gebhart/patrepeval huggingface dataset:
Lack of L‐selectin expression by cells transferring diabetes in NOD mice: insights into the mechanisms involved in diabetes prevention by Mel‐14 antibody treatment (1995)

The process of mononuclear cell extravasation from the blood into the islets of Langerhans in nonobese diabetic (NOD) mice is dependent on the expression of a set of molecules, most of which remain to be defined. The observation that vascular addressins are expressed in inflamed islets raises the issue of the involvement of one of their ligands, L-selectin, in the pathogenesis of autoimmune diabetes. Treatment of NOD females with Mel-14, an antibody specific for L-selectin, reduced the spontaneous development of both insulitis and diabetes. Pretreatment of diabetic donors with Mel-14 decreased the capacity of their splenocytes to transfer the disease. However, the treatment of recipients had no effect on the transfer of diabetes by untreated diabetogenic splenocytes. To reconcile these apparently conflicting results, we fractionated spleen T cells from diabetic mice according to L-selectin expression. Diabetogenic cells were found only in the L-selectin subpopulation. Thus, diabetogenic cells in adult mice share phenotypic characteristics with activated/memory cells, and enter the pancreas using L-selectin-independent migratory pathways.
Amyloid β-Peptide Impairs Glucose Transport in Hippocampal and Cortical Neurons: Involvement of Membrane Lipid Peroxidation (1997)

A deficit in glucose uptake and a deposition of amyloid beta-peptide (A beta) each occur in vulnerable brain regions in Alzheimer's disease (AD). It is not known whether mechanistic links exist between A beta deposition and impaired glucose transport. We now report that A beta impairs glucose transport in cultured rat hippocampal and cortical neurons by a mechanism involving membrane lipid peroxidation. A beta impaired 3H-deoxy-glucose transport in a concentration-dependent manner and with a time course preceding neurodegeneration. The decrease in glucose transport was followed by a decrease in cellular ATP levels. Impairment of glucose transport, ATP depletion, and cell death were each prevented in cultures pretreated with antioxidants. Exposure to FeSO4, an established inducer of lipid peroxidation, also impaired glucose transport. Immunoprecipitation and Western blot analyses showed that exposure of cultures to A beta induced conjugation of 4-hydroxynonenal (HNE), an aldehydic product of lipid peroxidation, to the neuronal glucose transport protein GLUT3. HNE induced a concentration-dependent impairment of glucose transport and subsequent ATP depletion. Impaired glucose transport was not caused by a decreased energy demand in the neurons, because ouabain, which inhibits Na+/K(+)-ATPase activity and thereby reduces neuronal ATP hydrolysis rate, had little or no effect on glucose transport. Collectively, the data demonstrate that lipid peroxidation mediates A beta-induced impairment of glucose transport in neurons and suggest that this action of A beta may contribute to decreased glucose uptake and neuronal degeneration in AD.
Modified Lagrangians and Monotone Maps in Optimization (1996)

Introduction to Convex Analysis Modified Lagrangian Functions for Convex Programming Problems Dual Methods Monotone Maps Gradient-Type Methods and Modification of a Monotone Map Saddle Gradient Methods Modified Lagrangian Functions for Smooth Mathematical Programming Problems and Related Dual Methods Bibliographic Comments References Index.
Sexual dysfunction in primary medical care: prevalence, characteristics and detection by the general practitioner (1997)

This study confirms the high prevalence of sexual disorders in the population. Many of these problems are concealed from GPs. Predictors in patients' notes could help GPs to detect those patients with more serious problems.
Pseudomonas aeruginosa SoxR Does Not Conform to the Archetypal Paradigm for SoxR-Dependent Regulation of the Bacterial Oxidative Stress Adaptive Response (2005)

