gebhart/patrepeval huggingface dataset:
Mechanism for multiple‐substrates recognition of α‐aminoadipate aminotransferase fromThermus thermophilus (2008)

Alpha-aminoadipate aminotransferase (AAA-AT), a homolog of mammalian kynurenine aminotransferase II (Kat II), transfers an amino group to 2-oxoadipate to yield alpha-aminoadipate in lysine biosynthesis through the alpha-aminoadipate pathway in Thermus thermophilus. AAA-AT catalyzes transamination against various substrates, including AAA, glutamate, leucine, and aromatic amino acids. To elucidate the structural change for recognition of various substrates, we determined crystal structures of AAA-AT in four forms: with pyridoxal 5'-phosphate (PLP) (PLP complex), with PLP and leucine (PLP/Leu complex), with N-phosphopyridoxyl-leucine (PPL) (PPL complex), and with N-phosphopyridoxyl-alpha-aminoadipate (PPA) at 2.67, 2.26, 1.75, and 1.67 A resolution, respectively. The PLP complex is in an open state, whereas PLP/Leu, PPL, and PPA complexes are in closed states with maximal displacement (over 7 A) of the alpha2 helix and the beta1 strand in the small domain to cover the active site, indicating that conformational change is induced by substrate binding. In PPL and PLP/Leu complexes, several hydrophobic residues on the alpha2 helix recognize the hydrophobic side chain of the bound leucine moiety whereas, in the PPA complex, the alpha2 helix rotates to place the guanidium moiety of Arg23 on the helix at the appropriate position to interact with the carboxyl side chain of the AAA moiety. These results indicate that AAA-AT can recognize various kinds of substrates using the mobile alpha2 helix. The crystal structures and site-directed mutagenesis revealed that intersubunit-electrostatic interactions contribute to the elevated thermostability of this enzyme.
Component-resolved diagnosis to optimize allergen-specific immunotherapy in the Mediterranean area. (2007)

Allergen-specific immunotherapy (SIT) is the only allergen-specific treatment for allergy. It can prevent progression of the disease and has a long-lasting therapeutic effect. Since SIT is allergen-specific, the identification of the disease-eliciting allergen is an essential prerequisite for the accurate prescription of treatment. Diagnostic tests based on allergen extracts consist of mixtures of various allergens of which some are specific for the allergen source and others occur as cross-reactive allergens in various unrelated allergen sources. It may therefore be difficult and sometimes impossible to identify the disease-causing allergen with such tests, particularly in patients who are sensitized to more than one allergen source. Sensitization to pollens from olive, grasses, and Parietaria in the Mediterranean area is frequently treated with SIT. Here, we describe allergen molecules from these sources that can be used for component-resolved diagnosis of allergy to facilitate the selection of patients for SIT and monitor the immunological effects of treatment.
Biochemistry: A Short Course (1997)

Partial table of contents: Molecules and Cells. Nucleic Acids. Proteins. Membranes. Nucleoprotein Complexes. Hemoglobin Illustrates Protein Behavior. Introduction to Enzymes. Regulation of Enzyme Activity by Noncovalent Changes. Regulation of Enzyme Activity by Covalent Changes. Proteins of the Cytoskeleton and the Extracellular Matrix. Glycolysis, Citric--Acid Cycle, and Electron Transport System. Gluconeogenesis. Fatty--Acid Metabolism: Catabolism. Lipid Metabolism: Synthesis and Transport. Metabolism of Other Aliphatic Amino Acids. Metabolism of Aromatic Amino Acids and Protein Economy. Purines, Pyrimidines, and Heme Metabolism. Genome Organization. DNA Replication. DNA Repair and Recombination. RNA Processing. Protein Synthesis. Protein Targeting and Turnover. Molecular Biology of Animal Viruses. Oncogenes and Human Cancer. Appendix. Glossary. Index.
Parkinson Phenotype in Aged PINK1-Deficient Mice Is Accompanied by Progressive Mitochondrial Dysfunction in Absence of Neurodegeneration (2009)

Thus, aging Pink1(-/-) mice show increasing mitochondrial dysfunction resulting in impaired neural activity similar to PD, in absence of overt neuronal death.
Serum-free medium for the in vitro growth of normal and malignant urinary bladder epithelial cells. (1982)

