gebhart/patrepeval huggingface dataset:
HLA-DQA1 and HLA-DQB1 alleles and haplotypes in two Brazilian Indian tribes: evidence of conservative evolution of HLA-DQ. (1998)

Nucleotide sequence polymorphism of the HLA-DQA1 and HLA-DQB1 class II genes was analyzed in the Kaingang and Guarani Amerindians from southern Brazil using PCR sequence-specific oligonucleotide typing methods. Four different DQA1-DQB1 haplotypes were found: DQA1*0401-DQB1*0402 (associated with DRB1*0802, DRB1*08041, and DRB1*0807), DQA1*0501-DQB1*0301 (associated with DRB1*1602, DRB1*1413, and DRB1*1402), DQA1*03-DQB1*0302 (associated with DRB1*0404 and DRB1*0411), and DQA1*03-DQB1*03032 (associated with DRB1*09012). These HLA-DQA1 and HLA-DQB1 alleles and haplotypes are common in many other populations of all major ethnic groups. Alleles and haplotypes introduced into the populations by post-Columbian admixture were seen at low frequency both in the Kaingang (3.2%) and in the Guarani (3.8%). No novel HLA-DQA1 and HLA-DQB1 alleles have thus far been identified in Amerindians. This differs from previous results for HLA-DRB1, another class II locus presenting novel alleles (i.e., alleles not found in other ethnic groups and probably generated after migration of paleo-Indians to the Americas) in the Guarani and in other South American Indian populations. The distribution of the HLA-DQ alleles and haplotypes in Amerindians indicates a weaker diversifying selective pressure on the HLA-DQ genes compared with HLA-DRB1 and HLA-B. The more conservative evolution of HLA-DQA1 and HLA-DQB1 compared with HLA-DRB1 is strong evidence of (still not well-defined) functional differences of these class II genes.
Regulating the Searching Behaviour of Parked Vehicles Attempting to Locate Moving, Missing Entities (2018)

In this work, feedback regulation is added to a system that otherwise consists of a large, high-density network of parked vehicles. When awoken by an administrative centre, this network proceeds to search for moving, missing entities of interest using RFID-based techniques. RIFD readers and antennae are placed within the vehicles, while RFID passive tags are carried on the entity of interest via some means, e.g., a wrist band. Specifically, we seek to regulate the number and geographical distribution of parked vehicles that are “Switched On”, and thus actively searching for the moving entity of interest. In doing so, we seek to conserve vehicular energy consumption while, at the same time, maintain good geographical coverage of the city such that the moving entity of interest is likely to be located within an acceptable time frame. Which vehicles are “Switched On” at any point in time is a matter determined periodically through the use of stochastic techniques. The regulated system is demonstrated through the use case of a missing Alzheimer's patient in inner-city Dublin, Ireland.
TRANSLOCATOR PROTEIN 18 DKA (TSPO) ENDOGENOUS LIGAND REGULATES THE METABOLISM OF HUMAN OSTEOBLAST (2008)

Introduction : The mitochondrial Translocator Protein 18 kDa (TSPO, previously named as the peripheral benzodiazepine receptor - PBR) is involved in cellular respiration, steroidogenesis and apoptosis. In our recent study we reported on the role of the synthetic pharmacological ligands to the TSPO in enhancing human osteoblast catabolism. There is also a previous evidence of the existence of an endogenous ligands to the TSPO, but their role in the human osteoblast physiology hasn’t been verified yet. Porphyrine IX has been found having affinity to the TSPO. Therefore we hypothesize that human osteoblast metabolism might be mediated by the porphyrine IX and the mode of its action is similar the synthetic ligand to the TSPO.

Methods : Cell cycle of the cultured human derived osteoblast- like cells, following exposure to Porphyrine IX, endogenous ligand to TSPO, and N,N-di-n-hexyl 2-(4- fluorophenyl)indole-3-acetamide (FGIN-1–27), synthetic ligand to the TSPO, was determined by flow cytometry (FACS). These ligands’ affect on cell number, metabolic activity, i.e. cellular fluorodeoxyglucose ([18F]-FDG) incorporation and alkaline phosphatase activity, and cell death rate, i.e. LDH activity in the culture media, were assayed. The semi-quantitative response of TSPO to exposure to these ligands was estimated by Western blotting. Six samples of cultured cells for each condition were used. The t test was implemented for the statistical analyses. P values below.05 considered as statistically significant

Results: Cell count significantly decreased following exposure to FGIN-1–27 or porphyrine IX. Cellular [18F]-FDG incorporation and alkaline phosphatase activity were suppressed by both ligands. Cell cycle analysis showed a significant decrease in the fraction of cells in the G1 and G2/M phases when exposed to each ligand with a higher proportion of necrotic and apoptotic cells.