SoxR is a transcriptional regulator that controls an oxidative stress response in Escherichia coli. The regulator is primarily activated by superoxide anion-dependent oxidation. Activated SoxR turns on transcription of a single gene, soxS, which encodes a transcriptional regulator that activates a regulon that includes dozens of oxidative stress response genes. SoxR homologues have been identified in many bacterial species, including the opportunistic pathogen Pseudomonas aeruginosa. However, the expected SoxR partner, SoxS, has not been found in P. aeruginosa. Thus, the primary gene target(s) of P. aeruginosa SoxR is unknown and the involvement of this regulator in the oxidative stress response of the bacterium remains unclear. We utilized transcriptome profiling to identify the P. aeruginosa SoxR regulon and constructed and characterized an unmarked P. aeruginosa DeltasoxR mutant. We provide evidence indicating that P. aeruginosa SoxR activates a six-gene regulon in response to O(2)(.-)-induced stress. The regulon includes three transcriptional units: (i) the recently identified mexGHI-ompD four-gene operon, which encodes a multidrug efflux pump system involved in quorum-sensing signal homeostasis; (ii) gene PA3718, encoding a probable efflux pump; and (iii) gene PA2274, encoding a probable monooxygenase. We also demonstrate that P. aeruginosa SoxR is not a key regulatory player in the oxidative stress response. Finally, we show that P. aeruginosa SoxR is required for virulence in a mouse model of intrapulmonary infection. These results demonstrate that the E. coli-based SoxRS paradigm does not hold in P. aeruginosa and foster new hypotheses for the possible physiological role of P. aeruginosa SoxR.
DEMONS—A NEW DECONVOLUTION METHOD FOR ESTIMATING DRUG ABSORBED AT DIFFERENT TIME INTERVALS AND/OR DRUG DISPOSITION MODEL PARAMETERS USING A MONOTONIC CUBIC SPLINE (1997)

DeMonS-a new numerical deconvolution method for estimating the amount of drug absorbed at different time intervals and/or drug disposition model parameters-is presented here. In DeMonS, the amount of drug absorbed at different time intervals and/or drug disposition model parameters are the unknown parameters to be calculated. The Fritsch-Butland non-decreasing cubic spline was constructed from the cumulative amount of drug absorbed-time data directly derived from the calculated amount of drug absorbed at different time intervals. The drug absorption rate, which is the derivative of this non-decreasing cubic spline, is therefore represented by a piecewise non-negative quadratic function. The drug concentrations were obtained by convoluting the drug absorption rate quadratic function with the drug disposition model function. The nonlinear optimization method with simple parameter bounds was used to estimate the optimal set of unknown parameters by minimizing the sum of squares of residuals between the observed and predicted drug concentrations. DeMonS has been applied to (i) the griseofulvin data for estimating drug absorbed at different time intervals when the drug disposition model parameters were determined separately from intravenous data, (ii) veralipride double-peak phenomenon data to estimate simultaneously the percentage of cumulative veralipride absorbed and the veralipride disposition model parameters without reference intravenous data, (iii) a comparative bioequivalence study of gastrointestinal therapeutic system (GITS) pseudoephedrine HCI (PeHCI) controlled-release oral dosage forms when the drug disposition model parameters were not available, and (iv) estimation of both drug disposition model parameters and the absorption rate of drug from Testoderm (testosterone transdermal system) in the presence of endogenous testosterone production. DeMonS was implemented using MATLAB and NAG MATLAB Toolbox, and is available for Windows 3.1.
A Protein-Based Method to Develop Allogeneic Chimeric Antigen Receptor T-Cells (2018)

