Miracle-dz/UniFAR-FTUs huggingface dataset:
MODELLING AND LIGAND INTERACTION STUDIES OF ENDO-1,4-BETA-XYLANASE FROM BACILLUS SUBTILIS

Xylanase is the name given to a class of enzymes which degrade the linear polysaccharide beta-1,4- xylan into xylose, thus breaking down hemicellulose, which is a major component of the cell wall of plants. The sequence of Xylanase from Bacillus subtilis was obtained from NCBI. The predicted domain was searched to find out the related protein structure to be used as a template by the Basic Local Alignment Search Tool (BLAST) program against Protein Databank (PDB). Sequence that showed maximum identity with high score and less e-value was aligned and used as a reference structure to build a 3D model for Xylanase. In order to understand the mechanisms of ligand binding and the interaction between the ligand and the Xylanase a three-dimensional (3D) model of the Xylanase is generated based on the crystal structure of the Template by using the Modeller. With the aid of the molecular mechanics and molecular dynamics methods, the final refined model is obtained and is further assessed by Profile-3D, which shows that the refined model is reliable. With this model, a flexible docking study is performed with the acetate ion as ligand. After the docking studies, important determined residues in binding are identified. The hydrogen bonds play an important role for the stability of the complex. These results may be helpful for further experimental investigations.
Comparison of two types of alginate microcapsules on stability and biocompatibility in vitro and in vivo

Transplantation of encapsulated living cells is a promising approach for the treatment of a wide variety of diseases, especially diabetes. Range-scale application of the technique, however, is hampered by insufficient stability of the capsules. It is difficult to find the optimal membrane to meet all the properties required for cell transplantation. To overcome these difficulties, it is necessary to compare characteristics such as mechanical strength, cell proliferation and biocompatibility of different membranes. We prepared Ca–alginate–poly-L-lysine–alginate (APA) and Ba–alginate–poly-L-lysine–alginate (BPA) microcapsules using the electrostatic droplet method. The integrity of the microcapsules was measured by suspending them in a saline buffer and shaking at 150 rpm for 48 h. The microcapsules were cultured in simulated body fluid to analyze the osmotic pressure stability and implanted in the leg muscle pouch of SD rats to test in vivo transplantation stability. The microcapsules were implanted in the intraperitoneal cavity; then the biocompatibility of microcapsules was identified through analyzing fibrosis formation of microcapsules. The proliferation of cells (Cos-7 and HL-60) cultured in the microcapsules was measured by MTT assay. After 48 h shaking at 150 rpm, the percentages of intact microcapsules of BPA and APA microcapsules were 98.5 ± 0.248% and 95.7 ± 0.221% (p < 0.05), respectively. The intact percentages of APA and BPA microcapsules were 96.9% and 97.7%, respectively, after being soaked in SBF at 37 °C for 15 days. The empty APA and BPA microcapsules were not adhered to the muscle and there was light cellular overgrowth. There is no difference on biocompatibility in implantation into peritoneal cavities. After the cells were cultured in microcapsules, A490 nm of the 8th week was significantly higher than that of 1 day, and the 4th week was at the peak of the cell proliferation curve. After culture for 2 to 6 weeks, spheroids started to develop gradually within the beads. The mechanical strength of BPA microcapsules was higher than that of APA microcapsules. However, there was no difference between the two kinds of capsules in biocompatibility. Microencapsulation did not affect cell proliferation or increase the quantity of cells. In conclusion, BPA microcapsules were more suitable for transplantation in vivo.
Analysis of Human C1q by Combined Bottom-up and Top-down Mass Spectrometry