Western blotting showed a decrease in TSPO abundance following treatment by both ligands. LDH activity in culture media significantly increased following exposure to FGIN-1–27 or porphyrine IX.

Discussion: We show that FGIN-1–27 and porphyrine IX have a similar cell death inducing affect on human osteoblast-like cell in vitro. This affect is parallel to the inhibition of the cellular metabolism. Since both ligands similarly reduce the availability of TSPO we postulate that their mode of action is similar by affecting this mitochondrial structure with sub sequential induction of cell death, i.e. apoptosis and necrosis. Therefore we suggest that human osteoblast metabolism and cell cycle are mediated through TSPO and that porphyrine IX might be an active endogenous ligand to the TSPO having a regulatory affect on the human bone cell cycle.
The Optimization and Biological Significance of a 29-Host-Immune-mRNA Panel for the Diagnosis of Acute Infections and Sepsis (2021)

In response to the unmet need for timely accurate diagnosis and prognosis of acute infections and sepsis, host-immune-response-based tests are being developed to help clinicians make more informed decisions including prescribing antimicrobials, ordering additional diagnostics, and assigning level of care. One such test (InSep™, Inflammatix, Inc.) uses a 29-mRNA panel to determine the likelihood of bacterial infection, the separate likelihood of viral infection, and the risk of physiologic decompensation (severity of illness). The test, being implemented in a rapid point-of-care platform with a turnaround time of 30 min, enables accurate and rapid diagnostic use at the point of impact. In this report, we provide details on how the 29-biomarker signature was chosen and optimized, together with its molecular, immunological, and medical significance to better understand the pathophysiological relevance of altered gene expression in disease. We synthesize key results obtained from gene-level functional annotations, geneset-level enrichment analysis, pathway-level analysis, and gene-network-level upstream regulator analysis. Emerging findings are summarized as hallmarks on immune cell interaction, inflammatory mediators, cellular metabolism and homeostasis, immune receptors, intracellular signaling and antiviral response; and converging themes on neutrophil degranulation and activation involved in immune response, interferon, and other signaling pathways.
Imide—Dimethylsiloxane block copolymers: Design and synthesis of a permanent buried oxygen ion etch barrier (1997)

Imide—siloxane multiblock copolymers were investigated. A key feature of these copolymers is the preparation of bis(aminopropyl) oligomers via anionic ring-opening polymerization. The molecular weights of the oligomers ranged from 1000 to 5000 g/mol. The oligomers were coreacted with 4,4′-oxydianaline (ODA) and pyromellitic dianhydride (PMDA) diethyl ester chloride in a N-methyl-2-pyrrolidone/THF—solvent mixture in the presence of N-methylmorpholine. The resulting amic ethyl ester siloxane copolymers were isolated and washed to remove homopolymer contamination. Copolymer compositions, determined by 1H-NMR, ranged from 20 to 65 wt % siloxane content and the measured compositions were close to those charged. Solutions of the copolymers were cast and cured (350°C) to effect imidization, producing clear films. The films showed tough ductile mechanical properties with moduli varying with siloxane content. The copolymers displayed good thermal stability with decomposition temperatures in the proximity of 450°C. Multiphase morphologies were observed irrespective of siloxane block lengths or compositions. © 1997 John Wiley & Sons, Inc. J Appl Polym Sci 66: 199–208, 1997
The Characteristic Modes and Structures of Bluff-Body Stabilized Flames in Supersonic Coflow Air (2012)

