gebhart/patrepeval huggingface dataset:
Succinate uptake and related proton movements in Escherichia coli K12 (1975)

1. The apparent Km values for succinate uptake by whole cells of Escherichia coli K12 depend on pH in the range 6.5-7.4.2. Uptake of succinate in lightly buffered medium is accompanied by proton uptake. 3. The apparent Km values for succinate uptake and for succinate-induced proton uptake are similar. 4. Approximately two protons enter the cell with each succinate molecule. 5. The pattern of inhibition of succinate uptake is similar to that of succinate-induced proton uptake. 6. Uptake of fumarate and malate, which share the succinate-transport system, is also accompanied by the uptake of approximately two protons per molecule of fumarate or malate. 7. Uptake of aspartate by the dicarboxylic acid-transport system is accompanied by the uptake of approximatley two protons per molecule of asparatate. 8. It is concluded that uptake of dicarboxylic acids by the dicarboxylic acid-transport system is obligatorily coupled to proton uptake such that succinate, malate and fumarate are taken up in electroneutral form and asparate is taken up in cationic form. 9. These results are consistent with, though they do not definitely prove, the energization of succinate uptake of the deltapH.
Rapid upregulation of fibroblast growth factor receptor 1 (flg) by rat photoreceptor cells after injury. (2000)

This body of evidence strongly suggests that the photoreceptor rescue effect elicited by retinal injury as well as by injection of exogenous bFGF is mediated, at least in part, by upregulation of the FGFR1 by the photoreceptor cells.
Development of the Tinnitus Handicap Inventory (1996)

The THI is a self-report measure that can be used in a busy clinical practice to quantify the impact of tinnitus on daily living.
Engineering aspects of extracorporeal photochemotherapy. (1990)

Photopheresis is a new extracorporeal photochemotherapy in which the patient's blood or certain blood fraction is exposed to light in the presence of a light-activatable drug. The major engineering elements involved for better system design and patient treatment, such as system model, cell separation, irradiation, and energy measurement, are discussed.
Structures and Bonding in Silane Derivatives with One Alkali Atom (2000)

The structures of silane derivatives with one alkali atom M, SiX3M, where X stands for hydrogen or halogen atoms and M is Li or Na, are studied ab initio with uncorrelated and correlated methods and a 6-311++G(3df,pd) basis set. Geometry, energetics, dipole moments, and topological features of the electron distribution are investigated at the B3LYP/6-311++G(3df,pd) level of the theory for both tetrahedral and inverted structures of these compounds. With the exception of SiH3Na, the inverted forms have been found to be more stable than the tetrahedral structures. The special geometrical features displayed by these inverted structures are analyzed, paying special attention to the information provided by the electron density. The nature of the bonding in these molecules is finally discussed.
Tales of Antigen Evasion from CAR Therapy (2016)

Both T cells bearing chimeric antigen receptors and tumor-specific antibodies can successfully target some malignancies, but antigen escape can lead to relapse. Two articles in this issue of Cancer Immunology Research explore what effective countermeasures may prevent it. Cancer Immunol Res; 4(6); 473-473. ©2016 AACRSee articles by Zah et al., p. 498, and Rufener et al., p. 509.
Tomographic Imaging with Nuclear Magnetic Resonance (1978)

A technique is described for obtaining tomographic images of hydrogen distribution in animals using nuclear magnetic resonance (NMR). Resonant frequency is proportional to magnetic field strength, so that spatial resolution is achieved by frequency selection and magnetic field shaping. The results of scanning a phantom and two rats are presented.
Potential Skin Layers for Membranes with Tunable Nanochannels (1997)

ADVERTISEMENT RETURN TO ISSUEPREVCommunication to the...Communication to the EditorNEXTPotential Skin Layers for Membranes with Tunable NanochannelsGuojun Liu, Jianfu Ding, Andrew Guo, Manfred Herfort, and David Bazett-JonesView Author Information Department of Chemistry, The University of Calgary, 2500 University Drive, NW, Calgary, Alberta, Canada T2N 1N4 Cite this: Macromolecules 1997, 30, 6, 1851–1853Publication Date (Web):March 24, 1997Publication History Received17 October 1996Revised24 January 1997Published online24 March 1997Published inissue 1 March 1997https://pubs.acs.org/doi/10.1021/ma961530bhttps://doi.org/10.1021/ma961530brapid-communicationACS PublicationsCopyright © 1997 American Chemical SocietyRequest reuse permissionsArticle Views638Altmetric-Citations84LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose SUBJECTS:Polymer films,Polymers,Thin films,Transmission electron microscopy,Trimethylsilyls Get e-Alerts
Human immunoglobulin heavy-chain minilocus recombination in transgenic mice: gene-segment use in mu and gamma transcripts. (1993)

