gebhart/patrepeval huggingface dataset:
Leukotrienes: Underappreciated Mediators of Innate Immune Responses (2005)

Leukotrienes are bronchoconstrictor and vasoactive lipid mediators that are targets in the treatment of asthma. Although they are increasingly recognized to exert broad proinflammatory effects, their role in innate immune responses is less well appreciated. These molecules are indeed synthesized by resident and recruited leukocytes during infection. Acting via cell surface G protein-coupled receptors and subsequent intracellular signaling events, they enhance leukocyte accumulation, phagocyte capacity for microbial ingestion and killing, and generation of other proinflammatory mediators. Interestingly, a variety of acquired states of immunodeficiency, such as HIV infection and malnutrition, are characterized by a relative deficiency of leukotriene synthesis. The data reviewed herein point to leukotrienes as underappreciated yet highly relevant mediators of innate immunity.
A genomic and clinical prognostic index for hepatitis C-related early-stage cirrhosis that predicts clinical deterioration (2014)

A genomic and clinical prognostic index readily available for clinical use was successfully validated, warranting further clinical evaluation for prognostic prediction and clinical trial stratification and enrichment for preventive interventions.
Hepatitis C Virus NS5A Protein Down-regulates the Expression of Spindle Gene Aspm through PKR-p38 Signaling Pathway (2008)

Hepatitis C virus often causes persistent infection and hepatocellular carcinoma. Studies have demonstrated the roles of viral nonstructural protein 5A (NS5A) in the induction of chromosome aneuploidy, but the molecular mechanisms are not clear. In this study, hydrodynamics-based in vivo transfection was applied to a mouse system. Mouse hepatocytes that successfully expressed NS5A protein were isolated by laser capture microdissection. Gene expression profiles of the NS5A-expressing hepatocytes were examined by an Affymetrix oligonucleotide microarray system. Aspm (abnormal spindle-like, microcephaly associated), which encodes the mitotic spindle protein ASPM, was identified to be differentially expressed in the absence and the presence of NS5A. The down-regulation of Aspm mRNA and ASPM protein was confirmed by real time polymerase chain reaction and Western blot analysis, respectively, both in mouse model systems and in viral subgenomic replicon and in vitro transfection culturing systems. In addition, cultured cells that constitutively expressed NS5A protein showed G(2)/M cell cycle block and chromosome aneuploidy. Overexpression of ASPM relieved the G(2)/M cell cycle block. Furthermore, NS5A protein repressed the promoter activity of Aspm gene in a dose-dependent manner. The regulatory effect was abolished when amino acid substitutions P2209L, T2214A, and T2217G known to interrupt the NS5A-PKR interaction were introduced into the NS5A protein. This indicates that the down-regulation of Aspm expression is via the PKR-p38 signaling pathway. These results suggest that NS5A protein down-regulates the expression of the mitotic spindle protein ASPM and induces aberrant mitotic cell cycle associated with chromosome instability and hepatocellular carcinoma.
Differences in gene copy number carried by different MHC ancestral haplotypes. Quantitation after physical separation of haplotypes by pulsed field gel electrophoresis. (1990)

We have examined the hypothesis that MHC ancestral haplotypes have a specific content of genes regulating the extent of autoimmune reactions. Gene copy number was quantitated by objective densitometry after PFGE was used to separate heterozygous AHs of different lengths. Initially we analyzed examples of known gene copy number at the C4 and 21 hydroxylase loci and showed that the approach provides predictable results. We then studied heterozygotes containing one characterized and one uncharacterized AH with particular attention to the gene copy number at the C4, Cyp21, and DRB loci. Each AH studied has a characteristic gene copy number at each locus studied. The same may be true of TNF, but other possibilities must be considered. AHs are markers for extensive chromosomal segments including particular numbers of several functional genes. Since AHs mark susceptibility to autoimmune disease, differences in gene copy number may be implicated.
Functional Resistance Training to Improve Knee Strength and Function After Acute Anterior Cruciate Ligament Reconstruction: A Case Study (2020)

FRT may serve as a viable approach to improve knee strength and function after ACL reconstruction.
<title>Using a new liquid-crystal polarization modulator for a polarimetric glucose sensor</title> (2005)

