gebhart/patrepeval huggingface dataset:
Proteases of the genus Bacillus. II. Alkaline proteases (1970)

Abstract The alkaline proteases of B. subtilis NRRL B3411, B. pumilis , and B. licheniformis have been isolated by fractionation followed by ion exchange chromatography and their homogeneity demonstrated. General enzyme properties of the B. sublitis NRRL B3411 alkaline protease have been studied and attempts made to differentiate a group of alkaline proteases. It is clear that the alkaline proteases known as Subtilisins or Subtilopeptidases are not, exclusive to B. subtilis but are common to many Bacilli and therefore the generic name Bacillopeptidases has been proposed. It is clear too that on the basis of the effect of pH on activity, amino acid composition, esterase activity, and immunological cross‐reactions the Bacillopeptidases can be divided into two groups or types: ( a ) Bacillopcptidase A (Subtilisin A or Subtilopeptidase A) which includes Subtilisin Carlsberg, B. licheniformis , and B. pumilis alkaline proteases; ( b ) Bacillopeptidase B (Subtilisin B or Subtilopeptidase B) which includes B subtilis NRRL B3411, Subtilisin Novo, Subtilisin BPN' (Nagarse), alkaline protease Daiwa Kasei, and (probably) B. subtilis var. amylosacchariticus . At present, no further differentiation is possible and whether or not the enzymes within group A or B are identical remains an open question. Methods for examination of crude enzyme mixtures or fermentation beers are described and from the examination of a number of crude enzymes and fermentation beers it appears that organisms producing Bacillopeptidase A do not produce neutral protease or amylase, while organisms producing Bacillopeptidase B produce a neutral protease and amylase as well.
Predictive Models to Identify Small Molecule Activators and Inhibitors of Opioid Receptors (2021)

Opioid receptors (OPRs) are the main targets for the treatment of pain and related disorders. The opiate compounds that activate these receptors are effective analgesics but their use leads to adverse effects, and they often are highly addictive drugs of abuse. There is an urgent need for alternative chemicals that are analgesics and to reduce/avoid the unwanted effects in order to relieve the public health crisis of opioid addiction. Here, we aim to develop computational models to predict the OPR activity of small molecule compounds based on chemical structures and apply these models to identify novel OPR active compounds. We used four different machine learning algorithms to build models based on quantitative high throughput screening (qHTS) data sets of three OPRs in both agonist and antagonist modes. The best performing models were applied to virtually screen a large collection of compounds. The model predicted active compounds were experimentally validated using the same qHTS assays that generated the training data. Random forest was the best classifier with the highest performance metrics, and the mu OPR (OPRM)-agonist model achieved the best performance measured by AUC-ROC (0.88) and MCC (0.7) values. The model predicted actives resulted in hit rates ranging from 2.3% (delta OPR-agonist) to 15.8% (OPRM-agonist) after experimental confirmation. Compared to the original assay hit rate, all models enriched the hit rate by ≥2-fold. Our approach produced robust OPR prediction models that can be applied to prioritize compounds from large libraries for further experimental validation. The models identified several novel potent compounds as activators/inhibitors of OPRs that were confirmed experimentally. The potent hits were further investigated using molecular docking to find the interactions of the novel ligands in the active site of the corresponding OPR.
Immunosuppressive drug‐free operational immune tolerance in human kidney transplant recipients: Part I. blood gene expression statistical analysis (2007)

Survival of solid organ grafts depends on life-long immunosuppression, which results in increased rates of infection and malignancy. Induction of tolerance to allografts would represent the optimal solution for controlling both chronic rejection (CR) and side effects of immunosuppression. Although spontaneous "operational tolerance" can occur in human kidney transplantation, the lack of noninvasive peripheral blood biological markers of this rare phenomenon precludes the identification of potentially tolerant patients in whom immunosuppression could be tapered as well as the development of new tolerance inducing strategies. Here, the potential of high throughput microarray technology to decipher complex pathologies allowed us to study the peripheral blood specific gene expression profile and corresponding EASE molecular pathways associated to operational tolerance in a cohort of human kidney graft recipients. In comparison with patients with CR, tolerant patients displayed a set of 343 differentially expressed genes, mainly immune and defense genes, in their peripheral blood mononuclear cells (PBMC), of which 223 were also different from healthy volunteers. Using the expression pattern of these 343 genes, we were able to classify correctly >80% of the patients in a cross-validation experiment and classified correctly all of the samples over time. Collectively, this study identifies a unique PBMC gene signature associated with human operational tolerance in kidney transplantation by a classical statistical microarray analysis and, in the second part, by a nonstatistical analysis.
Fluorination of MXene by Elemental F2 as Electrode Material for Lithium‐Ion Batteries (2019)