Abstract Introduction Anti-CD19 chimeric antigen receptor (CAR) T-cells are highly effective against B-cell malignancies. However, significant problems associated with autologous T-cells preclude more widespread adoption, including manufacturing failures, poor T-cell quality and cost/logistic issues. A solution could be allogeneic CAR T-cells generated from healthy donors, if these could be prevented from causing graft versus host disease (GvHD). GvHD is mediated by T-cell receptors (TCR) of donor T-cells. Previous approaches have used genome-editing to delete TCR expression, introducing complexity, expense and unpredictable genotoxicity. We developed an alternative, protein-based strategy: TCR-knockdown using an anti-TCR ScFv fused to a KDEL endoplasmic reticulum (ER)-retention domain. Results We cloned anti-TCR/CD3 ScFvs with C-terminal KDEL motifs, and introduced these to TCR-positive cell lines or primary T-cells. While clones OKT3 and BMA031 had no effect on TCR expression, cells expressing UCHT1-KDEL demonstrated loss of surface TCR. We subsequently generated constructs in which UCHT1-KDEL, a 2ndgeneration anti-CD19 CAR and RQR8 (a sort-suicide gene containing CD34 epitope) were co-expressed. We demonstrated obligate linkage of CAR expression and TCR downregulation in transduced T-cells. Following positive CD34 bead selection for RQR8, purity of RQR8+TCR-CAR+ T-cells was &gt;99.8%. In addition, we demonstrated that positive selection for RQR8 was routinely more stringent than depletion of TCR-positive cells. We demonstrated that CAR19-KDEL and conventional CAR19 cells demonstrated equivalent specificity, cytokine release and cytotoxicity in 48hr co-cultures with a panel of CD19-positive and CD19-negative cell lines. In addition, in long-term co-culture assays, no differences in proliferative capacity, markers of differentiation or exhaustion were seen. However, while conventional CAR19 cells proliferated in mixed lymphocyte reactions with irradiated allogeneic peripheral blood mononuclear cells (PBMCs), CAR19-KDEL cells did not. We compared CAR19 and CAR19-KDEL cells in vivo using the NSG-NALM6 tumour xenograft model. Both CAR19 and CAR19-KDEL were able to substantially delay tumour progression relative to control CAR or mock-transduced T-cells in a low-dose (0.2M) model. Finally, we developed a xeno-GvHD model in which irradiated NSG mice were injected with a high dose (5M) of CAR19 or CAR19-KDEL cells. While 100% of mice in the CAR19 group died of xeno-GvHD by D65, all CAR19-KDEL recipients were alive and healthy at D180. Conclusions We have developed a protein-based method which avoids genome editing for the rapid, simple and cost-effective generation of allogeneic CAR T-cells. Our positive selection strategy allows a highly stringent selection of TCR-negative cells. This process may bring the generation of 'off the shelf' CAR T-cells closer to clinical application. Disclosures Maciocia: Autolus: Equity Ownership, Patents &amp; Royalties: UCLB. Pule:UCLB: Patents &amp; Royalties; Autolus: Employment, Equity Ownership.
Complementary DNA cloning establishes microfibril-associated glycoprotein (MAGP) to be a discrete component of the elastin-associated microfibrils. (1991)

Affinity-purified antibodies to microfibril-associated glycoprotein (MAGP) were used to screen a random-primed, bovine nuchal ligament cDNA library in lambda gt11. A 303-base pair clone, cM5, was isolated which encoded an amino acid sequence homologous with that determined directly from a Lys-C peptide of MAGP. A 936-base pair cDNA clone, cM32, was identified in an oligo(dT)-primed cDNA library using plaque hybridization with clone cM5. Clone cM32 encoded amino acid sequences corresponding to sequences obtained from three Lys-C peptides of MAGP, indicating that the clone was an authentic cDNA for the glycoprotein. The cDNA coded for the entire MAGP polypeptide (21 kDa) of 183 amino acids including a putative signal peptide of 17-19 amino acids. This was confirmed by in vitro translation of synthetic mRNAs transcribed from cM32. The amino acid composition of the encoded protein was virtually identical to that previously published for MAGP. DNA sequence analysis of cM32 indicated that MAGP contains two structurally dissimilar regions, an amino-terminal domain containing high levels of glutamine, proline, and acidic amino acids and a carboxyl-terminal domain containing all 13 of the cysteine residues and most of the basic amino acids. Northern blot hybridization of poly(A+) RNA from fetal nuchal ligament with clone cM32 identified a single mRNA species for MAGP of approximately 1.1 kilobases. The evidence indicates that MAGP is a distinct component of 12-nm microfibrils and that it is not derived from a larger microfibrillar glycopolypeptide.
Cerebrospinal fluid neurofilament concentration reflects disease severity in frontotemporal degeneration (2013)

CSF NfL is elevated in symptomatic FTD and correlates with disease severity. This measurement may be a useful surrogate endpoint of disease severity in FTD clinical trials. Longitudinal studies of CSF NfL in FTD are warranted.
cDNA cloning of a novel cell adhesion protein expressed in human squamous carcinoma cells (1990)

A novel protein (SQM1 protein) present in human squamous epithelial cells has been found to be involved in cell adhesion in squamous epithelial cells, endothelial cells and extracellular matrix proteins. The corresponding cDNA that encodes a 135-residue polypeptide has been isolated. Sequence analysis indicates that the encoded polypeptide is distinct yet related to the beta subunit of integrins. A new sequence motif consisting of a heptadic repeat of positively-charged residues present in the polypeptide has been identified and is proposed to be important in protein-protein interaction. These results suggest that SQM1 protein, a new cell adhesion molecule expressed in squamous epithelial cells, may play an important role in tumor metastasis.
On the Active Site of α-Chymotrypsin (1970)

