gebhart/patrepeval huggingface dataset:
Filling Up the Heme Pocket Stabilizes Apomyoglobin and Speeds Up Its Folding (2014)

Wild type apomyoglobin folds in at least two steps: the ABGH core rapidly, followed much later by the heme-binding CDEF core. We hypothesize that the evolved heme-binding function of the CDEF core frustrates its folding: it has a smaller contact order and is no more complex topologically than ABGH, and thus, it should be able to fold faster. Therefore, filling up the empty heme cavity of apomyoglobin with larger, hydrophobic side chains should significantly stabilize the protein and increase its folding rate. Molecular dynamics simulations allowed us to design four different mutants with bulkier side chains that increase the native bias of the CDEF region. In vitro thermal denaturation shows that the mutations increase folding stability and bring the protein closer to two-state behavior, as judged by the difference of fluorescence- and circular dichroism-detected protein stability. Millisecond stopped flow measurements of the mutants exhibit refolding kinetics that are over 4 times faster than the wild type's. We propose that myoglobin-like proteins not evolved to bind heme are equally stable, and find an example. Our results illustrate how evolution for function can force proteins to adapt frustrated folding mechanisms, despite having simple topologies.
Point-source detection using 3D-position-sensitive semiconductor detectors with estimated background (2010)

In the detection of radiation sources, the combination of spectral and directional information can improve detection over using either one alone. Directional information found through probabilistic Compton-imaging methods helps to distinguish point sources from extended background sources. In this work, we use 3D-position-sensitive CdZn Te detectors to investigate the combination of these data for the automated detection, identification, and localization of point sources in a background where the spectral shape is known but its intensity may be unknown. If it is available, knowledge of the expected background energy distribution is shown to improve detection and identification performance compared with an unknown background. Such background estimates may be found from prior measurements or background tracking. Detection performance is compared with simple spectral methods as a function of false-alarm probability using experimental data from an 18-detector array system.
Dynamics of proinflammatory cytokine expression in the joints of mice with collagen-induced arthritis (CIA) (1997)

This report contains a description of the cellular localization and kinetics of proinflammatory cytokine expression in murine CIA, a model for rheumatoid arthritis. Tissue cryostat sections of undecalcified paws from type II collagen-immunized DBA/1 mice, taken 1-10 days after the onset of clinical arthritis, were examined for the presence of tumour necrosis factor-alpha (TNF-alpha), IL-1beta and IL-6 using an indirect immunoperoxidase technique. In parallel, interferon-gamma (IFN-gamma) production by lymph node cells, stimulated in vitro with type II collagen, was assessed as a marker of T cell activity. The main areas of TNF-alpha, IL-1beta and IL-6 expression were in the synovial lining layer and in tissue contiguous with cartilage and bone (the marginal zone), in particular at sites of pannus formation and joint erosion. There was a progressive increase in the number of TNF-alpha-, IL-1beta- and IL-6-positive cells from day 1 to day 10 of arthritis, during which time IFN-gamma production by CD4+ T cells from draining lymph nodes declined sharply. A further finding of potential significance was that TNF-alpha was consistently detected at day 1 of arthritis, whereas IL- 1beta-positive cells were not found until day 3, suggesting that the expression of TNF-alpha precedes that of IL-1beta.
Genomic copy number and expression variation within the C57BL/6J inbred mouse strain (2007)