The transformation of MXene sheets into TiOF<sub>2</sub> 2D sheets with superior electrochemical performance was developed. MXene synthesized from Ti<sub>3</sub> AlC<sub>2</sub> was fluorinated for 3, 6, and 24 h, respectively, by means of a direct fluorination process. Exposure of MXene powder to elemental fluorine for 3 h induced the formation of CF<sub>2</sub> groups and TiF<sub>3</sub> on the surface, which have beneficial effects on the electrochemical performance. X-ray photoelectron spectroscopy suggested that after fluorinating the MXene sample for 6 h Ti<sup>2+</sup> and Ti<sup>3+</sup> were not present on the surface but only Ti<sup>4+</sup> , indicating the formation of TiOF<sub>2</sub> . XRD indicated that TiOF<sub>2</sub> was present after fluorinating for 3 h, and after 24 h the MXene had transformed to TiOF<sub>2</sub> with minor impurities remaining, maintaining its 2D layer morphology. The 24 h fluorinated sample with its TiOF<sub>2</sub> phase showed superior capacity that increased with cycle number. It also had a better rate capability than non-2D-layered TiOF<sub>2</sub> , indicating the advantage of the 2D-layered morphology derived from the parent MXene phase.
Light shift of coherent population trapping resonances (1999)

We have measured the spectral position of the absorption minimum in a coherent population trapping resonance in thermal cesium vapor as a function of light intensity. The dependence of position on intensity is found to be almost linear. We have furthermore studied the dependence of this light shift on neon buffer gas pressure and find a strong reduction for higher pressures. So the addition of a buffer gas not only reduces the linewidth of the resonance but also a very important systematic effect for precision measurements.
Interpretation of the rainbow color scale for quantitative medical imaging: perceptually linear color calibration (CSDF) versus DICOM GSDF (2017)

Medical displays for primary diagnosis are calibrated to the DICOM GSDF<sup>1</sup> but there is no accepted standard today that describes how display systems for medical modalities involving color should be calibrated. Recently the Color Standard Display Function<sup>3,4</sup> (CSDF), a calibration using the CIEDE2000 color difference metric to make a display as perceptually linear as possible has been proposed. In this work we present the results of a first observer study set up to investigate the interpretation accuracy of a rainbow color scale when a medical display is calibrated to CSDF versus DICOM GSDF and a second observer study set up to investigate the detectability of color differences when a medical display is calibrated to CSDF, DICOM GSDF and sRGB. The results of the first study indicate that the error when interpreting a rainbow color scale is lower for CSDF than for DICOM GSDF with statistically significant difference (Mann-Whitney U test) for eight out of twelve observers. The results correspond to what is expected based on CIEDE2000 color differences between consecutive colors along the rainbow color scale for both calibrations. The results of the second study indicate a statistical significant improvement in detecting color differences when a display is calibrated to CSDF compared to DICOM GSDF and a (non-significant) trend indicating improved detection for CSDF compared to sRGB. To our knowledge this is the first work that shows the added value of a perceptual color calibration method (CSDF) in interpreting medical color images using the rainbow color scale. Improved interpretation of the rainbow color scale may be beneficial in the area of quantitative medical imaging (e.g. PET SUV, quantitative MRI and CT and doppler US), where a medical specialist needs to interpret quantitative medical data based on a color scale and/or detect subtle color differences and where improved interpretation accuracy and improved detection of color differences may contribute to a better diagnosis. Our results indicate that for diagnostic applications involving both grayscale and color images, CSDF should be chosen over DICOM GSDF and sRGB as it assures excellent detection for color images and at the same time maintains DICOM GSDF for grayscale images.
Morphological and electrophysiological characteristics of layer V neurons of the rat lateral entorhinal cortex (2002)

