gebhart/patrepeval huggingface dataset:
<i>Faecalibacterium</i>: a bacterial genus with promising human health applications (2023)

In humans, many diseases are associated with alterations in gut microbiota, namely increases or decreases in the abundance of specific bacterial groups. One example is the genus Faecalibacterium. Numerous studies have underscored that low levels of Faecalibacterium are correlated with inflammatory conditions, with inflammatory bowel disease (IBD) in the forefront. Its representation is also diminished in the case of several diseases, including colorectal cancer (CRC), dermatitis, and depression. Additionally, the relative presence of this genus is considered to reflect, at least in part, intestinal health status because Faecalibacterium is frequently present at reduced levels in individuals with gastrointestinal diseases or disorders. In this review, we first thoroughly describe updates to the taxonomy of Faecalibacterium, which has transformed a single-species taxon to a multispecies taxon over the last decade. We then explore the links discovered between Faecalibacterium abundance and various diseases since the first IBD-focused studies were published. Next, we examine current available strategies for modulating Faecalibacterium levels in the gut. Finally, we summarize the mechanisms underlying the beneficial effects that have been attributed to this genus. Together, epidemiological and experimental data strongly support the use of Faecalibacterium as a next-generation probiotic (NGP) or live biotherapeutic product (LBP).
<i>mRTVP-1</i>, a Novel p53 Target Gene with Proapoptotic Activities (2002)

We identified a novel mouse gene, mRTVP-1, as a p53 target gene using differential display PCR and extensive promoter analysis. The mRTVP-1 protein has 255 amino acids and differs from the human RTVP-1 (hRTVP-1) protein by two short in-frame deletions of two and nine amino acids. RTVP-1 mRNA was induced in multiple cancer cell lines by adenovirus-mediated delivery of p53 and by gamma irradiation or doxorubicin both in the presence and in the absence of endogenous p53. Analysis of RTVP-1 expression in nontransformed and transformed cells further supported p53-independent gene regulation. Using luciferase reporter and electrophoretic mobility shift assays we identified a p53 binding site within intron 1 of the mRTVP-1 gene. Overexpression of mRTVP-1 or hRTVP-1 induced apoptosis in multiple cancer cell lines including prostate cancer cell lines 148-1PA, 178-2BMA, PC-3, TSU-Pr1, and LNCaP, a human lung cancer cell line, H1299, and two isogenic human colon cancer cell lines, HCT116 p53(+/+) and HCT116 p53(-/-), as demonstrated by annexin V positivity, phase-contrast microscopy, and in selected cases 4',6'-diamidino-2-phenylindole staining and DNA fragmentation. Deletion of the signal peptide from the N terminus of RTVP-1 reduced its apoptotic activities, suggesting that a secreted and soluble form of RTVP-1 may mediate, in part, its proapoptotic activities.
Three-dimensional local binary patterns for hyperspectral imagery classification (2016)

Local binary patterns (LBP) features extracted from hyperspectral imagery (HSI) have gained impressive performance in hyperspectral classification tasks, for which LBP got considerable attention. However, existing LBP-based hyperspectral imagery classification methods utilized two-dimensional LBP (2DLBP) that could capture gray variation signal in space, which did not excavate the contextual information that hides in spectral-spatial structure considering that hyperspectral imagery characterizes by three dimension. Aimed at this problem, this paper presents a three-dimensional LBP-based (3DLBP) hyperspectral imagery classification method where 2DLBP textures histogram on three orthogonal planes are concatenated to form 3DLBP texture features to be classified by sparse representation. A serial of experiments are conducted on the Pavia university dataset, and the experimental results show that the performance of 3DLBP is significantly superior to that of 2DLBP.
Effect of a novel fluorapatite-forming calcium phosphate cement with calcium silicate on osteoblasts in comparison with mineral trioxide aggregate (2015)

