Miracle-dz/UniFAR-FTUs huggingface dataset:
Comparing Fragment Binding PosesPrediction Using HSP90 as a Key Study: When Bound Water Makes the Difference

Fragment-Based Drug Discovery (FBDD) approaches have gained popularitynot only in industry but also in academic research institutes. However, the computational prediction of the binding mode adopted by fragment-like molecules within a protein binding site is still a very challenging task. One of the most crucial aspects of fragment binding is related to the large amounts of bound waters in the targeted binding pocket. The binding affinity of fragmentsmay not be sufficientto displace the bound water molecules. In the present work, we confirmed the importance of the bound water molecules in the correct prediction of the fragment binding mode. Moreover, we investigate whether the use of methods based on explicit solvent molecular dynamics simulations can improve the accuracy of fragment posing. The protein chosen for this study is HSP-90.
Validation of the Unesp-Botucatu composite scale to assess acute postoperative abdominal pain in sheep (USAPS)

A scale with robust statistical validation is essential to diagnose pain and improve decision making for analgesia. This blind, randomised, prospective and opportunist study aimed to develop an ethogram to evaluate behaviour and validate a scale to assess acute ovine postoperative pain. Elective laparoscopy was performed in 48 healthy sheep, filmed at one preoperative and three postoperative moments, before and after rescue analgesia and 24 hours after. The videos were randomised and assessed twice by four evaluators, with a one-month interval between evaluations. Statistical analysis was performed using R software and differences were considered significant when p <0.05. Based on the multiple association, a unidimensional scale was adopted. The intra- and inter-observer reliability ranged from moderate to very good (intraclass correlation coefficient ≥ 0.53). The scale presented Spearman correlations > 0.80 with the numerical, simple descriptive, and visual analogue scales, and a correlation of 0.48 with the facial expression scale. According to the mixed linear model, the scale was responsive, due to the increase and decrease in pain scores of all items after surgery and analgesic intervention, respectively. All items on the scale demonstrated an acceptable Spearman item-total correlation (0.56–0.76), except for appetite (0.25). The internal consistency was excellent (Cronbach's α = 0.81) and all items presented specificity > 0.72 and sensitivity between 0.61–0.90, except for appetite. According to the Youden index, the cut-off point was ≥ 4 out of 12, with a diagnostic uncertainty zone of 4 to 5. The area under the curve > 0.95 demonstrated the excellent discriminatory capacity of the instrument. In conclusion, the Unesp-Botucatu pain scale in sheep submitted to laparoscopy is valid, reliable, specific, sensitive, with excellent internal consistency, accuracy, discriminatory capacity, and a defined cut-off point.
The biological characteristics of Agriphila aeneociliella and methods for monitoring and managing this pest

[Objectives]In recent years,a new wheat insect pest has occurred in Laizhou(Shandong) and Zezhou(Shanxi),which has been identified as Agriphila aeneociliella.This paper seeks to determine its biological characteristics and provide a basis for population monitoring and management. [Methods]The biological characteristics of A.aeneociliella,including annual life history and habits of each life-stage,were studied by field investigation,net-room observation,pair feeding and adult light trapping. [Results]In the wheat planting area of the Huang-Huai-Hai plain,this insect pest has one generation annually.The larvae over-winter as 2-3 instar larvae from November to February,feed on wheat seedlings in March and April,live through summer as cocoons,in which old larvae diapause from May to August,until September when they pupate.From late September to early October,the adults emerge,mate and lay their eggs;the hatching young larvae are the overwintering form.The adults have phototaxis and are inclined to lay eggs in/on soil.The larvae prefer tender parts of plants and have a "spot-and-sheet" distribution in the field.The overwintering larvae have high cold resistance,but the dispausing cocoons can't survive water-logging. [Conclusion]Knowledge of the timing of adult emergence in autumn,the initial damage caused by larvae in early spring and the summer dispause are crucial for population monitoring and management of this insect pest.
Transcriptomic and Quantitative Proteomic Profiling Reveals Signaling Pathways Critical for Pancreatic Islet Maturation.

