gebhart/patrepeval huggingface dataset:
Effect of adenine nucleotides on myo-inositol-1,4,5-trisphosphate-induced calcium release (1997)

The effects of a whole series of adenine nucleotides on Ins(1,4,5)P3-induced Ca2+ release were characterized in permeabilized A7r5 smooth-muscle cells. Several adenine nucleotides activated the Ins(1, 4,5)P3 receptor. It was observed that 3'-phosphoadenosine 5'-phosphoulphate, CoA, di(adenosine-5')tetraphosphate (Ap4A) and di(adenosine-5')pentaphosphate (Ap5A) were more effective than ATP. Ap4A and Ap5A also interacted with a lower EC50 than ATP. In order to find out how these adenine nucleotides affected Ins(1,4, 5)P3-induced Ca2+ release, we have measured their effect on the response of permeabilized A7r5 cells to a progressively increasing Ins(1,4,5)P3 concentration. Stimulatory ATP and Ap5A concentrations had no effect on the threshold Ins(1,4,5)P3 concentration for initiating Ca2+ release, but they stimulated Ca2+ release in the presence of supra-threshold Ins(1,4,5)P3 concentrations by increasing the co-operativity of the release process. Inhibition of the Ins(1,4,5)P3-induced Ca2+ release at higher ATP concentrations was associated with a further increase in co-operativity and also with a shift in threshold towards higher Ins(1,4,5)P3 concentrations. ATP had no effect on the non-specific Ca2+ leak in the absence of Ins(1,4,5)P3. We conclude that the adenine-nucleotide-binding site can be activated by many different adenine nucleotides. Binding of these compounds to the transducing domain of the Ins(1,4,5)P3 receptor increases the efficiency of transmitting Ins(1,4,5)P3 binding to channel opening. The inhibition by high ATP concentrations is exerted at a different site, related to Ins(1,4,5)P3 binding.
On GaN Crystallization by Ammonothermal Method (1996)

GaN crystals are grown using ammonothermal method at pressures below 5 kbar and temperatures below 550C. In this method, GaN is synthesised from high purity metallic gallium. The main role in the low temperature GaN crystallization is played by the chemically active and dense ammonia and dissolved mineralizer. Morphology of the obtained crystals as well as solubility experiments prove that gallium nitride is dissolved and crystallised from solution. Physical properties of GaN crystals obtained using ammonothermal method depend on the growth conditions and the type of mineralizer. All GaN samples reveal very intensive photoluminescence, also at room temperature. The spectra of crystals grown with lithium compound mineralizer are shifted towards higher energies in comparison to crystals grown with potassium based mineralizer. At helium temperatures, phosphorescence is also observed.
The 50- and 58-kdalton keratin classes as molecular markers for stratified squamous epithelia: cell culture studies. (1983)

The keratins are a highly heterogeneous group of proteins that form intermediate filaments in a wide variety of epithelial cells. These proteins can be divided into at least seven major classes according to their molecular weight and their immunological reactivity with monoclonal antibodies. Tissue-distribution studies have revealed a correlation between the expression of specific keratin classes and different morphological features of in vivo epithelial differentiation (simple vs. stratified; keratinized vs. nonkeratinized). Specifically, a 50,000- and a 58,000-dalton keratin class were found in all stratified epithelia but not in simple epithelia, and a 56,500- and a 65-67,000-dalton keratin class were found only in keratinized epidermis. To determine whether these keratin classes can serve as markers for identifying epithelial cells in culture, we analyzed cytoskeletal proteins from various cultured human cells by the immunoblot technique using AE1 and AE3 monoclonal antikeratin antibodies. The 56,500- and 65-67,000-dalton keratins were not expressed in any cultured epithelial cells examined so far, reflecting the fact that none of them underwent morphological keratinization. The 50,000- and 58,000-dalton keratin classes were detected in all cultured cells that originated from stratified squamous epithelia, but not in cells that originated from simple epithelia. Furthermore, human epidermal cells growing as a monolayer in low calcium medium continued to express the 50,000- and 58,000-dalton keratin classes. These findings suggest that the 50,000- and 58,000-dalton keratin classes may be regarded as "permanent" markers for stratified squamous epithelial cells (keratinocytes), and that the expression of these keratin markers does not depend on the process of cellular stratification. The selective expression of the 50,000- and 58,000-dalton keratin classes, which are synthesized in large quantities on a per cell basis, may explain the high keratin content of cultured keratinocytes.
Modification of Foaming Properties of Commercial Soy Protein Isolates and Concentrates by Heat Treatments (2016)