Abstract Cyclized α-tetrasubstituted substrates, 1-keto-3-methyl-3-carbomethoxytetrahydroisoquinoline, designated as Compound II-C, and methyl 3-methyl-3,4-dihydroisocoumarin-3-carboxylate, designated as Compound II-D, are hydrolyzed by α-chymotrypsin readily and highly stereospecifically in the R-D sense, kcat/Km = 1.8/0.0054 = 330 m-1 sec-1 and 2.7/0.0083 = 320 m-1 sec-1, respectively. The results indicate that d-cyclized substrates associate with the enzyme with the hetero ring at the α-hydrogen position, (h); the α-tetrasubstituted cyclized compounds place the α-methyl group at the l-α-acetamido site. Compounds II-C and II-D are less reactive by factors of 60 and 70 than the corresponding α-trisubstituted cyclized substrates. Factors of 9 and 20, respectively, may arise from the effect of the α-methyl group on the nonenzymic hydrolytic reactivity. The remaining factors are due to minor effects of the methyl group on Km. Noncyclized α-tetrasubstituted substrates, methyl N-acetyl-α-methyl-phenylalaninate, designated as Compound I-C, and methyl α-methyl-α-acetoxy-β-phenylpropionate, designated as Compound I-E, are inert to α-chymotrypsin, largely because they may place neither α substituent readily at h. However RS methyl α-methyl-β-phenyllactate, designated as Compound I-D, is a noncyclized α-tetrasubstituted compound which is hydrolyzed by α-chymotrypsin, kcat/ Km = 0.47/0.014 = 35 m-1 sec-1. It is hydrolyzed preferentially in the R-D sense like the cyclized compounds because, of the two α substituents, the α-hydroxyl is better accommodated at h. Interaction at the h part of the active site is with methionine 192. Absolute configurations of α-tetrasubstituted cyclized compounds are assigned by the proposed orientation in the active site and by optical rotatory dispersion correlations. Configurations of I-D and II-D are correlated by stereospecific conversion of I-D to II-D.
Increased mRNA expression of a laminin-binding protein in human colon carcinoma: complete sequence of a full-length cDNA encoding the protein. (1988)

Reliable markers to distinguish human colon carcinoma from normal colonic epithelium are needed particularly for poorly differentiated tumors where no useful marker is currently available. To search for markers we constructed cDNA libraries from human colon carcinoma cell lines and screened for clones that hybridize to a greater degree with mRNAs of colon carcinomas than with their normal counterparts. Here we report one such cDNA clone that hybridizes with a 1.2-kilobase (kb) mRNA, the level of which is approximately equal to 9-fold greater in colon carcinoma than in adjacent normal colonic epithelium. Blot hybridization of total RNA from a variety of human colon carcinoma cell lines shows that the level of this 1.2-kb mRNA in poorly differentiated colon carcinomas is as high as or higher than that in well-differentiated carcinomas. Molecular cloning and complete sequencing of cDNA corresponding to the full-length open reading frame of this 1.2-kb mRNA unexpectedly show it to contain all the partial cDNA sequence encoding 135 amino acid residues previously reported for a human laminin receptor. The deduced amino acid sequence suggests that this putative laminin-binding protein from human colon carcinomas consists of 295 amino acid residues with interesting features. Containing only two cysteine residues, the protein does not have consensus sequences for asparagine-linked glycosylation, amphipathic alpha-helix, or the N-terminal leader signal sequences for entry into endoplasmic reticulum, although hydrophobic segments for potential membrane associations exist. There is an unusual C-terminal 70-amino acid segment, which is trypsin-resistant (no lysine or arginine) and highly negatively charged (13 aspartic plus glutamic residues). Within this segment are five repeats of (Asp/Glu)-Trp-(Ser/Thr); two of these are nearly tandem repeats of Thr-Glu-Asp-Trp-Ser-Ala-Xaa-Pro.
EDEM1 accelerates the trimming of 1,2-linked mannose on the C branch of N-glycans (2010)