The intrinsic electrophysiological and morphological properties of lateral entorhinal area (LEA) layer V neurons were investigated by sharp electrode intracellular recording and biocytin labeling in vitro. The morphological analysis revealed that layer V of the LEA contains three distinct subtypes of principal neurons, which were classified as pyramidal, horizontal, and polymorphic neurons. Pyramidal cells were the most abundant subtype (57%) and could be further subdivided into neurons with large, small, and star-like somas. Similarly to pyramidal cells, horizontal neurons (11%) had a prominent apical dendrite. However, their distinctive basal dendritic plexus extended primarily in the horizontal plane. Polymorphic neurons (32%) were characterized by a multipolar dendritic organization. Electrophysiological analysis of neurons in the three categories demonstrated a diversity of electrophysiological profiles within each category and no significant differences between groups. Neurons in the three subgroups could display instantaneous and/or time-dependent inward rectification and different degrees of spike frequency adaptation. None of the recorded cells displayed an intrinsic oscillatory bursting discharge. Many neurons in the three subgroups, however, displayed slow (3.5-14 Hz), sustained, subthreshold membrane potential oscillations. The morphological and electrophysiological diversity of principal neurons in the LEA parallels that previously reported for the medial entorhinal area and suggests that, with respect to the deep layers, similar information processing is performed across the mediolateral extent of the entorhinal cortex. Layer V of the entorhinal cortex may undertake very complex operations beyond acting as a relay station of hippocampal processed information to the neocortex.
Distinct subcellular localization of calcium binding S100 proteins in human smooth muscle cells and their relocation in response to rises in intracellular calcium (1998)

Changes in cytosolic Ca2+ concentration control a wide range of cellular responses, and intracellular Ca2+-binding proteins are the key molecules to transduce Ca2+ signaling via interactions with different types of target proteins. Among these, S100 Ca2+-binding proteins, characterized by a common structural motif, the EF-hand, have recently attracted major interest due to their cell- and tissue-specific expression pattern and involvement in various pathological processes. The aim of our study was to identify the subcellular localization of S100 proteins in vascular smooth muscle cell lines derived from human aorta and intestinal smooth muscles, and in primary cell cultures derived from arterial smooth muscle tissue under normal conditions and after stimulation of the intracellular Ca2+ concentration. Confocal laser scanning microscopy was used with a specially designed colocalization software. Distinct intracellular localization of S100 proteins was observed: S100A6 was present in the sarcoplasmic reticulum as well as in the cell nucleus. S100A1 and S100A4 were found predominantly in the cytosol where they were strongly associated with the sarcoplasmic reticulum and with actin stress fibers. In contrast, S100A2 was located primarily in the cell nucleus. Using a sedimentation assay and subsequent electron microscopy after negative staining, we demonstrated that S100A1 directly interacts with filamentous actin in a Ca2+-dependent manner. After thapsigargin (1 microM) induced increase of the intracellular Ca2+ concentration, specific vesicular structures in the sarcoplasmic reticulum region of the cell were formed with high S100 protein content. In conclusion, we demonstrated a distinct subcellular localization pattern of S100 proteins and their interaction with actin filaments and the sarcoplasmic reticulum in human smooth muscle cells. The specific translocation of S100 proteins after intracellular Ca2+ increase supports the hypothesis that S100 proteins exert several important functions in the regulation of Ca2+ homeostasis in smooth muscle cells.
Monitoring the Aging of Industrial Motors by Geometric Trending of Frequency Domain Signatures (2014)

Abstract The characterization of the aging of electric motors using vibration measurements and a geometric interpretation of spectral domain signatures is presented. For comparison, two vibration signal records from a three-phase induction motor were acquired during degradation due to bearing fluting, following thermal and chemical aging sequences. Power spectral densities (PSD) of the vibration signals were calculated and linear approximations to the spectral signatures were used to observe the overall trend. The intersection point and slopes of these linear representations were used to extract certain critical frequencies in order to define convex regions (CR) and convex hulls (CH) as representatives of the aging (degradation) process. Furthermore, using these CRs and CHs, the functional readiness of motors could be determined by comparison of the signatures for initial and aged conditions.
Diagnosis of acute promyelocytic leukaemia by RT‐PCR: detection of PML‐RARA and RARA‐PML fusion transcripts (1992)