Pancreatic β-cell dysfunction and reduced insulin secretion play a key role in the pathogenesis of diabetes. Fetal and neonatal islets are functionally immature and have blunted glucose responsiveness and decreased insulin secretion in response to stimuli and are far more proliferative. However, the mechanisms underlying functional immaturity are not well-understood. Pancreatic islets are comprised of a mixture of different cell types and the microenvironment of islets and interactions between these cell types are critical for β-cell development and maturation. RNA-seq and quantitative proteomic data from intact islets isolated from fetal (e19) and 2-week old Sprague-Dawley rats were integrated in order to compare their gene and protein expression profiles. Ingenuity Pathway Analysis (IPA) was also applied to elucidate pathways and upstream regulators modulating functional maturation of islets. By integrating transcriptome and proteomic data, 917 differentially expressed genes/proteins were identified with a FDR <0.05. 411 and 506 of them were up- and down-regulated in 2-wk islets, respectively. IPA analysis revealed novel critical pathways associated with functional maturation of islets, such as AMPK and aryl hydrocarbon receptor signaling, as well as the importance of lipid homeostasis/signaling and neuronal function. Furthermore, we also identified many proteins enriched either in fetal or 2-wk islets related to extracellular matrix and cell communication suggesting that these pathways play critical roles in islet maturation. Our current study identified novel pathways for mature islet function in addition to confirming previously reported mechanisms and provided new mechanistic insights for future research on diabetes prevention and treatment.
Screening of Fish Cell Lines for Piscine Orthoreovirus-1 (PRV-1) Amplification: Identification of the Non-Supportive PRV-1 Invitrome

Piscine reovirus (PRV) is the causative agent of heart and skeletal muscle inflammation (HSMI), which is detrimental to Atlantic Salmon (AS) aquaculture, but so far has not been cultivatable, which impedes studying the disease and developing a vaccine. Homogenates of head kidney and red blood cells (RBC) from AS in which PRV-1 had been detected were applied to fish cell lines. The cell lines were from embryos, and from brain, blood, fin, gill, gonads, gut, heart, kidney, liver, skin, and spleen, and had the shapes of endothelial, epithelial, fibroblast, and macrophage cells. Most cell lines were derived from the Neopterygii subclass of fish, but one was from subclass Chondrostei. Cultures were examined by phase contrast microscopy for appearance, and by quantitative polymerase chain reaction (qPCR) for PRV-1 RNA amplification and for the capacity to transfer any changes to new cultures. No changes in appearance and Ct values were observed consistently or transferable to new cultures. Therefore, 31 cell lines examined were unable to support PRV-1 amplification and are described as belonging to the non-supportive PRV-1 invitrome. However, these investigations and cell lines can contribute to understanding PRV-1 cellular and host tropism, and the interactions between virus-infected and bystander cells.
The MAS-based Simulation of Bacterial Chemotaxis

Bacterial chemotaxis,such as Escherichia coli,is a typical case in signal transduction study.Acording to the biological phenomena and research progress of bacterial chemotaxis,the approach of MAS-based simulation of bacterial chemotaxis is presented in this paper by comparing with current approaches.The MAS-based simulation includes the simulation framework for signal transduction phenomena and the implementation process based on feedback agent stucture and multi-thread technology.At last an experiment for bacterial chemotaxis phenomena is designed based on the simulation framework,and the experiment result shows that this approach has good characteristics and broad application prospects in biological system simulations.
Polymorphisms of endothelial nitric oxide svnthase NOS3 4a/b and Hindm restriction site of the Y chromosome in essential hypertension