The C57BL/6J strain is one of the most widely used animal models for biomedical research, and individual mice within the strain are often assumed to be genetically identical after more than 70 yr of inbreeding. Using a single nucleotide polymorphism (SNP) genotyping panel, we assessed if copy number variations (CNVs) could be detected within the C57BL/6J strain by comparing relative allele frequencies in first generation (F(1)) progeny of C57BL/6J mice. Sequencing, quantitative PCR, breeding, and array comparative genomic hybridization (CGH) together confirmed the presence of two CNVs. Both CNVs span genes encoded on chromosome 19, and quantitative RT-PCR demonstrated that they result in altered expression of the insulin-degrading enzyme (Ide) and fibroblast growth factor binding protein 3 (Fgfbp3) genes. Analysis of 39 different C57BL/6J breeders revealed that 64% of mice from the Jackson Laboratory colony were heterozygous for the CNV spanning Ide. Homozygotes with and without the duplication were present in concordance with Hardy-Weinberg equilibrium (13% and 23%, respectively), and analysis of archived samples from the C57BL/6J colony suggests that the duplication has rapidly reached a high frequency in the colony since 1994. The identification of two CNVs in the small portion of the genome screened demonstrates that individual mice of highly inbred strains are not isogenic and suggests other CNVs may be segregating within C57BL/6J as well as other carefully maintained inbred strains. These differences can influence interpretations of physiological, biomedical, and behavioral experiments and can be exploited to model CNVs apparent in the human genome.
Montaje de aislamiento a ruido de impacto en edificación con lanas minerales (2011)

Mental processes related to visceral activity have gained growing interest during the last few years. The following study is the first to investigate possible interactions between interoceptive awareness and measures of attentional performance. We tested the hypothesis whether interoceptive awareness is positively related to indices of selective and divided attentional performances. Using a heartbeat perception task, 29 healthy female participants were separated into two groups scoring either high or low in an interoceptive awareness task. Attentional performance was assessed by several tests including the 'd2 test of attention' and subtests from the 'TAP: Test Battery for Attentional Performance'. We observed a significantly better performance in selective and divided attention for participants with high interoceptive awareness. Our data suggests that interoceptive awareness is related to a better performance especially in tasks assessing selective and divided attention. We conclude 1) that perception of bodily states might be a crucial determinant for the processing of external, visual stimuli, 2) that the ability to perceive internal signals might be an indicator of self-focused attention, and 3) that bodily signals may use, at least in part, similar processing resources as signals from the attention system.
Supplementary table 6 from Genomic Landscape of Somatic Alterations in Esophageal Squamous Cell Carcinoma and Gastric Cancer (2023)

&lt;p&gt;IVA disease analysis report&lt;/p&gt;
Magnetic Control of Macromolecular Conformations in Supramolecular Anionic Polysaccharide–Iron Complexes (2015)

Abstract The anionic iota carrageenan polysaccharide is enriched with Fe II and Fe III by ion exchange against FeSO 4 and FeCl 3 . With divalent iron, portions of polymer chains undergo a secondary structure transition from random coils to single helices. The single‐chain macromolecular conformations can be manipulated by an external magnetic field: upon exposure to 1.1 T, the helical portions exhibit 1.5‐fold stiffening and 1.1‐fold stretching, whereas the coil conformations respond much less as a result of lower contents of condensed iron ions. Along with the coil–helix transition, the trivalent iron triggers the formation of superstructures. The applicability of iron‐enriched iota carrageenan as functional ingredient for food fortification is tested by free Fe 2+ and Fe 3+ contents, respectively, with the most promising iota‐Fe III yielding 53 % of bound iron, which is due to the superstructures, where the ferric ions are chelated by the supramolecularly self‐assembled polymer host.
Enzyme-Mediated Preparation of the Enantiomerically Enriched Isomers of the Odorous Tetrahydropyranyl AcetatesJasmal® andJessemal®, and Their Olfactory Evaluation (2006)

All four stereoisomers of the fragrance Jasmal of structure 3,4,5,6-tetrahydro-3-pentyl-2H-pyran-4-yl acetate were prepared by enzymatic resolutions of the corresponding alcohols. The absolute configurations were unambiguously determined by comparison with the enantiomer (3R,4S)-1 prepared from L-tartaric acid. The four stereoisomers of the fragrance Jessemal of structure 3-butyl-5-methyl-3,4,5,6-tetrahydro-2H-pyran-4-yl acetate were obtained starting from the epoxy alcohol 10, which was obtained in an optically pure state by enzymatic resolution of the racemic mixture. The olfactory evaluations of all stereoisomers are reported. (1)H-NMR Conformational analysis of diastereoisomers (3RS,4RS,5RS)-2 and (3RS,4SR,5RS)-2 is also reported.
Rad is temporally regulated within myogenic progenitor cells during skeletal muscle regeneration (2005)