We compared the effects of treatment with fluorapatite-forming calcium phosphate cement (FA-forming CPC) containing tricalcium silicate (TCS) and those of mineral trioxide aggregate (MTA), the gold standard endodontic cement, on cultured osteoblast-like cells (ROS 17/2.8 cells; ROS cells). The FA-forming CPC powder consisted of 61.29% CaHPO4, 32.26% CaCO3, and 6.45% NaF. One part TCS was combined with nine parts FA-forming CPC powder to make FA-forming CPC with TCS. A 1.5-M phosphate solution was mixed as a cement liquid with a powder/liquid ratio of 2.22. Cell culture was carried out using cell culture inserts, whereby each test material was put on a porous membrane insert in the cell culture plate. Proliferation, morphologic changes, and alkaline phosphatase activity in ROS cells were measured in the presence of FA-forming CPC with TCS and MTA and compared. The logarithmic growth phase and cellular morphologic changes in ROS cells were identical in all experimental groups. Additionally, no significant difference in alkaline phosphatase activity was noted in ROS cells exposed to FA-forming CPC with TCS and those exposed to MTA. In conclusion, FA-forming CPC with TCS has characteristics identical to those of MTA under the present experimental conditions and may thus be useful for endodontic applications.
Coupled reactions of immobilized enzymes and immobilized substrates: clinical application as exemplified by amylase assay. (1978)

We described a partitioned enzyme-sensor system, which incorporates an immoblized substrate and three or more discrete immobilized enzymes. This instrument measures alpha-amylase activity by passing the solution containing alpha-amylase over a column packed with immobilized starch. The resulting oligosaccharides are successively exposed to a column or columns containing immobolized glucose oxidase, catalase, glucoamylase or maltase, and glucose oxidase. The resulting hydrogen peroxide is detected by a three-electrode amperometric cell. All immobilized reagents were immobilized on a particulate, porous alumina to allow rapid and constant flow rate. With use of less than optimum immobilized reagents, alpha-amylase activity has been measured from about 5 to 200 kU/liter with a 50 microliter sample size. Lack of sensitivity is predominantly attributable to the low activity and low stability of immobilized maltase and glucoamylase. We believe that a clinical test using this system is feasible and desirable because the immobilized reagent system should allow for testing of alpha-amylase with excellent precision, convenience to the operator, and low cost.
Piezoelectric Quartz Crystal Microbalance Sensor for Trace Aqueous Cyanide Ion Determination (2006)

Using selective reaction chemistry, our present research has developed an online, real-time sensor capable of monitoring toxic cyanide at both drinking water standard and environmental regulatory concentrations. Through the use of a flow cell, aqueous samples containing cyanide are reacted with a gold electrode of a piezoelectric crystal to indirectly sense cyanide concentration by the dissolution of metallic gold. The quartz crystal is an AT-cut wafer sandwiched between two neoprene O-rings within the liquid flow cell. The presence of cyanide in solution results in the selective formation of a soluble dicyano-gold complex according to the Elsner reaction: 4Au + 8CN- + 2H2O + O2 <=> 4Au(CN)2- + 4OH-. The resulting loss of gold from the electrode is detected by the piezoelectric crystal as a resonant frequency change. Since free cyanide is a weak acid (pKa = 9.3), available protons compete for cyanide ligands. Therefore, increased sample pH provides higher sensitivity. The detection limits at pH 12 are 16.1 and 2.7 ppb for analysis times of 10 min and 1 h, respectively. The incorporation of the flow cell improves both analyte sensitivity and instrument precision, with an average signal intensity drift of only 5% over a 2-h analysis. The calibrations show excellent linearity over a variety of cyanide concentrations ranging from low ppb to hundreds of ppm. This detection method offers the advantage of selectively detecting cyanides posing a biohazard while avoiding detection of stable metal cyanides. This aspect of the system is based on competitive exchange of available metals and gold with cyanide ligands. Stable metal cyanide complexes possess a higher formation constant than cyanoaurate. This detection system has been configured into a flow injection analysis array for simple adaptation to automation. Anions commonly found in natural waters have been examined for interference effects. Additionally, the sensor is free from interference by aqueous cyanide analogues including thiocyanate. The developed detection system provides rapid cyanide determinations with little sample preparation or instrument supervision.
Synthesis of Highly Crystalline sp<sup>2</sup>-Bonded Boron Nitride Aerogels (2013)

sp(2)-Bonded boron nitride aerogels are synthesized from graphene aerogels via carbothermal reduction of boron oxide and simultaneous nitridation. The color and chemical composition of the original gel change dramatically, while structural features down to the nanometer scale are maintained, suggesting a direct conversion of the carbon lattice to boron nitride. Scanning and transmission electron microscopies reveal a foliated architecture of wrinkled sheets, a unique morphology among low-density, porous BN materials. The converted gels display a high degree of chemical purity (>95%) and crystalline order and exhibit unique cross-linking structures.
Origin of Magnetic Properties in Amorphous Metals. (1979)

