549 cells can be used as a cell-based PDK inhibitor-distinction system to examine the relationship between PDH activity and cell death by established PDK inhibitors. Leelamine, huzhangoside A and otobaphenol induced PDH activity-dependent apoptosis, whereas AZD7545, VER-246608 and DCA effectively enhanced PDHA1 activity but little toxic to cancer cells. Furthermore, the activity of phosphomimetic PDHA1 revealed the complexity of its regulation, which requires further in-depth investigation.
Assessing the feasibility of a directional CRNS-sensor for estimating soil moisture

Cosmic Ray Neutron Sensing (CRNS) is a non-invasive tool for measuring hydrogen pools like soil moisture, snow, or vegetation. The intrinsic integration over a radial hectare-scale footprint is a clear advantage for averaging out small-scale heterogeneity, but on the other hand the data may become hard to interpret in complex terrain with patchy land use. This study presents a directional shielding approach to block neutrons from certain directions and explores its potential to gain a sharper view on the surrounding soil moisture distribution. 5 Using the Mont-Carlo code URANOS, we modelled the effect of additional polyethylene shields on the horizontal field of view and assessed its impact on the epithermal count rate, propagated uncertainties, and aggregation time. The results demonstrate that directional CRNS measurements are strongly dominated by isotropic neutron transport, which dilutes the signal of the targeted direction especially from the far field. For typical count rates of customary CRNS stations, directional shielding of halfspaces could not lead to acceptable precision at a daily time resolution. However, the mere statistical 10 distinction of two rates should be feasible.
Learning-by-Teaching Approach Improves Dengue Knowledge in Children and Parents

ABSTRACT. There is narrow evidence on which strategies are most effective for disseminating information on dengue prevention. This is particularly relevant because social habits have a great prevention capacity for dengue. We investigated how effective are children as health educators, and how much they learn as they teach. We recruited 142 children and 97 parents in Argentina’s tropical area for two cluster randomized parallel trials. In Study 1, we compared the dynamics of dengue knowledge of 10-year-old children who—after receiving a dengue talk—1) listened to an unrelated topic; 2) read a booklet with information about dengue, 3) taught their parents about dengue, or 4) taught their parents about dengue, using the booklet. In Study 2, we assessed whether the parents’ dengue knowledge changed after interacting with their children, in comparison with parents learning about dengue from an expert or about an unrelated topic. Children that taught their parents what they learned, using a booklet, showed 2.53 more correct responses (95% CI [0.20, 4.85]; P = 0.027) than children who listened to an unrelated topic. This style of teaching also serves to effectively propagate knowledge: parents learned from their children the same as from an expert; and significantly more than parents who learned about an unrelated topic. Parents learned from their children even if they were taught with booklets (1.49, 95% CI [0.01, 2.96]; P = 0.048) or without (1.94, 95% CI [0.44, 3.44]; P = 0.006). Specifically, after being taught by their children, parents showed on average 1.49 (if they were taught with a booklet) and 1.94 (without booklet) more correct responses than parents that learned about an unrelated topic. The simple action of prompting children to teach consolidated their own knowledge and broadcasted it effectively to their parents. This strategy is a potential low to no-cost method for sharing information about dengue prevention.
INTEGRATION AS A MULTI-WAY PROCESS: A CASE STUDY OF INNOVATIVE MIGRANT INTEGRATION PROJECTS IN SLOVENIA

This article explores innovative EU-funded migrant integration projects which emerged in Slovenia after the 2008 global economic crisis. It stems from sociological literature that conceptualises integration as a general societal phenomenon that shields against precarity. By conducting qualitative interviews with those running the studied projects and other stakeholders, this article explores the projects’ drivers, tactics, and their impact on established institutions. The findings show that the projects were established by proactive activists who utilised EU funds to professionalise their activities and engage in partnerships to develop needs-based, cross-sectional and networked provision that empowers migrants and benchmarks professional norms and standards for migrant integration. Its specific contribution lies in uncovering a multi-way integration process that moves away from mainstream approaches to integration, which segregate and demand change only from migrants, and also includes public institutions and servants, professionals and host societies as a whole.
Reasoning Paths Generation for Commonsense Question Answering

Commonsense question answering (QA) requires a model to acquire some necessary background knowledge about how the world operates and people interact with each others. A large number of works have been dedicated to resort the help from commonsense knowledge graphs. However, these methods do not consider the context of the questions while retrieving evidence from knowledge graphs. Moreover, knowledge graphs are known to be far from complete and might not contain the necessary knowledge for answering the questions. In this paper, we propose to learn a reasoning paths generator to generate structured evidence dynamically according to the questions. Our generator uses pre-trained language model as the backbone, leveraging the tremendous unstructured knowledge stored in the language model to alleviate the incompleteness of knowledge graph. In addition, we pro-pose to further train our whole framework to solve downstream tasks in a end-to-end fashion, greatly adjusting our generator to better serve the QA system. We further conduct experiments on commonsense QA dataset to demonstrate the effectiveness of our method.