We (N.L. and L.D.T.) have introduced a human heavy-chain minilocus into mice transgenically. Constructs contain 2 heavy-chain variable (VH; psi VH3-105 and VH5-251), 10 diversity (D), 6 heavy-chain joining (JH), and either constant (C)mu or C mu and C gamma gene segments. Several founder lines were established and studied before immunization. Seventy heavy-chain transcripts were cloned and sequenced from murine splenic B lymphocytes, and gene-segment use was assessed before and after class-switching. In general, the repertoire was "fetal" in appearance with little evidence of somatic mutation in any gene segment. The two VH gene segments were found rearranged to mu- and gamma-chain C segments, with a preference of VH5-251. We observed a preponderance of the most-J-proximal D gene (DHQ52) segments among the mu transcripts (44%). The JH gene-segment use mimics most patterns seen in human antibodies. Diversification in CDR3 was extensive and included clear examples of D inversions and D-D fusions. These data suggest that a human immunoglobulin minilocus can undergo recombinatorial processes in a manner analogous to that seen in the human fetal/preimmune repertoire. This model, in addition to providing a potential source of human monoclonal antibodies, is ideal for the study of further questions concerning immunoglobulin gene-segment recombination.
Tick-Borne Encephalitis with Hemorrhagic Syndrome, Novosibirsk Region, Russia, 1999 (2003)

Eight fatal cases of tick-borne encephalitis with an unusual hemorrhagic syndrome were identified in 1999 in the Novosibirsk Region, Russia. To study these strains, we sequenced cDNA fragments of protein E gene from six archival formalin-fixed brain samples. Phylogenetic analysis showed tick-borne encephalitis variants clustered with a Far Eastern subtype (homology 94.7%) but not with the Siberian subtype (82%).
l-2-Hydroxyglutaric Aciduria: Pattern of MR Imaging Abnormalities in 56 Patients (2009)

L2HGA has a distinct highly characteristic pattern of MR imaging abnormalities: a combination of predominantly subcortical cerebral WM abnormalities and abnormalities of the dentate nucleus, globus pallidus, putamen, and caudate nucleus. With increasing disease duration, WM abnormalities and basal ganglia signal intensity abnormalities become more diffuse and cerebral WM atrophy ensues.
Computational Approaches to the Chemical Conversion of Carbon Dioxide (2013)

The conversion of CO₂ into fuels and chemicals is viewed as an attractive route for controlling the atmospheric concentration and recycling of this greenhouse gas, but its industrial application is limited by the low selectivity and activity of the current catalysts. Theoretical modeling, in particular density functional theory (DFT) simulations, provides a powerful and effective tool to discover chemical reaction mechanisms and design new catalysts for the chemical conversion of CO₂, overcoming the repetitious and time/labor consuming trial-and-error experimental processes. In this article we give a comprehensive survey of recent advances on mechanism determination by DFT calculations for the catalytic hydrogenation of CO₂ into CO, CH₄, CH₃OH, and HCOOH, and CO₂ methanation, as well as the photo- and electrochemical reduction of CO₂. DFT-guided design procedures of new catalytic systems are also reviewed, and challenges and perspectives in this field are outlined.
Function of interleukin‐20 as a proinflammatory molecule in rheumatoid and experimental arthritis (2006)

IL-20 was up-regulated in the synovial fluid of RA patients and acted as a chemokine that attracted the migration of neutrophils and RASFs in vitro. The rat CIA model demonstrated that IL-20 was involved in the pathogenesis of arthritis, because sIL-20RI significantly reduced arthritis in rats with CIA. Thus, IL-20 may modulate the incidence and severity of arthritis and play important roles at local sites of inflammation.
The extracellular matrix at a glance (2010)