The magnetic properties of amorphous metals are examined relative to changes in composition and heat treatment of amorphous transition metal-metalloid alloys. The transition metals examined were iron and iron plus nickel. These were alloyed with the metalloids, boron, silicon and carbon. Significant effects of alloy variation were observed on magnetic properties and on the crystallization and stress relief of these materials. The effects of stress on magnetic properties was studied.
Detecting irregularities in images and in video (2005)

We address the problem of detecting irregularities in visual data, e.g., detecting suspicious behaviors in video sequences, or identifying salient patterns in images. The term "irregular" depends on the context in which the "regular" or "valid" are defined. Yet, it is not realistic to expect explicit definition of all possible valid configurations for a given context. We pose the problem of determining the validity of visual data as a process of constructing a puzzle: We try to compose a new observed image region or a new video segment ("the query") using chunks of data ("pieces of puzzle") extracted from previous visual examples ("the database "). Regions in the observed data which can be composed using large contiguous chunks of data from the database are considered very likely, whereas regions in the observed data which cannot be composed from the database (or can be composed, but only using small fragmented pieces) are regarded as unlikely/suspicious. The problem is posed as an inference process in a probabilistic graphical model. We show applications of this approach to identifying saliency in images and video, and for suspicious behavior recognition.
Copper(2+) Binding to the Surface Residue Cysteine 111 of His46Arg Human Copper−Zinc Superoxide Dismutase, a Familial Amyotrophic Lateral Sclerosis Mutant (2000)

Mutations in copper-zinc superoxide dismutase (CuZnSOD) cause 25% of familial amyotrophic lateral sclerosis (FALS) cases. This paper examines one such mutant, H46R, which has no superoxide dismutase activity yet presumably retains the gain-of-function activity that leads to disease. We demonstrate that Cu(2+) does not bind to the copper-specific catalytic site of H46R CuZnSOD and that Cu(2+) competes with other metals for the zinc binding site. Most importantly, Cu(2+) was found to bind strongly to a surface residue near the dimer interface of H46R CuZnSOD. Cysteine was identified as the new binding site on the basis of multiple criteria including UV-vis spectroscopy, RR spectroscopy, and chemical derivatization. Cysteine 111 was pinpointed as the position of the reactive ligand by tryptic digestion of the modified protein and by mutational analysis. This solvent-exposed residue may play a role in the toxicity of this and other FALS CuZnSOD mutations. Furthermore, we propose that the two cysteine 111 residues, found on opposing subunits of the same dimeric enzyme, may provide a docking location for initial metal insertion during biosynthesis of wild-type CuZnSOD in vivo.
Pre-clinical development of the human CD40 agonistic antibody ADC-1013 (2015)

Meeting abstracts Activation of CD40 on dendritic cells increases cross-presentation of tumor antigens and as a result the number of activated tumor directed T effector cells. CD40 agonists have been shown to generate powerful systemic anti-tumor responses when administered in situ. The pre-
A novel diagnostic test for arthritis: Multivariate analysis of infrared spectra of synovial fluid (1997)

Fourier transform infrared spectroscopy has been applied to the investigation of synovial fluids (SFs) aspirated from arthritic joints. Significant differences, related to differences in the composition of the fluid as a result of the disease processes, were found between spectra of SFs from joints affected by rheumatoid arthritis, osteoarthritis, spondyloarthropathies, and meniscal injuries. Linear discriminant analysis with leave-one-out cross validation was used to classify 239 SF film spectra obtained from 86 patients. Using a patient-based approach, in which the consensus of results obtained from three spectra of each fluid was taken as the diagnosis, multivariate analysis successfully classified spectra into four classes, in excellent agreement with clinical diagnosis (96.5% correct classification). These results demonstrate that when combined with a properly trained classifier, infrared spectra of SF films can be used as an aid in the diagnosis of arthritic disorders. © 1997 John Wiley & Sons, Inc. Biospect 3: 161–167, 1997
A general framework for process scheduling (2010)