This paper presents a new liquid-crystal polarization modulator comprising a nematic liquid-crystal variable retarder (LCVR) and two quarter-wave plates for the measurement of glucose concentrations. Rather than using a conventional Faraday modulator, this study firstly adopts a LCVR driven by sinusoidal signals to modulate the polarization angle of the light as a sinusoidal function. It is found that the variation frequency of the polarization angle doubles that of the driving signal, and the modulation depth is not proportional to the driving amplitude. These features are quite different from a Faraday modulator. Therefore, a signal demodulation algorithm which developed to adapt the particular features of the LC modulator enables the polarization rotation angle corresponding to the glucose concentration to be derived. The proposed measurement method has a minimum resolution of 0.05 degrees corresponding to a glucose concentration of 0.2 g/dl. Compared to its conventional counterparts, the developed polarimeter has a simpler structure, fewer optical elements, and a cheaper modulator component.
Ultraviolet Inactivation Kinetics of <i>Escherichia coli</i> and <i>Yersinia pseudotuberculosis</i> in Annular Reactors (2007)

Terrorist threats have precipitated the need for information on the ultraviolet (UV) resistance of potential biothreat agents in food processing, such as Yersinia pestis. The objective of this study was to characterize the resistance of the Yersinia species to UV treatment using a single-lamp annular UV reactor. A novel method is proposed to measure the inactivation kinetics of Yersinia pseudotuberculosis, a surrogate of Y. pestis. This proposed method can overcome the disadvantages of the traditional collimated beam approach for liquids with high absorptive properties, such as liquid foods. As a reference, an inactivation rate of Escherichia coli K12 in caramel model solutions was measured first. Both first-order and series-event inactivation models were used to fit UV inactivation data. For the series-event model, an inactivation constant of k(SE)= 0.675 cm(2)/mJ and threshold n= 4 were obtained for E. coli K12 with the coefficient of determination R(2)= 0.987 and the standard deviation of log(10) reductions sigma(y)= 0.133. For Y. pseudotuberculosis, k(SE)= 0.984 cm(2)/mJ and n= 3 were obtained with R(2)= 0.972 and sigma(y)= 0.212. In contrast, for the first-order inactivation model, the first-order inactivation constant k(1)= 0.325 cm(2)/mJ with R(2)= 0.907 and sigma(y)= 0.354 was found for E. coli; and k(1)= 0.557 cm(2)/mJ with R(2)= 0.916 and sigma(y)= 0.402 was obtained for Y. pseudotuberculosis. Based on R(2), sigma(y), and the maximum absolute and relative errors, the series-event inactivation model describes the UV inactivation kinetics of Y. pseudotuberculosis and E. coli better than the first-order model. It is apparent that Y. pseudotuberculosis is less resistant to UV light than E. coli K12.
Significance of Complement System in Ischemic Stroke: A Comprehensive Review (2019)

The complement system is an essential part of innate immunity, typically conferring protection via eliminating pathogens and accumulating debris. However, the defensive function of the complement system can exacerbate immune, inflammatory, and degenerative responses in various pathological conditions. Cumulative evidence indicates that the complement system plays a critical role in the pathogenesis of ischemic brain injury, as the depletion of certain complement components or the inhibition of complement activation could reduce ischemic brain injury. Although multiple candidates modulating or inhibiting complement activation show massive potential for the treatment of ischemic stroke, the clinical availability of complement inhibitors remains limited. The complement system is also involved in neural plasticity and neurogenesis during cerebral ischemia. Thus, unexpected side effects could be induced if the systemic complement system is inhibited. In this review, we highlighted the recent concepts and discoveries of the roles of different kinds of complement components, such as C3a, C5a, and their receptors, in both normal brain physiology and the pathophysiology of brain ischemia. In addition, we comprehensively reviewed the current development of complement-targeted therapy for ischemic stroke and discussed the challenges of bringing these therapies into the clinic. The design of future experiments was also discussed to better characterize the role of complement in both tissue injury and recovery after cerebral ischemia. More studies are needed to elucidate the molecular and cellular mechanisms of how complement components exert their functions in different stages of ischemic stroke to optimize the intervention of targeting the complement system.
Music Recommendations in Hyperbolic Space: An Application of Empirical Bayes and Hierarchical Poincaré Embeddings (2019)