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The extracellular matrix (ECM) is the non-cellular component present within all tissues and organs, and provides not only essential physical scaffolding for the cellular constituents but also initiates crucial biochemical and biomechanical cues that are required for tissue
The GP2 peptide: A HER2/neu‐based breast cancer vaccine (2012)

Preclinical studies suggest that GP2, a HER2/neu-derived peptide, is immunogenic. Subsequent phase I clinical trials demonstrated that GP2-based vaccines are safe and effective in stimulating peptide-specific immunity. A GP2 peptide vaccine is currently being evaluated in a phase II efficacy trial enrolling breast cancer patients. This article reviews initial studies characterizing GP2, clinical trials investigating GP2-based vaccines, and novel immunotherapy strategies incorporating GP2 in combination with other peptides or with the monoclonal antibody trastuzumab.
Intracisternal cyclodextrin prevents cerebellar dysfunction and Purkinje cell death in feline Niemann-Pick type C1 disease (2015)

Niemann-Pick type C1 (NPC) disease is a lysosomal storage disease caused by mutations in the NPC1 gene, leading to an increase in unesterified cholesterol and several sphingolipids, and resulting in hepatic disease and progressive neurological disease. We show that subcutaneous administration of the pharmaceutical excipient 2-hydroxypropyl-β-cyclodextrin (HPβCD) to cats with NPC disease ameliorated hepatic disease, but doses sufficient to reduce neurological disease resulted in pulmonary toxicity. However, direct administration of HPβCD into the cisterna magna of presymptomatic cats with NPC disease prevented the onset of cerebellar dysfunction for greater than a year and resulted in a reduction in Purkinje cell loss and near-normal concentrations of cholesterol and sphingolipids. Moreover, administration of intracisternal HPβCD to NPC cats with ongoing cerebellar dysfunction slowed disease progression, increased survival time, and decreased the accumulation of brain gangliosides. An increase in hearing threshold was identified as a potential adverse effect. These studies in a feline animal model have provided critical data on efficacy and safety of drug administration directly into the central nervous system that will be important for advancing HPβCD into clinical trials.
Recovery of Mitogenic Activity of a Growth Factor Mutant with a Nuclear Translocation Sequence (1990)

Heparin-binding growth factor-1 (HBGF-1) is an angiogenic polypeptide mitogen for mesoderm- and neuroectoderm-derived cells in vitro and remains biologically active after truncation of the amino-terminal domain (HBGF-1 alpha) of the HBGF-1 beta precursor. Polymerase chain reaction mutagenesis and prokaryotic expression systems were used to prepare a mutant of HBGF-1 alpha lacking a putative nuclear translocation sequence (amino acid residues 21 to 27; HBGF-1U). Although HBGF-1U retains its ability to bind to heparin, HBGF-1U fails to induce DNA synthesis and cell proliferation at concentrations sufficient to induce intracellular receptor-mediated tyrosine phosphorylation and c-fos expression. Attachment of the nuclear translocation sequence from yeast histone 2B at the amino terminus of HBGF-1U yields a chimeric polypeptide (HBGF-1U2) with mitogenic activity in vitro and indicates that nuclear translocation is important for this biological response.
Diagnosis of Arrhythmogenic Right Ventricular Cardiomyopathy/Dysplasia (2010)

URL: http://www.clinicaltrials.gov. Unique identifier: NCT00024505.
Characterization of collagen types XII and XIV from fetal bovine cartilage. (1992)