Objective To investigate the relationship to essential hypertension of NOS3 4a/b polymorphism and polymorphic Hind Ⅲ restriction site of the Y chromosome.Methods This study enrolled 345 young patients with essential hypertension and 281 young healthy subjects as controls.Genomic DNA was extracted from white blood cell.Segments of NOS3 and Y chromosome were amplified from genomic DNA by polymerase chain reaction(PCR). NOS3 PCR products were subjected to electrophoresis in 4% agarose gels.Y chromosome PCR products were restricted with HindⅢ at 37℃ and the digested products were subjected to electrophoresis on agarose gels and stained with ethidium bromide.Results The Hind Ⅲ (+)genotype was found in 55.4% of the patients with hypertension and in 67.3% of the controls.The frequency of Hind Ⅲ(-)genotype in the patients was significantly higher than that in the controls(P= 0.03). NOS3 4a/b allele and genotype frequencies did not differ significantly between the two groups(P 0.05). Conclusion Polymorphic Hind Ⅲ restriction site of the Y chromosome may be associated with essential hypertension.
DNA Damage Response and Immune Defense

DNA damage is the cause of numerous human pathologies including cancer, premature aging, and chronic inflammatory conditions. The DNA damage response (DDR), in turn, coordinates DNA damage checkpoint activation and promotes the removal of DNA lesions. In recent years, several studies have shown how the DDR and the immune system are tightly connected, revealing an important crosstalk between the two of them. This interesting interplay has opened up new perspectives in clinical studies for immunological diseases as well as for cancer treatment. In this review, we provide an overview, from cellular to molecular pathways, on how DDR and the immune system communicate and share the crucial commitment of maintaining the genomic fitness.
Vitrimer-Like Shape Memory Polymers: Characterization and Applications in Reshaping and Manufacturing

The shape memory effect (SME) refers to the ability of a material to recover its original shape, but only in the presence of a right stimulus. Most polymers, either thermo-plastic or thermoset, can have the SME, although the actual shape memory performance varies according to the exact material and how the material is processed. Vitrimer, which is between thermoset and thermo-plastic, is featured by the reversible cross-linking. Vitrimer-like shape memory polymers (SMPs) combine the vitrimer-like behavior (associated with dissociative covalent adaptable networks) and SME, and can be utilized to achieve many novel functions that are difficult to be realized by conventional polymers. In the first part of this paper, a commercial polymer is used to demonstrate how to characterize the vitrimer-like behavior based on the heating-responsive SME. In the second part, a series of cases are presented to reveal the potential applications of vitrimer-like SMPs and their composites. It is concluded that the vitrimer-like feature not only enables many new ways in reshaping polymers, but also can bring forward new approaches in manufacturing, such as, rapid 3D printing in solid state on space/air/sea missions.
Biomimetic Aspects of Oral and Dentofacial Regeneration

Biomimetic materials for hard and soft tissues have advanced in the fields of tissue engineering and regenerative medicine in dentistry. To examine these recent advances, we searched Medline (OVID) with the key terms “biomimetics”, “biomaterials”, and “biomimicry” combined with MeSH terms for “dentistry” and limited the date of publication between 2010–2020. Over 500 articles were obtained under clinical trials, randomized clinical trials, metanalysis, and systematic reviews developed in the past 10 years in three major areas of dentistry: restorative, orofacial surgery, and periodontics. Clinical studies and systematic reviews along with hand-searched preclinical studies as potential therapies have been included. They support the proof-of-concept that novel treatments are in the pipeline towards ground-breaking clinical therapies for orofacial bone regeneration, tooth regeneration, repair of the oral mucosa, periodontal tissue engineering, and dental implants. Biomimicry enhances the clinical outcomes and calls for an interdisciplinary approach integrating medicine, bioengineering, biotechnology, and computational sciences to advance the current research to clinics. We conclude that dentistry has come a long way apropos of regenerative medicine; still, there are vast avenues to endeavour, seeking inspiration from other facets in biomedical research.
Evolution of VOC and Sensory Characteristics of Stracciatella Cheese as Affected by Different Preservatives