Abstract Commercial soy protein isolates (SPIs; China 980A, China 880, ISP 974 and ADM 974) and soy protein concentrates (SPCs; SPC 700 and ARCON S) were used for comparing the effects of heat treatment (55C and 85C for 10–30 min) on the surface tension, surface hydrophobicity, viscosity, solubility at pH 3–8 and foaming properties. The foam capacity was highly positively correlated with the surface hydrophobicity, but negatively related to the surface tension, liquid percentage and foam maximum density. Heating commercial SPIs and SPCs improved the foam capacity, changed the surface hydrophobicity, solubility, foam maximum density and foam stability, and decreased the surface tension and viscosity. The heating temperatures had a greater influence on protein properties than did the heating time. Among soy protein products, heat‐modified China 980A had the best foam capacity and foam stability. Practical Applications Simple heating treatments improved foaming properties of commercial soy products with low level of surface tension and high level of surface hydrophobicity and solubility. In particular, heating improved surface tension, foaming capacity, liquid percentage, foam maximum density and not damaged foaming stability in most of samples. These results indicate that a relatively inexpensive, high quality foaming properties was obtained by the action of heating process that benefits the application of using commercial soy proteins as foaming agents in aerated food systems. Therefore, the foaming properties of heated soy proteins were dramatically different, showing great potential for improving tailor‐made proteins for various applications.
Pulsed Radiofrequency for Radicular Pain Due to a Herniated Intervertebral Disc—An Initial Report (2005)

Pulsed radiofrequency (PRF) has been used for the treatment of radicular pain, due to a herniated intervertebral disc, but so far the data are anecdotal. This is a retrospective study on 13 consecutive patients with this type of pain, at levels L3 to S1. All patients had a diagnosis confirmed by imaging, all had neurological abnormalities, and all were scheduled for surgical intervention. All 12 patients who had a profession had stopped working. Treatment consisted of application of PRF to the dorsal root ganglion of the affected segmental nerve, or in the case of S1 to the segmental nerve at the level of the S1 foramen. One patient underwent disc surgery, and one other patient underwent a spinal fusion 1 year following PRF treatment. He had no leg pain at the time of operation. The remaining patients did not require surgical intervention. The numeric rating scale (NRS) score fell from 7.83 to 2.25 over the first 2 weeks, followed by a gradual further fall to 0.27 at the final follow-up, 15.8 (11 to 23) months after the procedure. Compared with the initial NRS score the data were significant (P < 0.01) from 4 weeks after the procedure. Neurological abnormalities resolved except in one patient, who had decreased sensibility in a small area in the L3 dermatome at the last follow-up. All professionally active patients went back to work after 0.49 months (0.1 to 1). It is concluded that PRF may potentially be a viable alternative for epidural steroid injections in the treatment of acute radicular pain, due to a herniated intervertebral disc, and that further studies, including a control group, should be carried out to establish the value of this method.
Dextran Sodium Sulphate Colitis Mouse Model: Traps and Tricks (2012)

Inflammatory bowel disease (IBD) is a complex multifactorial disease of unknown etiology. Thus, dozens of different animal models of IBD have been developed in past decades. Animal models of IBD are valuable and indispensable tools that provide a wide range of options for investigating involvement of various factors into the pathogenesis of IBD and to evaluate different therapeutic options. However, the dextran sulphate sodium (DSS-) induced colitis model has some advantages when compared to other animal models of colitis. It is well appreciated and widely used model of inflammatory bowel disease because of its simplicity. It has many similarities to human IBD, which are mentioned in the paper. In spite of its simplicity and wide applicability, there are also traps that need to be taken into account when using DSS model. As demonstrated in the present paper, various factors may affect susceptibility to DSS-induced lesions and modify results.
Hereditary Early-Onset Parkinson's Disease Caused by Mutations in PINK1 (2004)