The successful use of myogenic progenitor cells for therapeutic applications requires an understanding of the intrinsic and extrinsic cues involved in their regulation. Herein we demonstrate the expression pattern and transcriptional regulation of Rad, a prototypical member of a family of novel Ras-related GTPases, during mammalian development and skeletal muscle regeneration. Rad was identified using microarray analysis, which revealed robust upregulation of its expression during skeletal muscle regeneration. Our current findings demonstrate negligible Rad expression with resting adult skeletal muscle; however, after muscle injury, Rad is expressed within the myogenic progenitor cell population. Rad expression is significantly increased and localized to the myogenic progenitor cell population during the early phases of regeneration and within the newly regenerated myofibers during the later phases of regeneration. Immunohistochemical analysis demonstrated that Rad and MyoD are coexpressed within the myogenic progenitor cell population of regenerating skeletal muscle. This expression profile of Rad during skeletal muscle regeneration is consistent with the proposed roles for Rad in the inhibition of L-type Ca(2+) channel activity and the inhibition of Rho/RhoA kinase activity. We also have demonstrated that known myogenic transcription factors (MEF2, MyoD, and Myf-5) can increase the transcriptional activity of the Rad promoter and that this ability is significantly enhanced by the presence of the Ca(2+)-dependent phosphatase calcineurin. Furthermore, this enhanced transcriptional activity appears to be dependent on the presence of a conserved NFAT binding motif within the Rad promoter. Taken together, these data define Rad as a novel factor within the myogenic progenitor cells of skeletal muscle and identify key regulators of its transcriptional activity.
TPR is required for the efficient nuclear export of mRNAs and lncRNAs from short and intron-poor genes (2020)

While splicing has been shown to enhance nuclear export, it has remained unclear whether mRNAs generated from intronless genes use specific machinery to promote their export. Here, we investigate the role of the major nuclear pore basket protein, TPR, in regulating mRNA and lncRNA nuclear export in human cells. By sequencing mRNA from the nucleus and cytosol of control and TPR-depleted cells, we provide evidence that TPR is required for the efficient nuclear export of mRNAs and lncRNAs that are generated from short transcripts that tend to have few introns, and we validate this with reporter constructs. Moreover, in TPR-depleted cells reporter mRNAs generated from short transcripts accumulate in nuclear speckles and are bound to Nxf1. These observations suggest that TPR acts downstream of Nxf1 recruitment and may allow mRNAs to leave nuclear speckles and properly dock with the nuclear pore. In summary, our study provides one of the first examples of a factor that is specifically required for the nuclear export of intronless and intron-poor mRNAs and lncRNAs.
Safety and efficacy of pemigatinib plus pembrolizumab combination therapy in patients (pts) with advanced malignancies: Results from FIGHT-101, an open-label phase I/II study. (2020)