The structurally related type XII-like collagen molecules TL-A and TL-B were recently identified in fetal bovine epiphyseal cartilage and subsequently shown to be collagen types XII and XIV, respectively. By indirect immunofluorescent staining of cartilage using monoclonal antibodies to the NC3 domains of each molecule, it was shown that type XII collagen was present predominantly around cartilage canals, the articular surface, subperichondrial margins, and the perichondrium, was less so in the remaining cartilage matrix, and was absent from the growth plate region. In the permanent cartilage of trachea, type XII stained somewhat more intensely in the margins beneath the loose connective tissue. Type XIV collagen localized more uniformly throughout the articular cartilage and was also absent from the growth plate region, whereas in tracheal cartilage, its distribution was similar to type XII. We have characterized the structure of these cartilage molecules and compared them with those from fetal bovine skin. Extraction of cartilage with 1 M NaCl and differential NaCl precipitation yields a fraction enriched for these two collagens. Analysis by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and immunoblotting with monoclonal antibodies to the large amino-terminal non-triple-helical domain, NC3, revealed the presence in cartilage of two forms of type XII collagen: type XIIB, the molecule previously identified in chick and bovine tissues, and type XIIA, a much larger form equivalent to the molecule recently identified in WISH-transformed epithelial cell culture medium (Lunstrum, G. P., McDonough, A. M., Marinkovich, M. P., Keene, D. R., Morris, N. P., and Burgeson, R. E. (1992) J. Biol. Chem. 267, 20087-20092). Digestion with bacterial collagenase shows that the increased mass is present in the NC3A domain. Additional purification by velocity sedimentation and observation of rotary-shadowed images demonstrates molecules with extended non-triple-helical arms approximately 80 nm in length analogous to the WISH cell molecules. Electrophoretic mobilities of bands corresponding to type XIIA, but not type XIIB, are sensitive to chondroitinase ABC, indicating that type XIIA is a chondroitin sulfate proteoglycan and that modification occurs predominantly within the NC3A domain distal to NC3B. Neither type XIIB from skin nor type XIIA from WISH cells are chondroitinase-sensitive. By similar analysis, a portion of the type XIV collagen chains in cartilage was also sensitive to chondroitinase digestion. Chondroitin sulfate is apparently not located on its NC3 domain. As in skin, collagen types XII and XIV have subtly different distributions within cartilage and type XII may have a tissue-specific structure.
PHOSPHORUS METABOLISM AND MANAGEMENT IN CHRONIC KIDNEY DISEASE: Lanthanum Carbonate as a First‐Line Phosphate Binder: The “Cons” (2007)

Controlling serum phosphorus levels in patients with renal failure is critical. The use of oral phosphate-binding agents is universal for patients with end-stage kidney disease to reduce phosphate absorption. The therapeutic goal is to reduce serum phosphorus levels without disturbing calcium homeostasis or promoting accumulation of potentially toxic elements from the medication. Aluminum hydroxide effectively reduces serum phosphorus, but has largely been abandoned as a first-line phosphate binder because of hazards associated with metal absorption and tissue accumulation. Traditional calcium-based phosphate binders tend to promote hypercalcemia and calcium overloading, and are linked to accelerated cardiovascular calcification. Interest in aluminum-free, calcium-free phosphate-binding agents continues to grow. Sevelamer hydrochloride, a metal-free, calcium-free hydrogel, is not absorbed, has been proven safe and efficacious in controlling serum phosphorus, and is associated with attenuated progression of cardiovascular calcification. Lanthanum carbonate is a newer aluminum-free, calcium-free phosphate-binding agent. Lanthanum is a rare-earth trace metal with industrial and agricultural applications. As a therapeutic, this metal-based binder appears effective in reducing serum phosphorus, yet concerns remain about lanthanum accumulation in tissues during long-term oral administration. Similar to the metal aluminum, lanthanum is absorbed in the intestine and accumulates in body tissues, especially in the liver, bone, muscle, kidney, and brain. Moreover, the rate of intestinal absorption of lanthanum is enhanced in chronic renal failure. Our experience with aluminum hydroxide suggests caution regarding the long-term use of another metal-based agent that displays enhanced absorption in the uremic state and progressive tissue accumulation.
Dynamic Response of Dye-Sensitized Nanocrystalline Solar Cells:  Characterization by Intensity-Modulated Photocurrent Spectroscopy (1997)

The frequency-dependent photocurrent response of dye-sensitized TiO2 cells to modulated illumination is analyzed. Analytical expressions are derived that describe generation, collection, and recombination of electrons in a thin layer nanocrystalline solar cell under conditions of steady illumination and with a superimposed small amplitude modulation. The analysis considers illumination from the contact side and from the counter electrode side, and characteristic differences in the intensity-modulated photocurrent response are predicted for the two cases. The attenuation of the ac photocurrent by the RC time constant of the cell is also considered. The theoretical analysis shows that intensity modulated photocurrent spectroscopy (IMPS) can provide new insight into the dynamics of electron transport and collection in the dye-sensitized solar cell. Experimental IMPS data measured for high-efficiency dye-sensitized cells are fitted to the theoretical model using Bode plots in order to derive values of the lifetime (2 × 10-2 s) and diffusion coefficient (5 × 10-5 cm2 s-1) of photoinjected electrons.
Ocular Biomechanics and Biotransport (2004)