C1q is a subunit of the C1 complex, a key player in innate immunity that triggers activation of the classical complement pathway. Featuring a unique structural organization and comprising a collagen-like domain with a high level of post-translational modifications, C1q represents a challenging protein assembly for structural biology. We report for the first time a comprehensive proteomics study of C1q combining bottom-up and top-down analyses. C1q was submitted to proteolytic digestion by a combination of collagenase and trypsin for bottom-up analyses. In addition to classical LC-MS/MS analyses, which provided reliable identification of hydroxylated proline and lysine residues, sugar loss-triggered MS3 scans were acquired on an LTQ-Orbitrap (Linear Quadrupole Ion Trap-Orbitrap) instrument to strengthen the localization of glucosylgalactosyl disaccharide moieties on hydroxylysine residues. Top-down analyses performed on the same instrument allowed high accuracy and high resolution mass measurements of the intact full-length C1q polypeptide chains and the iterative fragmentation of the proteins in the MSn mode. This study illustrates the usefulness of combining the two complementary analytical approaches to obtain a detailed characterization of the post-translational modification pattern of the collagen-like domain of C1q and highlights the structural heterogeneity of individual molecules. Most importantly, three lysine residues of the collagen-like domain, namely Lys59 (A chain), Lys61 (B chain), and Lys58 (C chain), were unambiguously shown to be completely unmodified. These lysine residues are located about halfway along the collagen-like fibers. They are thus fully available and in an appropriate position to interact with the C1r and C1s protease partners of C1q and are therefore likely to play an essential role in C1 assembly.
Absolute Cardiovascular Disease Risk and Shared Decision Making in Primary Care: A Randomized Controlled Trial

PURPOSE We wanted to determine the effect of promoting the effective communication of absolute cardiovascular disease (CVD) risk and shared decision making through disseminating a simple decision aid for use in family practice consultations. METHODS The study was based on a pragmatic, cluster randomized controlled trial (phase III) with continuing medical education (CME) groups of family physicians as the unit of randomization. In the intervention arm, 44 physicians (7 CME groups) consecutively recruited 550 patients in whom cholesterol levels were measured. Forty-seven physicians in the control arm (7 CME groups) similarly included 582 patients. Four hundred sixty patients (83.6%) of the intervention arm and 466 patients (80.1%) of the control arm were seen at follow-up. Physicians attended 2 interactive CME sessions and received a booklet, a paper-based risk calculator, and individual summary sheets for each patient. Control physicians attended 1 CME-session on an alternative topic. Main outcome measures were patient satisfaction and participation after the index consultation, change in CVD risk status, and decisional regret at 6 months’ follow-up. RESULTS Intervention patients were significantly more satisfied with process and result (Patient Participation Scale, difference 0.80, P<.001). Decisional regret was significantly lower at follow-up (difference 3.39, P = .02). CVD risk decreased in both groups without a significant difference between study arms. CONCLUSION A simple transactional decision aid based on calculating absolute individual CVD risk and promoting shared decision making in CVD prevention can be disseminated through CME groups and may lead to higher patient satisfaction and involvement and less decisional regret, without negatively affecting global CVD risk.
Asymptotic Analysis of Large Auctions

We study private-value auctions with a large number of bidders. We calculate approximations of the equilibrium bids and the seller's revenue in first-price auctions regardless of whether the bidders are symmetric or asymmetric, or risk-neutral or risk-averse. Furthermore, we show that first-price auctions with asymmetric bidders, or risk-averse bidders, are asymptotically revenue equivalent to wide classes of standard auctions.
Monitoring cytomegalovirus IE‐1 and pp65‐specific CD4+ and CD8+ T‐cell responses after allogeneic stem cell transplantation may identify patients at risk for recurrent CMV reactivations

We studied the recovery of CMV‐specific CD4+ and CD8+ T‐cell immunity in 52 recipients of allogeneic stem cell transplantation (SCT). The proportions of IFN‐γ‐producing CD4+ and CD8+ T cells upon in vitro activation using peptide pools representing the CMV pp65 and IE‐1 proteins were assessed at multiple time points post SCT, and correlated with the occurrence of CMV reactivation. In a retrospective analysis, recurrent CMV reactivations occurred in 9 patients and were associated with low pp65‐specific CD4+ T‐cell and low IE‐1‐specific CD8+ T‐cell reactivities, whereas patients without detectable CMV reactivation (n = 30) or a single reactivation (n = 13) showed a better recovery of these immune responses. CD4+ T‐cell responses to IE‐1 were infrequent in most patients, whereas CD8+ T‐cell responses to pp65 occurred frequently, but did not correlate with protection against (recurrent) reactivation. Prospectively, CMV‐specific T‐cell responses could be studied prior to 14 reactivation episodes in 8 patients. CD4+ T‐cell responses to IE‐1 and pp65 were positive in only 1 and 2 episodes, respectively. CD8+ T‐cell responses against IE‐1 were positive in 4, but against pp65 in 12 episodes, again showing that CD8+ T‐cell reactivity against pp65 did not prevent CMV reactivation. Thus, monitoring of particular CMV‐specific CD4+ and CD8+ T‐cell responses after allogeneic SCT may identify patients at risk for recurrent CMV reactivations. © 2008 Clinical Cytometry Society
An improved PCR-based method for site directed mutagenesis using megaprimers.