Acute promyelocytic leukaemia (APL; AML M3) is identified by a unique t(15;17) translocation which fuses the PML gene to the retinoic acid receptor alpha gene (RARA). Reverse transcription coupled with the polymerase chain reaction (RT-PCR) has been used to develop a diagnostic test for APL based on the PML-RARA fusion message. Separate PCR assays were designed to amplify either PML-RARA (15q+ derived) or RARA-PML (17q- derived) chimaeric transcripts. PML-RARA transcripts were detected in every case from a series of 18 APL patients with cytogenetically confirmed t(15;17) translocations, whereas RARA-PML messages were detected in only 67% (12/18) of these patients. This suggests that it is the 15q+ derivative which mediates leukaemogenesis. Furthermore the PCR approach (or Southern analysis) may be used to identify in which of the alternative PML introns the breakpoint occurs; 52% of cases (15/29 patients) utilize a 5' PML intron and 48% the 3' intron (14/29 cases). Neither the choice of PML intron nor the expression of the 17q- derivative could be correlated with the microgranular variant of APL (M3V), overall survival rate, age, sex or presence of coagulopathy. Finally, the fusion message is undetectable in five remission samples. This indicates a possible use for RT-PCR in monitoring remission patients for evidence of relapse.
CCMP (2010)

This paper presents the design and implementation of CCMP, a conference management protocol currently under standardization within the IETF, conceived at the outset as a lightweight protocol allowing conferencing clients to access and manipulate objects describing a centralized conference. The CCMP is a state-less, XML-based, client-server protocol carrying in its request and response messages conference information in the form of XML documents and fragments conforming to the centralized conferencing data model schema. It represents a powerful means to control basic and advanced conference features such as conference state and capabilities, participants and relative roles and details. We first focus on the design of the protocol and then discuss how it has been integrated in the Meetecho collaborative framework developed at the University of Napoli as an active playground for IETF standardization activities in the field of real-time applications and infrastructure.
InvasiveHaemophilus influenzaeDisease in Utah Children: An 11‐Year Population‐Based Study in the Era of Conjugate Vaccine (2010)

H. influenzae continues to cause invasive disease in Utah children. Hia is the primary cause of the overall increased incidence of invasive H. influenzae disease and leads to disease similar to Hib. Isolated cases of Hib disease demonstrate a continued reservoir. The success of the Hib conjugate vaccine may therefore be vulnerable to vaccine shortages and refusal of vaccination.
Coherent electron cooling: Status of single-pass simulations (2013)

Advances in nuclear physics depend on experiments that employ hadron accelerators with dramatically increased luminosity. Stochastic cooling is currently used to increase hadron beam luminosity, but this approach faces serious difficulties at the high intensities and high energies proposed for high-energy election-ion colliders. The novel concept of coherent electron cooling (CeC) promises to cool hadron beams at a much faster rate. Simulations of a single pass through a CeC system are key to its experimental demonstration. Here we validate the primary components of these simulations.
Helicobacter pylori Cytotoxin-Associated Gene A Activates the Signal Transducer and Activator of Transcription 3 Pathway In vitro and In vivo (2009)