The stability and structure of bluff-body stabilized hydrogen flames were investigated numerically and experimentally. The velocity of coflowing air was varied from subsonic velocity to a supersonic velocity of Mach 1.8. OH PLIF images and Schlieren images were used for analysis. Flame regimes were used to classify the characteristic flame modes according to the variation of the fuel-air velocity ratio, into jet-like flame, central-jet-dominated flame, and recirculation zone flame. Stability curves were drawn to find the blowout regimes and to show the improvement in flame stability with increasing lip thickness of the fuel tube, which acts as a bluff-body. These curves collapse to a single line when the blowout curves are normalized by the size of the bluff-body. The variation of flame length with the increase in air flow rate was also investigated. In the subsonic coflow condition, the flame length decreased significantly, but in the supersonic coflow condition, the flame length increased slowly and finally reached a near-constant value. This phenomenon is attributed to the air-entrainment of subsonic flow and the compressibility effect of supersonic flow. The closed-tip recirculation zone flames in supersonic coflow had a reacting core in the partially premixed zone, where the fuel jet lost its momentum due to the high-pressure zone and followed the recirculation zone; this behavior resulted in the long characteristic time for the fuel-air mixing.
Localization of the Activation Gate for Small Conductance Ca2+-activated K+Channels (2002)

Small conductance Ca2+-activated K+ (SK) channels open in response to increased cytosolic Ca2+ and contribute to the afterhyperpolarization in many excitable cell types. Opening of SK channels is initiated by Ca2+ binding to calmodulin that is bound to the C terminus of the channel. Based on structural information, a chemomechanical gating model has been proposed in which the chemical energy derived from Ca2+ binding is transduced into a mechanical force that restructures the protein to allow K+ ion conduction through the pore. However, the residues that comprise the physical gate of the SK channels have not been identified. In voltage-gated K+ (Kv) channels, access to the inner vestibule is controlled by a bundle crossing formed by the intracellular end of the sixth transmembrane domain (S6) of each of the four channel subunits. Probing SK channels with internally applied quaternary amines suggests that the inner vestibules of Kv and SK channels share structural similarity. Using substituted cysteine accessibility mutagenesis, the relatively large molecule [2-(trimethylammonium)] methanethiosulfonate accessed positions near the putative bundle crossing more rapidly in the open than the closed state but did not modify S6 positions closer to the selectivity filter. In contrast, the smaller compound, 2-(aminoethyl) methanethiosulfonate (MTSEA), modified a position predicted to lie in the lumen immediately intracellular to the selectivity filter equivalently in the open and closed states. The pore blocker tetrabutylammonium impeded MTSEA access to this position in both open and closed channels. The results suggest that the SK channel gate is not formed by the cytoplasmic end of S6 but resides deep in the channel pore in or near the selectivity filter.
Proposed digital holographic 3D mapping of coral beds (2008)

Digital Holography is a technique which provides a measurement of the complex field reflecting from a coherently illuminated object. When the measurement is performed with two carefully chosen wavelengths a phase difference map can be created providing a three dimensional map of the object. We present results from a laboratory experiment where the surface contours of coral are measured in seawater. Contour maps with step sizes on the order of 0.1 mm can easily be obtained. We propose that this technique be used to remotely monitor the growth of coral in an effort to quantify the health of coral beds. The technique is effective from space, aircraft, ships, buoys or rigid platforms such as a pier. In the last few years we have been successfully using this technique to measure objects through very turbulent atmosphere at ranges of up to 700 meters and we are now applying the concept to shoreline applications.
Melanoma Inhibits Macrophage Activation by Suppressing Toll-like Receptor 4 Signaling (2005)

Melanoma inhibits macrophage activation by suppressing TLR-4 signaling downstream of the TLR-4 receptor.
GABA(A) receptors containing (alpha)5 subunits in the CA1 and CA3 hippocampal fields regulate ethanol-motivated behaviors: an extended ethanol reward circuitry (2001)