An improved protocol for site-directed mutagenesis based on the two-step polymerase chain reaction (PCR) megaprimer method is described. Compared to previously published protocols, the protocol described in this article ensures consistently a success rate of at least 85% with essentially no introduction of unwanted secondary mutations. The essential features of this protocol include an optimization of the template-primer amounts and ratio that allows the use of a reduced number of PCR cycles and the use of proof-reading thermostable DNA polymerases.
Outcomes of patients with metastatic melanoma treated with immunotherapy prior to or after BRAF inhibitors

The immunotherapy (IT) agents ipilimumab and interleukin‐2 as well as BRAF inhibitors (BRAFi) vemurafenib and dabrafenib, with or without trametinib (MEK inhibitors), are all FDA‐approved treatments for BRAF metastatic melanoma, but there are few studies to guide optimal sequencing. This retrospective analysis describes the outcomes of patients treated with either BRAFi before IT or IT before BRAFi.
Dynamic Specification Mining with Out-of-Scope E ect Awareness and Result Classification

Dynamic speci cation mining techniques attempt to ll gaps in missing or decaying documentation of software systems to support software maintenance tasks such as testing or bug xing. Current dynamic mining techniques are blind to common coding styles, and in particular to design patterns that involve dynamic data structures such as lists of listeners for event noti cation. Because they cannot recover properties involving these dynamic structures, they may produce incomplete or misleading speci cations (e.g., suggesting a method may be “pure” because its e ects are produced indirectly through event noti cation). We have devised an extension to current dynamic speci cation mining techniques that ameliorates this shortcoming. The key insight is to monitor not only values dynamically, but also properties to track dynamic data structures commonly used in design patterns. We have implemented this approach as an extension to the instrumentation component of Daikon, the leading example of dynamic invariant mining in the research literature. We have applied our tool to widely used software systems published on GitHub to illustrate and evaluate the usefulness of this pliable monitoring for elucidating the overall behavior of target systems.
Micro-Doppler analysis of small UAVs

Coherent radar measures micro-Doppler properties of moving objects. The micro-Doppler signature depends on parts of an object moving and rotating in addition to the main body motion (e.g. rotor blades) and is therefore characteristic for the type of object. In this study, the micro-Doppler signature (i.e. the object spectrogram) is exploited to classify small, unmanned helicopters and multicopters.
The Werner syndrome protein contributes to induction of p53 by DNA damage

Mutations in the p53 tumor‐suppressor gene promote increased genomic instability and cancer. Mutations in the WRN gene, encoding a DNA helicase, underlie the segmental progeroid Werner syndrome (WS). WS is also associated with increased genomic instability and elevated cancer risk. The p53 and WRN proteins can engage in direct protein‐protein interactions. We report that excess WRN elicits increased cellular p53 levels and potentiates p53‐mediated apoptosis. Importantly, cells derived from WS patients exhibit an attenuated and delayed induction of p53 by UV or by the topoisomerase I inhibitor camptothecin. These results suggest that WRN may participate in the activation of p53 in response to certain types of DNA damage. Furthermore, the failure to induce p53 effectively may contribute to enhanced genomic instability and elevated cancer risk in WS patients.
Efficient Neutralization of Anthrax Toxin by Chimpanzee Monoclonal Antibodies against Protective Antigen