Undesired volatile organic compounds (VOCs) can negatively affect the flavor of fresh food products; especially those characterized by a mild and delicate aroma. Finding connections between chemical and sensory analyses is a useful way to better understand the arising of off-flavors. A study was conducted on stracciatella; a traditional Italian cream cheese that is emerging on international markets. Samples were prepared by adding two different preservatives (alone or combined): sorbic acid and an olive leaf extract. Their influence on flavor preservation during refrigerated storage was investigated by chemical, microbiological and sensory analyses. A strong change of the VOC profile was ascertained after 8 days in the control cheese and in the sample added with leaf extract alone. The samples containing sorbic acid, alone or in combination with leaf extract, gave the best chemical and sensory results, demonstrating a significant shelf-life extension. In particular, these samples had lower concentrations of undesired metabolites, such as organic acids and volatiles responsible for off-flavor, and received better scores for odor and taste. Ex and Ex-So samples had significantly higher antioxidant activity than Ctr and So throughout the entire storage period, and the color parameter shows no differences among samples taken on the same day. The use of the olive leaf extract, at the concentration tested, seemed to be interesting only in the presence of sorbic acid due to possible synergic effect that mainly acted against Enterobacteriaceae.
Spontaneous Self-Assembly of Single-Chain Amphiphilic Polymeric Nanoparticles in Water

Single-chain polymeric nanoparticles (SCPNs) have great potential as functional nanocarriers for drug delivery and bioimaging, but synthetic challenges in terms of final yield and purification procedures limit their use. A new concept to modify and improve the synthetic procedures used to generate water-soluble SCPNs through amphiphilic interactions has been successfully exploited. We developed a new ultrahigh molecular weight amphiphilic polymer containing a hydrophobic poly(epichlorohydrin) backbone and hydrophilic poly(ethylene glycol) side chains. The polymer spontaneously self-assembles into SCPNs in aqueous solution and does not require subsequent purification. The resulting SCPNs possess a number of distinct physical properties, including a uniform hydrodynamic nanoparticle diameter of 10–15 nm, extremely low viscosity and a desirable spherical-like morphology. Concentration-dependent studies demonstrated that stable SCPNs were formed at high concentrations up to 10 mg/mL in aqueous solution, with no significant increase in solution viscosity. Importantly, the SCPNs exhibited high structural stability in media containing serum or phosphate-buffered saline and showed almost no change in hydrodynamic diameter. The combination of these characteristics within a water-soluble SCPN is highly desirable and could potentially be applied in a wide range of biomedical fields. Thus, these findings provide a path towards a new, innovative route for the development of water-soluble SCPNs.
Defining Pre-Clinical Psoriatic Arthritis in an Integrated Dermato-Rheumatology Environment

In excess of three quarters of patients with psoriatic arthritis (PsA) have preceding psoriasis (PsO), which offers a clinical biomarker for the recognition of early PsA. Numerous surveys have shown a remarkably high frequency of clinically occult musculoskeletal symptoms in psoriasis patients. Imaging studies, particularly ultrasound, show a high prevalence of subclinical enthesitis and other inflammatory changes in psoriasis subjects. Since a serum biomarker, such as the case of anti-citrullinated protein antibodies (ACPA) in rheumatoid arthritis, neither exists nor seems biologically plausible at this point, this article explores how integration of rheumatological and dermatological assessment can be facilitated for the early recognition of potential PsA. Given that scalp disease is a PsA predictor, but may be managed in the community, then a particular need to access this group is needed. An integrated approach between rheumatology and dermatology can involve joint clinics, parallel clinics with discussion of relevant cases or virtual contact between specialties. Early therapy evaluation and integrated strategies have considerable implications for minimizing suffering and joint damage in PsA.
TSOL18 vaccine and oxfendazole for control of Taenia solium cysticercosis in pigs: A field trial in endemic areas of Tanzania