3606 Background: Pemigatinib (INCB054828) is a selective fibroblast growth factor receptor (FGFR) 1–3 inhibitor with demonstrated efficacy as monotherapy in phase 1/2 (FIGHT-101) and phase 2 (FIGHT-201, -202, -203) trials in pts with advanced cancer. Here, we present preliminary safety, efficacy, and pharmacokinetic (PK) data for pemigatinib (PEMI) combined with pembrolizumab (PEMBRO), a programmed cell death protein-1 (PD-1) inhibitor, in pts with refractory advanced malignancies enrolled in the ongoing FIGHT-101 trial (NCT02393248). Methods: FIGHT-101 includes monotherapy (part 1 and 2) and combination therapy (part 3) cohorts. This analysis is based on pts enrolled in the PEMI + PEMBRO combination dose finding (3a) and dose expansion (3b) cohorts. Eligible adults had advanced malignancies who had progressed after prior therapy and for whom PEMBRO treatment was relevant; pts in part 3b had FGF/FGFR alterations. Pts received oral PEMI at 9 mg or 13.5 mg QD on an intermittent dosing (ID) schedule (21-day cycle, 14-day on/7-day off), or 13.5 mg QD on a continuous dosing (CD) schedule, plus PEMBRO 200 mg IV on day 1 of each 21-day cycle. Results: At data cutoff (August 30, 2019), 23 pts had received PEMI + PEMBRO; 22 (96%) had discontinued therapy (disease progression, 70%). Most frequent tumors were NSCLC (n = 3), bladder (n = 3), pancreatic, testicular, and sarcoma (each n = 2). Of 19 enrolled pts with baseline FGF/FGFR data; 5 had FGFR mutations or rearrangements. No dose-limiting toxicities occurred with PEMI + PEMBRO. The recommended PEMI dose combined with PEMBRO was 13.5 mg QD. Most frequent all-cause, all-grade (Gr) adverse events for ID (n = 17) were hyperphosphatemia (n = 14 [82%]; Gr ≥3, n = 0), anemia (n = 9 [53%]; Gr ≥3, n = 3 [18%]), and decreased appetite (n = 9 [53%]; Gr ≥3, n = 0); for CD (n = 6), hyperphosphatemia (n = 5 [83%]; Gr ≥3, n = 0), and dry mouth (n = 4 [67%]; Gr ≥3, n = 0). One pt discontinued, 2 reduced dose, and 13 interrupted dose due to AEs (none for hyperphosphatemia; dose interruption mainly for gastrointestinal AEs [n = 5]). One fatal AE occurred (suicide, not treatment-related). PK parameters for PEMI in the PEMI + PEMBRO combination were comparable with those for PEMI monotherapy. Five pts had partial response (3 had FGFR rearrangements or mutations); 5 pts had stable disease. Conclusions: PEMI + PEMBRO combination therapy was tolerable with no new safety signals, and demonstrated preliminary antitumor activity in pts with advanced malignancies including those with FGF/FGFR alterations. Clinical trial information: NCT02393248 .
Vitamin E in Heart Transplantation: Effects on Cardiac Gene Expression (2006)

Based on transcript profiling, we propose a novel role of vitamin E in transplant surgery. Our findings warrant further studies to explore its clinical application.
Demonstration of T15 idiotype‐positive effector and suppressor T cells for phosphorylcholine‐specific delayed‐type hypersensitivity response in CBA/N or (CBA/N X BALB/c)F<sub>1</sub> male mice (1981)

Subcutaneous immunization of CBA/N or (CBA/N X BALB/c)F1 (NBF1) male mice, which were defective in phosphorylcholine (PC)-specific humoral antibody response, with PC-conjugated syngeneic spleen cells induced a PC-specific delayed-type hypersensitivity (DTH) response, while intravenous administration of the same cells induced PC-specific suppressor T cells for the DTH response. Treatment of PC-specific effector or suppressor T cells for the DTH response induced in NBF1 male mice with anti-T15 idiotypic antibody inactivated effector or suppressor functions of these T cells implying that PC-specific T cells in NBF1 mice expressed T15 idiotypic determinants on their surface. Enrichment of PC-specific suppressor T cells was also shown by employing anti-T15 antibody-coated dishes.
Ab Initio Study of Electronic Structure and Jahn-Teller Effect of Tetrachloromethane Cation (1995)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTAb Initio Study of Electronic Structure and Jahn-Teller Effect of Tetrachloromethane CationJ. M. Garcia de la Vega, E. Mena, B. Miguel, and E. San FabianCite this: J. Phys. Chem. 1995, 99, 32, 12135–12140Publication Date (Print):August 1, 1995Publication History Published online1 May 2002Published inissue 1 August 1995https://pubs.acs.org/doi/10.1021/j100032a014https://doi.org/10.1021/j100032a014research-articleACS PublicationsRequest reuse permissionsArticle Views76Altmetric-Citations5LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access options Get e-Alerts
The <i>Escherichia coli</i> NadR Regulator Is Endowed with Nicotinamide Mononucleotide Adenylyltransferase Activity (1999)