Abstract Existing methods for process scheduling can be broadly classified as network‐based or sequential. The former are used to address problems where different batches of the same or different tasks are freely mixed or split, whereas the latter are used to address problems where batch mixing/splitting is not allowed. A framework is proposed that allows us to: (1) express scheduling problems in facilities that consist of network and sequential, as well as continuous subsystems, (2) formulate mixed‐integer programming (MIP) scheduling models for such problems, and (3) solve the resulting MIP formulations effectively. The proposed framework bridges the gap between network and sequential approaches, thereby addressing the major formulation challenge in the area of process scheduling, namely, the development of a framework that can be used to address a wide spectrum of problems. © 2010 American Institute of Chemical Engineers AIChE J, 57: 695–710, 2011
Discovery of Stereospecific PARP-1 Inhibitor Isoindolinone NMS-P515 (2019)

Poly(ADP-ribose) polymerase-1 (PARP-1) is an enzyme involved in signaling and repair of DNA single strand breaks. PARP-1 employs NAD<sup>+</sup> to modify substrate proteins via the attachment of poly(ADP-ribose) chains. PARP-1 is a well established target in oncology, as testified by the number of marketed drugs (e.g., Lynparza, Rubraca, Zejula, and Talzenna) used for the treatment of ovarian, breast, and prostate tumors. Efforts in investigating an uncharted region of the previously identified isoindolinone carboxamide series delivered (<i>S</i>)-<b>13</b> (NMS-P515), a potent inhibitor of PARP-1 both in biochemical (<i>K</i> <sub>d</sub>: 0.016 μM) and cellular (IC<sub>50</sub>: 0.027 μM) assays. Cocrystal structure allowed explaining NMS-P515 stereospecific inhibition of the target. After having ruled out potential loss of enantiopurity in vitro and in vivo, NMS-P515 was synthesized in an asymmetric fashion. NMS-P515 ADME profile and its antitumor activity in a mouse xenograft cancer model render the compound eligible for further optimization.
Time reversal optical tomography: locating targets in a highly scattering turbid medium (2011)

A time reversal optical tomography (TROT) method for near-infrared (NIR) diffuse optical imaging of targets embedded in a highly scattering turbid medium is presented. TROT combines the basic symmetry of time reversal invariance and subspace-based signal processing for retrieval of target location. The efficacy of TROT is tested using simulated data and data obtained from NIR imaging experiments on absorptive and scattering targets embedded in Intralipid-20% suspension in water, as turbid medium. The results demonstrate the potential of TROT for detecting and locating small targets in a turbid medium, such as, breast tumors in early stages of growth.
Pattern Recognition-Driven Automatic Drainage Region Mapping to Accelerate Reservoir Simulations (2023)

Abstract History matching is widely considered as the most time- and resource-consuming phase of reservoir simulation modeling. Even with the advent of modern, computer-assisted, history matching methods, the dynamic calibration of large-scale simulation models represents a considerable computational undertake. The challenges become even more pronounced with incorporation of subsurface and production uncertainty. This paper outlines a step forward in acceleration of reservoir simulation studies by applying a split/merge approach constrained by no-flow boundary drainage region. The method transforms the history-matching process into an accelerated progressive sequence of dynamic model updates in time and space. Each segment defined as distinctive drainage region, the boundaries of the drainage regions are mapped based on no-flow conditions. Each segment is dynamically calibrated and history matched simultaneously in parallel. Lastly, the segments are merged back to reconstruct the original model to run the prediction phase. The detail of the workflow is described, as well as the implementation of the workflow in a synthetic model. A comparison between the conventional approach and the new approach is discussed. Recommendation and a way forward are shared to capitalize on the accelerated method for future reservoir studies.
Nanomolar-Potency 1,2,4-Triazoloquinoxaline Inhibitors of the Kidney Urea Transporter UT-A1 (2018)

Urea transporter A (UT-A) isoforms encoded by the Slc14a2 gene are expressed in kidney tubule epithelial cells, where they facilitate urinary concentration. UT-A1 inhibition is predicted to produce a unique salt-sparing diuretic action in edema and hyponatremia. Here we report the discovery of 1,2,4-triazoloquinoxalines and the analysis of 37 synthesized analogues. The most potent compound, 8ay, containing 1,2,4-triazolo[4,3- a]quinoxaline-substituted benzenesulfonamide linked by an aryl ether, rapidly and reversibly inhibited UT-A1 urea transport by a noncompetitive mechanism with IC<sub>50</sub> ≈ 150 nM; the IC<sub>50</sub> was ∼2 μM for the related urea transporter UT-B encoded by the Slc14a1 gene. Molecular modeling suggested a putative binding site on the UT-A1 cytoplasmic domain. In vitro metabolism showing quinoxaline ring oxidation prompted the synthesis of metabolically stable 7,8-difluoroquinoxaline analogue 8bl, which when administered to rats produced marked diuresis and reduced urinary osmolality. 8bl has substantially improved UT-A1 inhibition potency and metabolic stability compared with prior compounds.
Human Immunodeficiency Virus (HIV) Antigen-Antibody Combination Assays: Evaluation of HIV Seroconversion Sensitivity and Subtype Detection (2002)