GABA receptors within the mesolimbic circuitry have been proposed to play a role in regulating alcohol-seeking behaviors in the alcohol-preferring (P) rat. However, the precise GABA A receptor subunit(s) mediating the reinforcing properties of EtOH remains unknown. We examined the capacity of intrahippocampal infusions of an α5 subunit-selective (∼75-fold) benzodiazepine (BDZ) inverse agonist [i.e., RY 023 (RY) (tert-butyl 8-(trimethylsilyl) acetylene-5,6-dihydro-5-methyl-6-oxo-4H-imidazo [1,5a] [1,4] benzodiazepine-3-carboxylate)] to alter lever pressing maintained by concurrent presentation of EtOH (10% v/v) and a saccharin solution (0.05% w/v). Bilateral (1.5–20 μg) and unilateral (0.01–40 μg) RY dose-dependently reduced EtOH-maintained responding, with saccharin-maintained responding being reduced only with the highest doses (e.g., 20 and 40 μg). The competitive BDZ antagonist ZK 93426 (ZK) (7 μg) reversed the RY-induced suppression on EtOH-maintained responding, confirming that the effect was mediated via the BDZ site on the GABA A receptor complex. Intrahippocampal modulation of the EtOH-maintained responding was site-specific; no antagonism by RY after intra-accumbens [nucleus accumbens (NACC)] and intraventral tegmental [ventral tegmental area (VTA)] infusions was observed. Because the VTA and NACC contain very high densities of α1 and α2 subunits, respectively, we determined whether RY exhibited a “negative” or “neutral” pharmacological profile at recombinant α1β3γ2, α2β3γ2, and α5β3γ2 receptors expressed in Xenopus oocytes. RY produced “classic” inverse agonism at all α receptor subtypes; thus, a neutral efficacy was not sufficient to explain the failure of RY to alter EtOH responding in the NACC or VTA. The results provide the first demonstration that the α5-containing GABA A receptors in the hippocampus play an important role in regulating EtOH-seeking behaviors.
G (Gross) and H-2 Cell-Surface Antigens: Location on Gross Leukemia Cells by Electron Microscopy with Visually Labeled Antibody (1970)

The hybrid-antibody method of locating cell-surface antigens in electron micrographs, with either ferritin or southern bean mosaic virus as the visual marker, was applied to the cells of a transplanted murine leukemia induced by Gross virus. The two antigens studied were (a) G (Gross) cell-surface antigen, which is a specific component of cells infected with Gross virus and is identified by cytotoxic hyperimmune C57BL/6 antiserum, and (b) H-2 antigen, which is the major histocompatibility determinant of the mouse. Both antigens were represented on the cell surface in discrete circumscribed areas. Neither antigen was present on free Gross virions or on virions in the process of budding from the cell surface. Thus G cell-surface antigen identified by C57BL mouse cytotoxic antiserum is not a constituent of the viral envelope, which accounts for the poor virus-neutralizing capacity of such antibody. Virus maturation may take place preferentially at regions of the cell surface where H-2 and G antigens are absent, for budding was seldom seen in H-2(+) sectors and never convincingly in G(+) sectors. In other experiments, serum from an untreated NZB mice aged 16 months gave labeling of the virion only, showing that this mouse strain, in contrast to C57BL and other strains, forms antibody to envelope antigen of Gross virus.
Novel Bat Influenza Virus NS1 Proteins Bind Double-Stranded RNA and Antagonize Host Innate Immunity (2015)

We demonstrate that novel bat HL17NL10 and HL18NL11 influenza virus NS1 proteins are effective interferon antagonists but do not block general host gene expression. Solving the RNA-binding domain structures revealed the canonical NS1 symmetrical homodimer, and RNA binding required conserved basic residues in this domain. Interferon antagonism was strictly dependent on RNA binding, and chimeric bat influenza viruses expressing NS1s defective in this activity were highly attenuated in interferon-competent cells but not in cells unable to establish antiviral immunity.
A common antigenic motif recognized by naturally occurring human VH5–51/VL4–1 anti-tau antibodies with distinct functionalities (2018)

Misfolding and aggregation of tau protein are closely associated with the onset and progression of Alzheimer’s Disease (AD). By interrogating IgG+ memory B cells from asymptomatic donors with tau peptides, we have identified two somatically mutated VH5–51/VL4–1 antibodies. One of these, CBTAU-27.1, binds to the aggregation motif in the R3 repeat domain and blocks the aggregation of tau into paired helical filaments (PHFs) by sequestering monomeric tau. The other, CBTAU-28.1, binds to the N-terminal insert region and inhibits the spreading of tau seeds and mediates the uptake of tau aggregates into microglia by binding PHFs. Crystal structures revealed that the combination of VH5–51 and VL4–1 recognizes a common Pro-Xn-Lys motif driven by germline-encoded hotspot interactions while the specificity and thereby functionality of the antibodies are defined by the CDR3 regions. Affinity improvement led to improvement in functionality, identifying their epitopes as new targets for therapy and prevention of AD.
A complementarity‐based vapor‐liquid equilibrium formulation for equation‐oriented simulation and optimization (2023)