Parkinson's disease (PD) is a neurodegenerative disorder characterized by degeneration of dopaminergic neurons in the substantia nigra. We previously mapped a locus for a rare familial form of PD to chromosome 1p36 (PARK6). Here we show that mutations in PINK1 (PTEN-induced kinase 1) are associated with PARK6. We have identified two homozygous mutations affecting the PINK1 kinase domain in three consanguineous PARK6 families: a truncating nonsense mutation and a missense mutation at a highly conserved amino acid. Cell culture studies suggest that PINK1 is mitochondrially located and may exert a protective effect on the cell that is abrogated by the mutations, resulting in increased susceptibility to cellular stress. These data provide a direct molecular link between mitochondria and the pathogenesis of PD.
Regenerating Cells in Human Airway Surface Epithelium Represent Preferential Targets for Recombinant Adenovirus (1995)

To investigate the efficiency of adenovirus-mediated gene delivery in regenerating human respiratory epithelium, we have performed infections with an E1- and E3-deleted type 5 recombinant adenovirus containing the Escherichia coli LacZ reporter gene on different culture models of regenerating human nasal polyp surface epithelium. These models included: (i) an ex vivo organ culture of nasal polyp tissue, (ii) an explant outgrowth cell culture, and (iii) an in vitro wound repair model, on dissociated cells. In ex vivo nasal polyp tissue, transduced cells were not detected in normal pseudostratified areas, but were found in areas of the surface epithelium with a morphology reminiscent of regenerating airway tissue. In the explant outgrowth cell culture, adenovirus-infected cells were preferentially detected at the periphery of the outgrowth. These transducible epithelial cells, representative of epithelial cells present in vivo during the process of surface airway epithelium regeneration, were shown to be migrating and poorly differentiated cells, which were proliferating or not. In the in vitro wound repair model, the efficiency of cell transduction was much higher in cells present in the wound area than in those far from the wound area. These results indicate that regenerating cells from human airway surface epithelium represent preferential targets for transgene expression, and suggest that efficiency of CFTR gene transfer by recombinant adenovirus vectors may be higher in regenerating CF airway mucosa than in normal tissue. However, since these cells do not show endogenous CFTR expression, the relevance of their preferential transduction for the functional correction of the ion transport defect in cystic fibrosis needs further investigations.
Multiple Retinol and Retinal Dehydrogenases Catalyze All-trans-retinoic Acid Biosynthesis in Astrocytes (2010)

All-trans-retinoic acid (atRA) stimulates neurogenesis, dendritic growth of hippocampal neurons, and higher cognitive functions, such as spatial learning and memory formation. Although astrocyte-derived atRA has been considered a key factor in neurogenesis, little direct evidence identifies hippocampus cell types and the enzymes that biosynthesize atRA. Here we show that primary rat astrocytes, but not neurons, biosynthesize atRA using multiple retinol dehydrogenases (Rdh) of the short chain dehydrogenase/reductase gene family and retinaldehyde dehydrogenases (Raldh). Astrocytes secrete atRA into their medium; neurons sequester atRA. The first step, conversion of retinol into retinal, is rate-limiting. Neurons and astrocytes both synthesize retinyl esters and reduce retinal into retinol. siRNA knockdown indicates that Rdh10, Rdh2 (mRdh1), and Raldh1, -2, and -3 contribute to atRA production. Knockdown of the Rdh Dhrs9 increased atRA synthesis ∼40% by increasing Raldh1 expression. Immunocytochemistry revealed cytosolic and nuclear expression of Raldh1 and cytosol and perinuclear expression of Raldh2. atRA autoregulated its concentrations by inducing retinyl ester synthesis via lecithin:retinol acyltransferase and stimulating its catabolism via inducing Cyp26B1. These data show that adult hippocampus astrocytes rely on multiple Rdh and Raldh to provide a paracrine source of atRA to neurons, and atRA regulates its own biosynthesis in astrocytes by directing flux of retinol. Observation of cross-talk between Dhrs9 and Raldh1 provides a novel mechanism of regulating atRA biosynthesis.
Metabolism of receptor-bound and matrix-bound basic fibroblast growth factor by bovine capillary endothelial cells. (1988)