In this study, we evaluated the performance of two prototype human immunodeficiency virus (HIV) antigen-antibody (Ag-Ab) combination assays, one from Abbott Laboratories (AxSYM HIV Ag-Ab) and the other from bioMerieux (VIDAS HIV Duo Ultra), versus five combination assays commercially available in Europe. The assays were Enzygnost HIV Integral, Genscreen Plus HIV Ag-Ab, Murex HIV Ag-Ab Combination, VIDAS HIV Duo, and Vironostika HIV Uniform II Ag-Ab. All assays were evaluated for the ability to detect p24 antigen from HIV-1 groups M and O, antibody-positive plasma samples from HIV-1 groups M and O, HIV-2, and 19 HIV seroconversion panels. Results indicate that although all combination assays can detect antibodies to HIV-1, group M, subtypes A to G, circulating recombinant form (CRF) A/E, and HIV-1 group O, their sensitivity varied considerably when tested using diluted HIV-1 group O and HIV-2 antibody-positive samples. Among combination assays, the AxSYM, Murex, and VIDAS HIV Duo Ultra assays exhibited the best antigen sensitivity (at ∼25 pg of HIV Ag/ml) for detection of HIV-1 group M, subtypes A to G and CRF A/E, and HIV-1 group O isolates. However, the VIDAS HIV Duo Ultra assay had a lower sensitivity for HIV-1 group M and subtype C, and was unable to detect subtype C antigen even at 125 pg of HIV Ag/ml. The HIV antigen sensitivity of the VIDAS HIV Duo and Genscreen Plus combination assays was ∼125 pg of HIV Ag/ml for detection of all HIV-1 group M isolates except HIV-1 group O while the sensitivity of Vironostika HIV Uniform II Ag-Ab and Enzygnost HIV Integral Ag-Ab assays for all the group M subtypes was >125 pg of HIV Ag/ml. Among the combination assays, the AxSYM assay had the best performance for detection of early seroconversion samples, followed by the Murex and VIDAS HIV Duo Ultra assays.
Backscattering target detection in a turbid medium by use of circularly and linearly polarized light (2005)

The polarization properties of the backscattered light from a turbid medium containing large-diameter (10.143-microm) and small-diameter (0.202-microm) spherical polystyrene particles are studied. It is shown that the difference in the polarization properties of the emerging light that originates at the target and that is backscattered from the medium allows for improvement of image contrast by use of polarized light. Based on the images obtained by the CCD camera, the polarization memory effect with circularly polarized light is demonstrated to have an advantage over the linear polarization technique in imaging a highly reflective target inside a turbid medium containing large particles.
Identifying potentially shockable rhythms without interrupting cardiopulmonary resuscitation* (2008)

The algorithm fulfilled the potential lifesaving advantages of allowing for uninterrupted chest compression, avoiding pauses for automated rhythm analyses before prompting delivery of an electrical shock.
A Novel Method for Mouse Retinal Temperature Determination Based on ERG Photoresponses (2017)

This study introduces a novel retinal temperature determination method based on the temperature dependent properties of photoresponses recorded by electroretinography (ERG). The kinetics and amplitudes of ERG photoresponses depend on retinal temperature. Additionally, raising retinal temperature increases the probability of long-wavelength photon absorption, which manifests as temperature dependence of photoreceptor sensitivity. In this study we extract a number of features that represent these properties from the a- and b-waves of mouse ex vivo ERG flash responses and construct three multivariable regression models between temperature and the selected features. The performance of these models was evaluated against a separate test dataset and for two of the models, an RMS temperature determination error of less than 0.50 °C could be reached. Our results demonstrate that the method can be successfully used for reliable retinal temperature determination ex vivo. The method, reflecting the temperature of distal retina, can be applied also in the estimation of retinal pigment epithelium temperature.