Abstract Four single-chain variable fragments (scFvs) against protective antigen (PA) and 2 scFvs against lethal factor (LF) of anthrax were isolated from a phage display library generated from immunized chimpanzees. Only 2 scFvs recognizing PA (W1 and W2) neutralized the cytotoxicity of lethal toxin in a macrophage lysis assay. Full-length immunoglobulin G (IgG) of W1 and W2 efficiently protected rats from anthrax toxin challenge. The epitope recognized by W1 and W2 was conformational and was formed by C-terminal amino acids 614–735 of PA. W1 and W2 each bound to PA with an equilibrium dissociation constant of 4×10-11 mol/L to 5 × 10−11 mol/L, which is an affinity that is 20–100-fold higher than that for the interaction of the receptor and PA. W1 and W2 inhibited the binding of PA to the receptor, suggesting that this was the mechanism of protection. These data suggest that W1 and W2 chimpanzee monoclonal antibodies may serve as PA entry inhibitors for use in the emergency prophylaxis against and treatment of anthrax
The in Vitro Action of Dapsone and its Derivatives on Normal and G6PD‐deficient Red Cells

Summary. In an attempt to define the mechanism of dapsone‐induced haemolysis the in vitro action of dapsone (4,4′, diaminodiphenylsulphone) and some of its derivatives on normal and G6PD‐deficient red cells has been investigated. Dapsone, its N′ acetyl‐ and hydroxy‐derivatives have no measurable effect on metabolism, haemoglobin or the membrane in either normal or G6PD‐deficient red cells. 4, hydroxylamino‐4′ aminodiphenylsulphone (HADS) and 4, hydroxylamino‐4′ acetaminodiphenylsulphone (HMDS) have oxidant effects on red cells. Both of these compounds readily form methaemoglobin but in normal red cells higher levels of methaemoglobin are achieved with HMDS than with HADS. With both compounds less methaemoglobin is formed in glucose‐deprived or in G6PD‐deficient red cells. In normal red cells hexose monophosphate pathway (HMP) activity is increased, HADS being a more potent stimulus than HMDS. It is suggested that methaemoglobin formation is dependent upon the recycling of these compounds via the HMP.
Development and Validation of Videotaped Scenarios

Researchers using scenarios often neglect to validate perceived content and salience of embedded stimuli specifically with intended participants, even when such meaning is integral to the study. For example, sex and aggression stimuli are heavily influenced by culture, so participants may not perceive what researchers intended in sexual aggression scenarios. Using four studies, the authors describe the method of scenario validation to produce two videos assessing alcohol-related sexual aggression. Both videos are identical except for the presence in one video of antiforce cues that are extremely salient to the young heterosexual men. Focus groups and questionnaires validate these men's perceptions that (a) the woman was sexually interested, (b) the sexual cues were salient, (c) the antiforce cues were salient (antiaggression video only), and (e) these antiforce cues inhibited acceptance of forced sex. Results show the value of carefully selecting and validating content when assessing socially volatile variables and provide a useful template for developing culturally valid scenarios.
Sem and Tem Study of the Armed Male Terminal Genitalia of the Tapeworm Paraechinophallus japonicus (Cestoda: Bothriocephalidea)

For the first time, the ultrastructure of the armed cirrus of an echinophallid cestode, Paraechinophallus japonicus (Yamaguti, 1934), has been studied with the use of scanning and transmission electron microscopy. Two sets of eversible copulatory organs (≈300 μm in length and ≈130 μm in width) are present on the dorsal side of each segment near the lateral margin of the strobila. Except for the terminal portion, the cirrus is covered with large spines (up to 40 μm long, measured from SEM photomicrographs) composed of 2 parts. The basal portion contains a lobed electron-dense outer region that gives way to a reticular meshwork of electron-dense material. The apical region of the spines, composed of a homogeneous, moderately electron-dense matrix, is slightly curved distally. Spines are covered with a cortical zone. Between the spines, the distal cytoplasm is covered with microvilli of about 1.2 μm in length. The wall of the cirrus sac, which is ≈500 μm long and ≈250 μm wide, is composed of 2 layers of muscles, i.e., an internal layer of circular muscles and external longitudinal muscles. Microvilli on the cirrus of P. japonicus are reported for the first time in the Cestoda, whereas the spines on the cirrus may represent a synapomorphy of bothriocephalidean cestodes of the Echinophallidae.
Positive and negative control of nod gene expression in Rhizobium meliloti is required for optimal nodulation

We show that expression of common nodulation genes in Rhizobium meliloti is under positive as well as negative control. A repressor protein was found to be involved in the negative control of nod gene expression. Whereas the activator NodD protein binds to the conserved cis‐regulatory element (nod‐box) required for coordinated regulation of nod genes, the repressor binds to the overlapping nodD1 and nodA promoters, at the RNA polymerase binding site. A model depicting the possible interaction of the plant‐derived nod gene inducer (luteolin), the NodD and the repressor with the nod promoter elements is presented. Mutants lacking the repressor exhibited delayed nodulation phenotype, indicating that fine tuning of nod gene expression is required for optimal nodulation of the plant host.
A robust homogeneous binding assay for alpha4beta2 nicotinic acetylcholine receptor.