Bovine capillary endothelial (BCE) cells were incubated at 4 degrees C with 5 ng/ml 125I-basic fibroblast growth factor (bFGF) to equilibrate 125I-bFGF with high affinity cell surface receptors and low affinity matrix binding sites. 67% of the added 125I-bFGF bound to the matrix and 7% bound to receptors. The fate of bound bFGF was followed after cells were incubated in bFGF-free medium and were shifted to 37 degrees C to restore cell metabolism. 125I-bFGF bound to receptors decreased rapidly while the amount of 125I-bFGF bound to matrix was reduced more slowly. The rapid decrease in receptor-bound 125I-bFGF appeared to be due to a down-regulation of bFGF receptors; cells that had been treated for 5 h with bFGF had 60% fewer high affinity receptors than untreated cells. Despite the initial high level of 125I-bFGF binding to matrix, most of this 125I-bFGF was mobilized and metabolized by the cells. 125I-bFGF was internalized by the cells at 37 degrees C, leading to a constant accumulation of 125I-bFGF within the cell. Internalized bFGF was rapidly cleaved from an 18-kD form to a 16-kD form. The 16-kD form was more slowly degraded with a half-life of approximately 8 h. Degradation of internalized 125I-bFGF was inhibited by chloroquine, suggesting that the digestion occurred in a lysosomal compartment. The role of matrix binding sites in the internalization process was investigated. Binding to matrix sites seemed not to be directly involved in the internalization process, since addition of heparin at a concentration that blocked 95% of the binding to matrix had no effect on the initial rate of internalization of bFGF. BCE cells also released a substance that competed for the binding of bFGF to matrix but not to receptors. This substance bound to DEAE-cellulose and was sensitive to heparinase treatment, suggesting that it was a heparinlike molecule. Thus, heparinlike molecules produced by BCE cells can modulate the cellular interaction with bFGF. Matrix-associated heparinlike molecules bind bFGF which can later be metabolized by the cell, and secreted heparinlike molecules release bFGF from matrices.
Correction: Comparative Expression Profile of miRNA and mRNA in Primary Peripheral Blood Mononuclear Cells Infected with Human Immunodeficiency Virus (HIV-1) (2012)

Host cells respond to exogenous infectious agents such as viruses, including HIV-1. Studies have evaluated the changes associated with virus infection at the transcriptional and translational levels of the cellular genes involved in specific pathways. While this approach is useful, in our view it provides only a partial view of genome-wide changes. Recently, technological advances in the expression profiling at the microRNA (miRNA) and mRNA levels have made it possible to evaluate the changes in the components of multiple pathways. To understand the role of miRNA and its interplay with host cellular gene expression (mRNA) during HIV-1 infection, we performed a comparative global miRNA and mRNA microarray using human PBMCs infected with HIV-1. The PBMCs were derived from multiple donors and were infected with virus generated from the molecular clone pNL4-3. The results showed that HIV-1 infection led to altered regulation of 21 miRNAs and 444 mRNA more than 2-fold, with a statistical significance of p,0.05. Furthermore, the differentially regulated miRNA and mRNA were shown to be associated with host cellular pathways involved in cell cycle/proliferation, apoptosis, T-cell signaling, and immune activation. We also observed a number of inverse correlations of miRNA and mRNA expression in infected PBMCs, further confirming the interrelationship between miRNA and mRNA regulation during HIV-1 infection. These results for the first time provide evidence that the miRNA profile could be an early indicator of host cellular dysfunction induced by HIV-1.
The Periodontal Microflora of Juvenile Diabetics: Culture, Immunofluorescence, and Serum Antibody Studies (1983)

These studies demonstrate a unique constellation of organisms populating the subgingival area in periodontitis lesions of patients with juvenile or insulin-dependent diabetes mellitus (IDDM). The cultivable microflora was predominated by Capnocytophaga and anaerobic vibrios in the patients studied. In some patients, Actinobacillus actinomycetemcomitans were also found. This distinguishes the subgingival flora of IDDM patients suffering from periodontitis from that of patients with localized juvenile periodontitis (LJP), and that of adult periodontitis patients. In LJP most patients harbor both A actinomycetemcomitans and Capnocytophaga subgingivally; and in periodontitis lesions from nondiabetic adults, black-pigmented Bacteroides such as B gingivalis or B melaninogenicus subspecies intermedius are often found. Antibiotic susceptibility patterns suggest that penicillin or tetracycline or its analogs such as minocycline may be effective against the predominant cultivable microflora in periodontal lesions of IDDM patients; however, individual patients may harbor flora with significant resistance to these antibiotics.
Force field parameters for sulfates and sulfamates based onab initiocalculations: Extensions of AMBER and CHARMm fields (1995)