Persistent infection with Helicobacter pylori confers an increased risk for the development of gastric cancer. However, the exact mechanisms whereby this bacterium causes carcinogenesis have not been completely elucidated. Recent evidence indicates that aberrant activation of the signal transducers and activators of transcription 3 (STAT3) signaling pathway may play a role in gastric carcinogenesis. Therefore, we hypothesized that H. pylori infection modulates STAT3 signaling, favoring gastric cancer development. In epithelial cells infected with H. pylori, STAT3 was activated, as assessed by immunoblotting for phosphorylated STAT3, immunofluorescence of translocated STAT3, fluorescence recovery after photobleaching, and luciferase activation in transfected cells. Activation was dependent on translocation but not phosphorylation of cytotoxin-associated gene A (CagA) in host cells. Activation seemed to be receptor-mediated because preincubation of cells with the interleukin-6 (IL-6) receptor superantagonist sant7 or inhibition of gp130 by a monoclonal antibody prevented H. pylori-mediated STAT3 activation. However, activation was not related to autocrine activation by IL-6 or IL-11. CagA+ wild-type H. pylori, but not the noncarcinogenic cagA- mutant, activated STAT3 in gastric epithelial cells in vivo in the gerbil model of H. pylori-mediated gastric carcinogenesis. Collectively, these results indicate that H. pylori CagA activates the STAT3 signaling pathway in vitro and in vivo, providing a potential mechanism by which chronic H. pylori infection promotes the development of gastric cancer.
Enhancement of Crude Oil Biodegradation by Immobilizing of different Bacterial Strains on Porous PVA Hydrogels or Combining of them with their produced Biosurfactants (2014)

The degradation of the crude oil in wastewater by each of freely microorganisms and by immobilized them on each of crosslinked poly (vinyl alcohol) hydrogel (CPVA) and its foam (CPVAF) was reported. Also, it was studied by using biosurfactants (Bio s ) with free cells. The macroporous CPVAF was prepared by adding CaCO 3 as poreforming agent and epichlorohydrin as crosslinker. The prepared polymers are examining by FTIR, XRD, TGA, DSC and SEM analysis. The microorganisms of B.l., R.e. and P.x. isolated from contaminated effluents were investigated. The ability of these microorganisms to degrade the n-paraffin and PAHs was assessed by GC and HPLC analysis, respectively. Moreover, their stabilities and activities were tested in the growth count of bacteria study. The crosslinked CPVA carrier demonstrated better thermal stability and improvement in the microorganism efficiency with respect to hydrocarbons degradation than these of the CPVAF carrier. Scanning electron microscopy showed the presence of extracellular structures that could play an important role in the immobilization stability of cells on polymers. As well, GC analysis revealed that the percentage biodegradation ability of immobilized cells R.e. on CPVAF for the total n-paraffin was approximately, 100%. While, the HPLC analysis showed that the percentage biodegradation of cells for PAHs was enhancement by immobilized them on CPVA and also, at adding Bio s to them. The results suggest that the potential of using each of CPVA, PVAF as cell carriers and Bio s separately, to free cells to enhancing the biodegradation of petroleum hydrocarbons in an open marine environment.
Bone mineral density and vitamin D status in older women with and without metabolic syndrome (2012)

This study investigated associations between serum 25‐ hydroxyvitamin D [25(OH)D] and bone mineral density (BMD) in women &gt;50 years of age with and without metabolic syndrome (MetS). MetS as defined by the International Diabetes Foundation was waist &gt;88 cm with two additional factors from elevated blood pressure, serum triglycerides or glucose or decreased HDL‐cholesterol. Forty women, half with metabolic syndrome (MetS), had whole body, lumbar spine, hip and forearm BMD assessed by dual‐energy X‐ray absorptiometry (DEXA) scan. Serum 25(OH)D concentrations were assessed by enzyme‐linked immunosorbent assay (Immunodiagnostics Systems Ltd., Fountain Hills, AZ). No women had 25(OH)D &lt;25 nmol/L, 15% were between 25 ‐ &lt;50, 55% were between 50‐&lt;75, and 30% had ≥ 75 nmol/L. Mean (SD) for 25(OH)D was 62 (18) for women with MetS and was not significantly different (p&lt;0.10) from the mean of 71 (15) for control women. Z scores for BMD for age were higher in the lumbar spine ( p &lt;0.0004) and hip regions ( p &lt;.0024) for women in the MetS group and BMD tended to be higher (p&lt;0.06) in the whole body in the MetS group. BMD was not significantly different in the forearm between control and MetS groups. Overall, serum 25(OH)D did not correlate significantly with BMD in the sites measured. (Supported by Wentz Foundation and Oklahoma Agricultural Experiment Station, W2002)