The first identification and characterization of a catalytic activity associated with NadR protein is reported. A computer-aided search for sequence similarity revealed the presence in NadR of a 29-residue region highly conserved among known nicotinamide mononucleotide adenylyltransferases. The Escherichia coli nadR gene was cloned into a T7-based vector and overexpressed. In addition to functionally specific DNA binding properties, the homogeneous recombinant protein catalyzes NAD synthesis from nicotinamide mononucleotide and ATP.
Morphometric and demographic differences between tropical and temperate Norway rats (<i>Rattus norvegicus</i>) (2015)

Rattus norvegicus (Norway rat) is one of the most abundant and geographically widespread mammals. Ecological studies focusing on urban Norway rat populations are restricted to temperate regions, and data describing populations from tropical cities are lacking. We compared the morphometrics and demographic characteristics of rats captured in urban low-income settlements in Salvador, Brazil, to a season, environmental area of capture, and sex-matched sample from Baltimore, Maryland. Norway rats of both sexes were significantly smaller in Salvador, although the threshold mass marking sexual maturity was equivalent for both cities. Pregnancy rates were comparable (~50%); however, juveniles were commonly trapped in Salvador (20%) while they were rarely trapped in Baltimore during winter months (2%). These findings suggest that tropical and temperate rats differ with respect to body metrics, while size at sexual maturity is similar. Further studies conducted over different seasons are required before any firm conclusions are reached; however, this study provides preliminary support for Bergmann’s rule that species at higher absolute latitude are larger than the same species sampled at lower latitudes.
Simplified Model of Variable Speed Wind Turbine Generator for Dynamic Simulation Analysis (2015)

This paper presents simplified models to represent a grid connected wind farm composed of variable speed wind turbines with Doubly Feed Induction Generator (DFIG) and Permanent Magnet Synchronous Generator (PMSG) for dynamic simulation study. Aim of the simplified models is to diminish the complexity and simulation time of the analysis of grid connected wind farm. The proposed simplified models can be used as an aggregated and individual wind generator model representations. Simulation analyses in time domain have been performed for steady state and transient scenarios to demonstrate the accuracy of the proposed model. Comparative analysis between the proposed simplified and detailed models is also performed and presented. The simulation results show that the simplified models have sufficient accuracy in both steady state and transient conditions.
Mechanism of Internet of Things (IoT) Integrated with Radio Frequency Identification (RFID) Technology for Healthcare System (2022)

Radio frequency identification (RFID) technology has already demonstrated its use. RFID is used in many productions for different applications, for example, apparatus chasing, personal and vehicle access panels, logistics, baggage, and safety items in departmental stores. The main benefits of RFID are optimizing resources, quality customer service, improved accuracy, and efficient business and healthcare procedures. In addition, RFID can help to recognize appropriate information and help advance the probability of objects for certain functions. Nevertheless, RFID components need to be studied for use in healthcare. Antennas, tags, and readers are the main components of RFID. The study of these elements provides an understanding of the usage and integration of these components in healthcare environments. The security of the patient is now a global alarm for public health, particularly among older people who need integrated and technologically integrated physiological health monitoring systems to monitor medical needs and manage them. This paper proposes using Internet of Things (IoT) and RFID tags as an effective healthcare monitoring system. In this method, we utilize RFID dual-band protocols that are useful for identifying individual persons and are used to monitor body information using high frequency. The patient’s physiological data are monitored and collected by sensors to recognize the patient, using an RFID tag. The IoT-based RFID healthcare provides the elderly and people with physiological information. The aim is also to secure patient health records using the signing algorithm based on the hyperelliptic curve (HEC) and to provide the physician with access to health information for patients. Furthermore, the confidentiality of the medical records for patients of variable length is provided. The evaluation reveals the algorithm proposed for optimum health care with different genus curves.