Abstract Ab initio self‐consistent field (SCF) Hartree‐Fock calculations of sulfates R OSO 3 (−1) ( R = Me, Et, i‐Pr) and sulfamates R NHSO 3 (−1) ( R = H, Me, Et, i‐Pr) were performed at the 4‐31G(*S*N) //3‐21G(*S*N) basis set levels, where asterisks indicate d functions on sulfur and nitrogen atoms. These standard levels were determined by comparing calculation results with several basis sets up to MP2/6‐31G*//6‐31G*. Several conformations per compound were studied to obtain molecular geometries, rotational barriers, and potential derived point charges. In methyl sulfate, the rotational barrier around the CO bond is 1.6 kcal/mol at the MP2 level and 1.4 kcal/mol at the standard level. Its ground state has one of three HCOS torsion angles trans and one of three COSO torsion angles trans. Rotation over 60° around the single OS bond in the sulfate group costs 2.5 kcal/mol at the MP2 and 2.1 kcal/mol at the standard level. For ethyl sulfate, the calculated rotational barrier in going from the ground state, which has its CCOS torsion angle trans, to the syn‐periplanar conformation (CCOS torsion angle cis) is 4.8 kcal/mol. However, a much lower barrier of 0.7 kcal/mol leads to a secondary gauchelike conformation about 0.4 kcal/mol above the ground state, with the CCOS torsion angle at 87.6°. Again, one of the COSO torsion angles is trans in the ground state, and the rotational barrier for a 60° rotation of the sulfate group amounts to 1.8 kcal/mol. For methyl sulfamate, the rotational barriers are 2.5 kcal/mol around the CN bond and 3.3 kcal/mol around the NS bond. This is noteworthy because sulfamate itself has a calculated rotational barrier around the NS bond of only 1.7 kcal/mol. These and other data were used to parameterize the well‐known empirical force fields AMBER and CHARMm. When the new fields were tested by means of vibrational frequency calculations at the 6‐31G*//6‐31G* level for methyl sulfate, sulfamate, and methyl sulfamate ground states, the frequencies compared favorably with the AMBER and CHARMm calculated frequencies. The transferability of the force parameters to β‐ D ‐glucose‐6‐sulfate and isopropyl sulfate appears to be better than to isopropyl sulfamate. © 1995 by John Wiley &amp; Sons, Inc.
Redirection of antileukemic reactivity of peripheral T lymphocytes using gene transfer of minor histocompatibility antigen HA-2-specific T-cell receptor complexes expressing a conserved alpha joining region (2003)

Donor-derived T lymphocytes directed against minor histocompatibility antigens (mHags) exclusively expressed on cells of the hematopoietic lineages can eliminate hematologic malignancies. Transfer of T-cell receptors (TCRs) directed against these mHags into T lymphocytes may provide a strategy to generate antileukemic T cells. To investigate the feasibility of this strategy the TCR usage of mHag HA-2-specific T-cell clones was characterized. Thirteen different types of HA-2-specific T-cell clones were detected, expressing TCRs with diversity in TCR alpha- and beta-chain usage, however, containing in the TCR alpha chain a single conserved gene segment J alpha 42, indicating that J alpha 42 is involved in HA-2-specific recognition. We transferred various HA-2 TCRs into T lymphocytes from HLA-A2-positive HA-2-negative individuals resulting in T cells with redirected cytolytic activity against HA-2-expressing target cells. Transfer of chimeric TCRs demonstrated that the HA-2 specificity is not only determined by the J alpha 42 region but also by the N-region of the alpha chain and the CDR3 region of the beta chain. Finally, when HA-2 TCRs were transferred into T cells from HLA-A2-negative donors, the HA-2 TCR-modified T cells exerted potent antileukemic reactivity without signs of anti-HLA-A2 alloreactivity. These results indicate that HA-2 TCR transfer may be used as an alternative strategy to generate HA-2-specific T cells to treat hematologic malignancies of HLA-A2-positive, HA-2-expressing patients that received transplants from HLA-A2-matched or -mismatched donors.