AIM To develop a homogeneous high-throughput screening (HTS) assay based on scintillation proximity assay (SPA) technology for identification of novel alpha4beta2 nicotinic acetylcholine receptor (nAChR) modulators. METHODS Membrane preparation of HEK293 cells expressing alpha4beta2 nAChR, [(3)H]cytisine and wheat germ agglutinin (WGA)-coupled microbeads were used to develop an HTS assay based on SPA technology. This method was validated against a conventional filter binding approach and applied to large-scale screening of a library containing 32 000 synthetic compounds. Intracellular calcium measurement was carried out to verify the bioactivities of the hits found by the SPA assay. RESULTS IC(50) values of 2 reference compounds (epibatidine and RJR 2403) determined by SPA and filter binding methods were comparable and consistent with those reported elsewhere. A total of 54 compounds, showing more than 60% competitive inhibition on [(3)H]cytisine binding to alpha4beta2 nAChR, were identified initially following an HTS campaign. Secondary screening confirmed that 17 compounds with novel chemical structures possessed relatively high binding affinity to alpha4beta2 nAChR (K(i)<2 micromol/L). Eight compounds displayed antagonistic effects with >50% inhibition on ABT-594-induced calcium mobilization while none showed any agonist activity. CONCLUSIONS This homogeneous binding assay is a highly efficient, amenable to automation and robust tool to screen potential alpha4beta2 nAChR modulators in an HTS setting. Its application may be expanded to other membrane receptors and ion channels.
[An integrated perspective of the organisational context and experience of stress].

OBJECTIVES Investigating scientific production regarding the concept of occupational stress in periodicals indexed in international databases and analysing questions related to the heart of this phenomenon as seen from the perspective of individual and collective interpretation. METHOD Most articles were obtained from Medline, Lilacs and PsycINFO databases covering 1998 to 2008 using the following keywords: stress, well-being, burnout, organisation and presenteeism. RESULTS 33 articles were identified; 21 of them were selected and 18 located. Speaking about stress in daily-life is already commonplace, associated as it is with constant changes and the accelerated rhythm ruling society nowadays; this leads to profound transformations in an individual's behaviour patterns, attitudes and values. Stress can therefore be seen as a cultural symbol of the present, leading to feelings of uncertainty regarding an individual's perception of the future. CONCLUSIONS The analysis of the literature allowed the sources of intrinsic/extrinsic stress on an individual to be discriminated and an analysis of the main repercussions, of which presenteeism and burnout are worth special mention. This reinforced the need for primary prophylactic intervention, starting from recognising those risk factors which make certain individuals more vulnerable.
Influence of tissue biotype in the morpho- esthetic-functional behavior of the peri-implant tissue: A literature review

Introduction: The current focus of Implantology is the planning of a rehab contemplating, besides the function, the esthetical success. The expectation is to create an esthetic restoration that is indistinguishable from the natural tooth, as well as returning the contour of peripheral structures (peri-implant mucosa and papilla) that resemble the same contralateral structures. It is a field of multiple variables in which the identification of tissue biotype is a factor that competes for the achievement of such success. Objective: The purpose of this present work was to review the influence of gingival biotype on morpho-functional and esthetic behavior of peri-implant tissues, indicating protocols of diagnosis and management of these tissues. It was used as source of research the data base of PubMed, selecting articles published from March 2008 to June 2011. Conclusion: Within the limits of this review, it was possible to conclude that tissue biotype has influence on the esthetic in the therapy with implants, specially on the facial peri-implant mucosa levels; presenting the thin biotype greater susceptibility to recession. In this condition, the conversion of a thin biotype into a thick biotype, through grafting of conjunctive tissue seems to positively influence on the level of facial marginal mucosa. On the other hand, the tissue biotype showed little influence on the height of the interproximal papilla.