Matrix Factorization (MF) is a common method for generating recommendations, where the proximity of entities like users or items in the embedded space indicates their similarity to one another. Though almost all applications implicitly use a Euclidean embedding space to represent two entity types, recent work has suggested that a hyperbolic Poincaré ball may be more well suited to representing multiple entity types, and in particular, hierarchies. We describe a novel method to embed a hierarchy of related music entities in hyperbolic space. We also describe how a parametric empirical Bayes approach can be used to estimate link reliability between entities in the hierarchy. Applying these methods together to build personalized playlists for users in a digital music service yielded a large and statistically significant increase in performance during an A/B test, as compared to the Euclidean model.
Cortical and Subcortical Correlates of Electroencephalographic Alpha Rhythm Modulation (2004)

Neural correlates of electroencephalographic (EEG) alpha rhythm are poorly understood. Here, we related EEG alpha rhythm in awake humans to blood-oxygen-level-dependent (BOLD) signal change determined by functional magnetic resonance imaging (fMRI). Topographical EEG was recorded simultaneously with fMRI during an open versus closed eyes and an auditory stimulation versus silence condition. EEG was separated into spatial components of maximal temporal independence using independent component analysis. Alpha component amplitudes and stimulus conditions served as general linear model regressors of the fMRI signal time course. In both paradigms, EEG alpha component amplitudes were associated with BOLD signal decreases in occipital areas, but not in thalamus, when a standard BOLD response curve (maximum effect at approximately 6 s) was assumed. The part of the alpha regressor independent of the protocol condition, however, revealed significant positive thalamic and mesencephalic correlations with a mean time delay of approximately 2.5 s between EEG and BOLD signals. The inverse relationship between EEG alpha amplitude and BOLD signals in primary and secondary visual areas suggests that widespread thalamocortical synchronization is associated with decreased brain metabolism. While the temporal relationship of this association is consistent with metabolic changes occurring simultaneously with changes in the alpha rhythm, sites in the medial thalamus and in the anterior midbrain were found to correlate with short time lag. Assuming a canonical hemodynamic response function, this finding is indicative of activity preceding the actual EEG change by some seconds.
Reverse transcription polymerase chain reaction for the rearranged retinoic acid receptor alpha clarifies diagnosis and detects minimal residual disease in acute promyelocytic leukemia. (1992)

The characteristic t(15;17) of acute promyelocytic leukemia (APL) fuses the retinoic acid receptor alpha (RAR-alpha) gene on chromosome 17 to a gene on chromosome 15 called PML, a putative transcription factor. This distinct translocation results in a fusion mRNA detected by Northern analysis. Two cDNAs have been isolated that differ in the extent of 3' PML nucleic acid sequence contained. This study describes a reverse transcription polymerase chain reaction (RT-PCR) assay for the PML/RAR-alpha fusion transcript, which amplifies PML/RAR-alpha mRNA from APL cells with either reported breakpoint. DNA sequencing of the predominant RT-PCR products from 6 patients showed identical RAR-alpha exonic breakpoints and two PML breakpoints. This RT-PCR assay was positive in leukemic cells from 30/30 APL patients with the molecular rearrangement confirmed by cytogenetics or Northern analysis. In leukemic cells of patients with a morphologic diagnosis of APL lacking the t(15;17) by routine cytogenetics, a positive RT-PCR assay predicted clinical response to all-trans-retinoic acid (RA) therapy. Dilutional studies with leukemic cells that express (NB4) or do not express (HL-60) a PML/RAR-alpha fusion mRNA reveal that this RT-PCR assay detects the transcript from as little as 50 pg of total RNA. In APL cells from 5/6 patients treated with RA alone, a complete response by clinical and cytogenetic criteria accompanied a persistently positive RT-PCR assay. This preceded relapse by 1-6 months. RT-PCR for PML/RAR-alpha mRNA provides a more-sensitive test for the t(15;17) than routine cytogenetics or Northern analysis. This molecular rearrangement detected by RT-PCR best defines this RA-responsive malignancy. The RT-PCR assay for the PML/RAR-alpha transcript yields important diagnostic and prognostic information in the management of APL patients.
The site of action of N-<i>alpha</i>-tosyl-<scp>l</scp>-lysyl-chloromethyl-ketone (TLCK) on cloned cytotoxic T lymphocytes. (1983)