Glycoprotein folding and degradation in the endoplasmic reticulum (ER) is mediated by the ER quality control system. Mannose trimming plays an important role by forming specific N-glycans that permit the recognition and sorting of terminally misfolded conformers for ERAD (ER-associated degradation). The EDEM (ER degradation enhancing alpha-mannosidase-like protein) subgroup of proteins belonging to the Class I alpha1,2-mannosidase family (glycosylhydrolase family 47) has been shown to enhance ERAD. We recently reported that overexpression of EDEM3 enhances glycoprotein ERAD with a concomitant increase in mannose-trimming activity in vivo. Herein, we report that overexpression of EDEM1 produces Glc(1)Man(8)GlcNAc(2) isomer C on terminally misfolded null Hong Kong alpha1-antitrypsin (NHK) in vivo. Levels of this isomer increased throughout the chase period and comprised approximately 10% of the [(3)H]mannose-labeled N-glycans on NHK after a 3-h chase. Furthermore, overexpression of EDEM1 E220Q containing a mutation in a conserved catalytic residue essential for alpha1,2-mannosidase activity did not yield detectable levels of Glc(1)Man(8)GlcNAc(2) isomer C. Yet, the same extent of NHK ERAD-enhancement was observed in both EDEM1 and EDEM1 E220Q overexpressing cells. This can be attributed to both wild-type and mutant EDEM1 inhibiting aberrant NHK dimer formation. We further analyzed the N-glycan profile of total cellular glycoproteins from HepG2 cells stably overexpressing EDEM1 and found that the relative amount of Man(7)GlcNAc(2) isomer A, which lacks the terminal B and C branch mannoses, was increased compared to parental HepG2 cells. Based on this observation, we conclude that EDEM1 activity trims mannose from the C branch of N-glycans in vivo.
Controllable excimer-laser fabrication of conical nano-tips on silicon thin films (2004)

We have found conditions for the reproducible, direct laser fabrication of sharp conical tips with heights of about 1 μm and apical radii of curvature of several tens of nanometers. An individual cone is formed when single-crystalline silicon on a silica substrate is irradiated with a single pulse from a KrF excimer laser, homogenized and shaped to a circular spot several microns in diameter. Atomic force microscopy and field-emission scanning electron microscopy were used to characterize these structures. A simple mechanism of formation based on movement of melted material is proposed. Our results suggest that this technique could produce even smaller structures by optimizing the laser processing geometry.
Prevalence of hyperinsulinaemia in patients with high blood pressure (1992)

A total of 41 patients with hypertension were identified in a survey of 732 healthy factory workers. Twenty-three of these individuals were receiving antihypertensive medication, whereas 18 cases were newly discovered. Plasma glucose and insulin responses to oral glucose and fasting plasma triglyceride (TG), cholesterol, and high-density-lipoprotein (HDL) cholesterol concentrations of these 41 individuals were compared with those of 41 other factor workers, with normal blood pressure, matched with the hypertensive group in terms of gender, age, degree of obesity, job in the factory, and leisure-time activity. Patients with hypertension had significantly higher plasma glucose (P less than 0.05) and insulin (P less than 0.05) concentrations in response to oral glucose, as well as a higher plasma TG concentration (P less than 0.05). Similar findings were obtained when the treated and untreated hypertensive groups were analysed separately and compared with their respective control groups. However, there were no differences between the treated and untreated hypertensive groups. Ninety per cent of the normotensive group had a plasma insulin concentration of less than 500 pmol l-1 2 h after the glucose load. Using this value as the criterion for definition of hyperinsulinaemia, 41% of the patients with high blood pressure were hyperinsulinaemic. In addition to meeting this cut-off point, the patients with hypertension and hyperinsulinaemia were also glucose intolerant and dyslipidaemic. In conclusion, approximately 50% of an unselected group of patients with hypertension were hyperinsulinaemic. Insulin levels were comparable in treated and untreated patients with high blood pressure, and hyperinsulinaemic patients also tended to be glucose intolerant and dyslipidaemic.
Polymer diodes with high rectification (1999)

Polymer diodes made using a bilayer of doped poly(3,4-ethylenedioxythiophene) and a semiconducting polymer in a sandwich structure with two low-work-function metals are reported. The conducting polymer layer acted as a modifier of the injection properties of the low-work-function metal, allowing easy hole injection. Upon insertion of the conducting polymer layer, the contact-limited current flow became bulk limited. With this anode, the fabrication of diodes with a rectification ratio of seven orders of magnitude was possible. We present patterned microdiodes made with crossing of 10 μm lines, showing similar performance as the mm-size diode.
When a Victim's a Victim: Making Reference to Victims and Sex-Crime Prosecution (2005)

7 Id.at 4. 8 Id. 9 Id. at 5-6.Interestingly, the court found it important to note that the attendant admitted to engaging in sexual intercourse with another man two days prior to the incident with Bryant.