Abstract Vapor‐liquid equilibrium (VLE) is a cornerstone of computer‐aided process engineering (CAPE). Embedded within process system models, VLE calculations are inherently procedural with non‐smooth behavior that frequently requires discrete decisions. Traditionally, these features resist the incorporation of VLE within efficient, large‐scale equation‐oriented (EO) process simulation and optimization strategies. On the other hand, recent reformulation of VLE models through the incorporation of complementarity constraints has broadened its scope to deal seamlessly with phase transitions and even supercritical excursions in process simulation and optimization. In this study, we extend these VLE complementarity models to EO frameworks where procedural thermodynamic property libraries are still required. Here we develop an efficient, non‐intrusive, and intuitive “square‐flash” equation system that has been implemented within the IDAES Integrated Platform (IDAES‐IP). The effectiveness of this modular approach is demonstrated on case studies for non‐ideal flash calculations and distillation optimization, with disappearing phases and supercritical transitions.
Study of ultramicroporous carbons by high-pressure sorption. Part 4.—Isotherms and kinetic transport in activated carbons (1989)

Low-pressure hystereses, shown to exist for both nitrogen and carbon dioxide on as-received TCM carbon, disappear upon slight activation. These hystereses are related, in the case of nitrogen, to protracted penetration of restricted regions and, in the case of carbon dioxide, to dilation of tiny constrictions. A highly oxygen-activated carbon (19% weight loss) showed minute hysteresis in CO2 sorption experiments, while the more activated carbon (32% weight loss) formed by nitric acid activation showed more extreme hysteresis. These hystereses are related to swelling of the progressively weakened carbon matrix. Nitrogen, which is a poor swelling agent, does not show any hysteresis with these highly activated carbons. A series of TCM carbons which were progressively activated by oxygen showed a maximum in their sorption affinity constant with respect to the degree of activation. This maximum is related to either the greater accessibility of new small-pore regions or to the gradual opening of tiny constrictions that regulate transport into these regions.The lack of internal pore resistance to transport in a slightly activated carbon provides conditions conducive to observation of transient barriers formed in the entrances to the outermost pores immediately after applying a pressure step.
CONDENSATION OF CINNAMALDEHYDE WITH CROTONIC ESTER (1954)

Condensation of cinnamaldehyde with methyl crotonate in the presence of alcohol-flee potassium methoxide gives,after hydrolysis,p-phenyl-benzoic acid in low yield.Its structure has been ascertained by direct comparison with an au- thentic sample.
Numerical Investigation of Edge Flame Structure of Counterflow Nonpremixed Flames with Local Extinction Due to Flame Stretch (2005)

Laminar counterflow nonpremixed flames with local extinction caused by nonuniform inflows are numerically investigated in two-dimensions in a system governed by Lewis numbers of unity and assuming a single-step, irreversible, finite-rate reaction. A numerical method based on the SIMPLE algorithm is used. Edge flame structures are investigated through the introduction of a new progress variable defined as the normalized integral of the mass fraction of a product in the mixture fraction Z space and which expresses the progress of the chemical reaction. Calculation results reveal that the edge flame structure can be classified into three regions; fully burning flame, weakened flame with a low reaction rate, and a non-reacting preheat region. Under these conditions, and in terms of the energy balance, the edge flame structure is dependent on the Z-directional heat diffusion transport, heat consumption (given by the progress variable), and heat production by chemical reaction. It is found that each type of flame structure can be well characterized by three parameters; the mixture fraction, the stoichiometric scalar dissipation rate, and the progress variable. These three parameters are identified as important factors affecting the edge flame structure of nonpremixed flames with local extinction.
Structure activity relationship studies of cinnamic acid derivatives as inhibitors of human neutrophil elastase revealed by ligand docking calculations. (2003)

Structure-activity relationship of cinnamic acid derivatives as inhibitors of the human neutrophil elastase is reported. Comparison of the inhibitory concentrations (IC50 values) with the results of the ligand docking calculations revealed that the structure element of the aromatic ortho-dihydroxy groups combined with a lipophilic residue seems to be a prerequisite for an optimal binding within the active site.