N-alpha-tosyl-L-lysyl-chloromethyl-ketone (TLCK), an irreversible inhibitor of trypsin-like serine proteases, is a potent, nontoxic inhibitor of cytotoxic T lymphocyte (CTL) activity with half-maximal inhibition of an alloreactive CTL clone occurring at [TLCK] = 30 microM. We have utilized TLCK as an affinity probe for functionally important CTL surface molecules by raising rabbit antibodies specific for the tosyl group and employing them as immunoprecipitating reagents. When 125I-labeled cloned CTL were treated with TLCK, immunoprecipitation with rabbit anti-tosyl antibodies and analysis by polyacrylamide gel electrophoresis revealed a small number of TLCK-binding proteins. Prior alkylation of radiolabeled CTL with iodoacetamide inhibited TLCK binding only slightly, suggesting that TLCK binding did not occur via free sulfhydryl groups. Thymocytes and a second CTL clone both had very similar patterns of TLCK-binding proteins; in contrast the TLCK-binding proteins of B cells differed greatly. Sequential immunoprecipitation experiments identified the predominant CTL TLCK-binding protein as T200. Lymphocyte function-associated antigen-1 also reacted with TLCK but to a lesser extent. The inhibitory role of cell-surface bound TLCK (vs intracellular TLCK) was demonstrated by protection experiments using Concanavalin A, a reversible ligand of the CTL cell surface. These experiments suggest that T200 may be required for cytotoxic activity of CTL.
Growth of single diamond crystallites around nanometer-scale silicon wires (1995)

Diamond crystallites were nucleated and grown from the vapor phase on silicon substrates previously processed into arrays of nanometer-scale silicon wires. We found that the nanowires did not aid nucleation, and that the nucleation density on the nanowire base was very low (&lt;104 cm−2). Most importantly, we discovered that single diamond crystallites grew around the nanowires, infiltrating the nanowire arrays, forming new composite structures. This discovery clearly shows how inclusions can be trapped in vapor grown diamond crystallites, and challenges the common assumption that growth precursors on the diamond surface are relatively immobile.
P,O-Phosphinophenolate zinc(<scp>ii</scp>) species: synthesis, structure and use in the ring-opening polymerization (ROP) of lactide, ε-caprolactone and trimethylene carbonate (2015)

The P,O-type phosphinophenol proligands (1·H, 2-PPh2-4-Me-6-Me-C6H2OH; 2·H, 2-PPh2-4-Me-6-(t)Bu-C6H2OH) readily react with one equiv. of ZnEt2 to afford in high yields the corresponding Zn(II)-ethyl dimers of the type [(κ(2)-P,O)Zn-Et]2 (3 and 4) with two μ-OPh bridging oxygens connecting the two Zn(II) centers, as determined by X-ray diffraction (XRD) studies in the case of 3. Based on diffusion-ordered NMR spectroscopy (DOSY), both species 3 and 4 retain their dimeric structures in solution. The alcoholysis reaction of Zn(II) alkyls 3 and 4 with BnOH led to the high yield formation of the corresponding Zn(II) benzyloxide species [(κ(2)-P,O)Zn-OBn]2 (5 and 6), isolated in a pure form as colorless solids. The centrosymmetric and dimeric nature of Zn(II) alkoxides 5 and 6 in solution was deduced from DOSY NMR experiments and multinuclear NMR data. Though the heteroleptic species 5 is stable in solution, its analogue 6 is instable in CH2Cl2 solution at room temperature to slowly decompose to the corresponding homoleptic species 8via the transient formation of (κ(2)-P,O)2Zn2(μ-OBn)(μ–κ(1):κ(1)-P,O) (6′). Crystallization of compound 6 led to crystals of 6′, as established by XRD analysis. The reaction of ZnEt2 with two equiv. of 1·H and 2·H allowed access to the corresponding homoleptic species of the type [Zn(P,O)2] (7 and 8). All gathered data are consistent with compound 7 being a dinuclear species in the solid state and in solution. Data for species 8, which bears a sterically demanding P,O-ligand, are consistent with a mononuclear species in solution. The Zn(II) alkoxide species 5 and the [Zn(P,O)2]-type compounds 7 and 8 were evaluated as initiators of the ring-opening polymerization (ROP) of lactide (LA), ε-caprolactone (ε-CL) and trimethylene carbonate (TMC). Species 5 is a well-behaved ROP initiator for the homo-, co- and ter-polymerization of all three monomers with the production of narrow disperse materials under living and immortal conditions. Though species 7 and 8 are ROP inactive on their own, they readily polymerize LA in the presence of a nucleophile such as BnOH to produce narrow disperse PLA, presumably via an activated-monomer ROP mechanism.
BCAT1 expression associates with ovarian cancer progression: possible implications in altered disease metabolism (2015)