The eye transduces light, and we usually do not think of it as a biomechanical structure. Yet it is actually a pressurized, thick-walled shell that has an internal and external musculature, a remarkably complex internal vascular system, dedicated fluid production and drainage tissues, and a variety of specialized fluid and solute transport systems. Biomechanics is particularly involved in accommodation (focusing near and far), as well as in common disorders such as glaucoma, macular degeneration, myopia, and presbyopia. In this review, we give a (necessarily brief) overview of many of the interesting biomechanical aspects of the eye, concluding with a list of open problems.
Identification of a novel region of homozygous deletion on chromosome 9p in squamous cell carcinoma of the lung: the location of a putative tumor suppressor gene. (1997)

Cytogenetic and molecular studies have implied the presence of tumor suppressor genes (TSGs) on chromosome 9p that are critical in the development of lung and other cancers. The p16/CDKN2 gene, a cyclin dependent kinase inhibitor, is a well-defined TSG on 9p21. Although the frequency of mutations in the p16/CDKN2 gene has been detected in approximately 30% of non-small cell lung cancer, loss of heterozygosity on 9p has been observed in greater than 70% of non-small cell lung cancers. These and other deletion mapping studies have suggested the existence of additional TSGs on 9p. This study examined chromosome 9p for TSG loci by analyzing 23 squamous cell carcinomas of the lung with 21 microsatellite markers. Loss of heterozygosity was detected in all of the tumors, and homozygous deletions of the p16/ CDKN2 locus were observed in 6 of the 23 tumors (26%). In addition, a novel region of homozygous deletion was detected in six tumors (26%) at D9S126, approximately 2.5 cM proximal to p16/CDKN2. A single tumor contained a homozygous deletion at both the p16/CDKN2 locus and the D9S126 locus. The possibility of homozygous loss was confirmed by multiplex PCR using both the D9S126 marker and a chromosome 9p control marker. Fluorescence in situ hybridization analysis with P1 and cosmid probes containing D9S126 also confirmed these data. The minimum region of homozygous deletion was determined by testing markers immediately proximal and distal to the D9S126 region. The data identify a homozygous loss on the short arm of chromosome 9 suggesting the presence of a novel TSG locus, proximal to p16/CDKN2 and located between D9S265 and D9S259.
Cloning, expression, and crystallization of recoverin, a calcium sensor in vision. (1992)

Recoverin, a recently discovered 23-kDa calcium-binding protein, activates retinal rod guanylate cyclase when the calcium level is lowered in the submicromolar range. We report here the cloning and sequencing of a cDNA for recoverin from a bovine retinal expression library. The recoverin coding sequence was inserted into a pET-11a expression vector under control of the T7 phage promoter. A second expression system, in which the coding sequence was placed under control of the lambda phage PR promoter, gave 10-fold higher yields (10 mg of purified recoverin per liter of Escherichia coli culture). The finding that retinal recoverin is myristoylated at its amino terminus led us to coexpress the recombinant protein and N-myristoyltransferase (EC 2.3.1.97). Myristoylated recombinant recoverin formed in this way in E. coli is like retinal recoverin in exhibiting a large calcium-induced shift in its tryptophan fluorescence emission spectrum. The availability of abundant protein enabled us to crystallize unmyristoylated recombinant recoverin and initiate x-ray studies. The space group of tetragonal crystals obtained from 75% saturation ammonium sulfate is I4 with unit cell dimensions a = 85.1 A and c = 59.8 A. These crystals of the calcium-bound form of the protein diffracted to a resolution of 2.2 A. The expression systems described here open the door to high-resolution x-ray crystallographic and nuclear magnetic resonance studies of this new member of the EF-hand superfamily and to the elucidation of its precise mode of action as a calcium switch.