A field trial was conducted in Tanzania to determine the effectiveness of TSOL18 vaccine used concurrently with oxfendazole (OFZ), and of OFZ alone, on T. solium cysticercosis determined by organ and half carcase dissection of slaughter age pigs. This study followed a quasi-experimental group design. Suitable trial sites were randomly allocated to either treatment group T1 (OFZ treatment alone [30mg/kg, Paranthic 10%]) or T2 (TSOL18 [1ml, Cysvax] plus OFZ). Three 4-monthly treatments were administered to eligible pigs. A random selection of pigs were necropsied at baseline and at endline, 2–3.5 months after the final treatment. Additionally, untreated pigs from T1 and T2 areas were necropsied at endline to provide contemporaneous comparisons with T1 and T2 pigs. Baseline prevalence of viable T. solium cysticerci for T1 was 25.5% (Exact 95% CI: 13.9, 40.3; n = 12/47), and for T2 was 12.0% (CI: 6.4, 20.0; n = 12/100). At endline, prevalence was 2.8% for T1 (CI: 0.1, 14.5, n = 1/36) and 0% for T2 (CI: 0, 4.7, n = 0/77). Among untreated pigs, three had viable cysticerci, one from T1 area (12.5%, CI: 0.3, 52.7; n = 1/8) and two from T2 area (5.7%, CI: 0.7, 19.2, n = 2/35). Fisher’s exact test showed significant changes in prevalence from baseline to endline in both groups (T1: p = 0.005, T2: p = 0.001). Firth’s penalized Maximum Likelihood method suggested the changes were not significant relative to their controls (T1: p = 0.245, T2: p = 0.076). These findings showed a significant reduction in the prevalence of viable cysticerci from baseline to endline after both interventions. However, the changes could not be definitively attributed to the interventions due, in part, to small numbers of control pigs. Concurrent administration of the TSOL18 and OFZ cleared infection among assessed pigs whereas infection remained after treatment with OFZ only. Further studies including larger sample sizes would be required for more definitive conclusions. A One Health approach is recommended for rapid and sustainable impact.
Physiological changes in retinal layers thicknesses measured with swept source optical coherence tomography

Purpose To evaluate the physiological changes related with age of all retinal layers thickness measurements in macular and peripapillary areas in healthy eyes. Methods Wide protocol scan (with a field of view of 12x9 cm) from Triton SS-OCT instrument (Topcon Corporation, Japan) was performed 463 heathy eyes from 463 healthy controls. This protocol allows to measure the thickness of the following layers: Retina, Retinal nerve fiber layer (RNFL), Ganglion cell layer (GCL +), GCL++ and choroid. In those layers, mean thickness was compared in four groups of ages: Group 1 (71 healthy subjects aged between 20 and 34 years); Group 2 (65 individuals aged 35–49 years), Group 3 (230 healthy controls aged 50–64 years) and Group 4 (97 healthy subjects aged 65–79 years). Results The most significant thinning of all retinal layers occurs particularly in the transition from group 2 to group 3, especially in temporal superior quadrant at RNFL, GCL++ and retinal layers (p≤0.001), and temporal superior, temporal inferior, and temporal half in choroid layer (p<0.001). Curiously group 2 when compared with group 1 presents a significant thickening of RNFL in temporal superior quadrant (p = 0.001), inferior (p<0.001) and temporal (p = 0.001) halves, and also in nasal half in choroid layer (p = 0.001). Conclusions Excepting the RNFL, which shows a thickening until the third decade of life, the rest of the layers seem to have a physiological progressive thinning.
Self-perception of shyness and its relation to aspects of public speaking.

PURPOSE To determine the prevalence of shyness in university students and to analyze among the sociodemographic and public communication factors, those that are most related to their presence. METHOD A cross-sectional analytical study was carried out with 1124 university students aged between 17 and 63 years old. It was used a questionnaire with questions related to sociodemographic characteristics; frequency of participation in public speaking activities; self-report of fear of speaking; self-perception of non-verbal aspects of oral communication: tone of voice, speed of speech, voice intensity, vocal projection, eye contact with the audience during the speech, use hands in public presentations; self-assessment of public speaking (Scale for Self-Assessment in Public Speaking) and self-perception of shyness (Revised Shyness Scale). The analysis of factors associated with shyness and with the other variables was performed by Pearson's chi-square test and univariate and multivariate logistic regression. The level of significance adopted was 5%. RESULTS The majority of the university population self-reported traces of shyness and fear of speaking in public. There was an association of shyness with the age of 17 to 30 years, fear of speaking in public, little participation in public speaking activities, negative self-perception of speech and with non-verbal communication aspects. CONCLUSION Shyness is prevalent in young university students, who participate in few public speaking activities, who are afraid to speak in public, self-report speaking at low intensity and who are unable to use their hands naturally during public presentations.