Previously, we have identified the branched chain amino-acid transaminase 1 (BCAT1) gene as notably hypomethylated in low-malignant potential (LMP) and high-grade (HG) serous epithelial ovarian tumors, compared to normal ovarian tissues. Here we show that BCAT1 is strongly overexpressed in both LMP and HG serous epithelial ovarian tumors, which probably correlates with its hypomethylated status. Knockdown of the BCAT1 expression in epithelial ovarian cancer (EOC) cells led to sharp decrease of cell proliferation, migration and invasion and inhibited cell cycle progression. BCAT1 silencing was associated with the suppression of numerous genes and pathways known previously to be implicated in ovarian tumorigenesis, and the induction of some tumor suppressor genes (TSGs). Moreover, BCAT1 suppression resulted in downregulation of numerous genes implicated in lipid production and protein synthesis, suggesting its important role in controlling EOC metabolism. Further metabolomic analyses were indicative for significant depletion of most amino acids and different phospho- and sphingolipids following BCAT1 knockdown. Finally, BCAT1 suppression led to significantly prolonged survival time in xenograft model of advanced peritoneal EOC. Taken together, our findings provide new insights about the functional role of BCAT1 in ovarian carcinogenesis and identify this transaminase as a novel EOC biomarker and putative EOC therapeutic target.
Robust transmission of variable-length encoded sources (2003)

Digital communications systems commonly use compression (source coding) and error control (channel coding) to allow efficient and robust transmission of data over noisy channels. When compression is imperfect, some residual redundancy remains in the transmitted data and can be exploited at the decoder to improve the decoder's probability-of-error performance. A new approach to joint source-channel maximum a posteriori probability (MAP) decoding applicable to systems employing variable-length source codes (VLCs) was previously developed by the authors-the resulting joint decoder's structure is similar to that of the conventional Viterbi decoder. This paper extends the authors' previous work to address the problem of error propagation, an inherent problem with using VLCs. Options considered include list decoding, trellis-pruning, and composite schemes. Simulation results presented show that the proposed techniques can result in significant improvement in decoding performance.
Advances in the Development of Bradykinin Receptor Ligands (2006)

Kinins are blood-derived local-acting peptides that elicit specific cellular effects via the stimulation of two related G protein coupled receptors. While the B(2)receptor subtype, constitutively expressed in various tissues, is believed to mediate most of the physiological actions of kinins in healthy conditions, the B(1) receptor, highly regulated during inflammation, has been associated with the sustained actions of these peptides in various pathological situations. Potent peptide and nonpeptide modulators of both kinin receptors have been produced as pharmacological tools and potential therapeutics over the last three decades. More recently, the accumulating evidence suggesting that B(1) receptor blockade could be useful for the treatment of pain and inflammatory disorders has led to a shift in drug development efforts toward the synthesis of orally bioavailable nonpeptide B(1) receptor antagonists. Nonpeptide ligands of either receptor subtype produced by several industrial organizations often possess significant structural commonalities that can lead to the definition of a pharmacophore, especially when the receptor docking models are compared. The field of kinin receptors ligands research has reached an exciting step of its history, as the near future will reveal whether these molecules are therapeutically beneficial in various human diseases. This review will concisely summarize our current understanding of the biology of kinins and their receptors, before discussing the recent medicinal chemistry developments and challenges that bring new kinin receptor ligands closer to clinical applications.
Partially-methylated amyloses as effective hosts for inclusion complex formation with polymeric guests (2007)

Partially 2,3-O-methylated amyloses efficiently form inclusion complexes with polytetrahydrofuran and poly(epsilon-caprolactone) by simply mixing them in DMSO-H(2)O (1 : 9) solution, in contrast to the case of the parent amylose in which the corresponding inclusion complexes are only slightly formed.