A serum-free medium, DH-S1, is described which is valuable for the establishment of primary cultures of normal and malignant transitional epithelium (transitional cell carcinoma of the bladder). Growth of epithelial cells in DH-S1 is facilitated but that of fibroblasts is suppressed. Another established human transitional cell carcinoma cell line, 647V, has grown continually in DH-S1 for over 36 passages. Morphological and antigenic studies comparing 647V cells growing in serum-containing and serum-free medium reveal differences which are pronounced at low cell density but which almost disappear at higher densities. A new human transitional cell carcinoma cell line, LA-B1, is described whose initial growth was supported by this serum-free medium.
Effect of Aromatherapy on Symptoms of Dysmenorrhea in College Students: A Randomized Placebo-Controlled Clinical Trial (2006)

These findings suggest that aromatherapy using topically applied lavender, clary sage, and rose is effective in decreasing the severity of menstrual cramps. Aromatherapy can be offered as part of the nursing care to women experiencing menstrual cramps or dysmenorrhea.
Creutzfeldt-Jakob, Parkinson, Lewy Body Dementia and Alzheimer Diseases: From Diagnosis to Therapy (2009)

Depositions of proteins in form of amyloid and non-amyloid plaques are common pathogenic signs of more than 20 degenerative diseases affecting the central nervous system or a variety of peripheral tissues. Among the neuropathological conditions, Alzheimer's, Parkinson's and the prion diseases, such as Creutzfeldt-Jakob disease (CJD), present ambiguities as regarding their differential diagnosis. At present, their diagnosis must be confirmed by post-mortem examination of the brain. Currently the ante-mortem diagnosis is still based on the integration of multiple data (clinical, paraclinical and biological analyses) because no unique marker exists for such diseases. The detection of specific biomarkers would be useful to develop a differential diagnostic, distinguishing not only different neurodegenerative diseases but also the disease from the non-pathological effects of aging. Several neurodegenerative biomarkers are present at very low levels during the early stages of the disease development and their ultra-low detection is needed for early diagnosis, which should permit more effective therapeutic interventions, before the disease concerned can progress to a stage where considerable damage to the brain has already occurred. In the case of prion diseases, there are concerns regarding not only patient care, but the wider community too, with regard to the risk of transmission of prions, especially during blood transfusion, for which, four cases of variant CJD infection associated with transfusion of non-leukocyte-depleted blood components have been confirmed. Therefore the development of techniques with high sensitivity and specificity represent the major challenge in the field of the protein misfolding diseases. In this paper we review the current analytical and/or biochemical diagnostic technologies used mainly in prion, but also in Alzheimer and Parkinson diseases and emphasizing work on the protein detection as a surrogates and specific biomarker in the body fluid of patients (urine, CSF and blood). This review highlights the urgency of the development of early and sensitive diagnostics in terms of therapeutic challenge.
Dual-Chemiresistor GC Detector Employing Monolayer-Protected Metal Nanocluster Interfaces (2002)

The synthesis and testing of two gold-thiolate monolayer-protected (nano)clusters as interfacial layers on a dual-chemiresistor vapor sensor array are described. Responses (changes in dc resistance) to each of 11 organic solvent vapors are rapid, reversible, and linear with concentration at low vapor concentrations, becoming sublinear at higher concentrations. Limits of detection (LODs) range from 0.1 to 24 parts per million and vary inversely with solvent vapor pressure. When configured as a GC detector and used to analyze 0.5-L preconcentrated samples of the 11-vapor mixture, the array provides LODs of < or = 700 parts per trillion for most vapors, comparing favorably with those from an integrated array of polymer-coated surface acoustic wave sensors configured and tested similarly. This first report on the use of such an array as a GC detector shows that the combination of response patterns and GC retention times improves capabilities for vapor recognition compared to the sensor array alone or to single-detector GC systems. Spray-coated nanocluster thin films can be deposited reproducibly and exhibit response stability in air that ranges from fair to excellent for up to several months. Scaling the active device area down by a factor of 16 has no significant effect on sensitivity. Implications of these results for portable vapor sensing systems are discussed.
Direct in vivo adenovirus-mediated gene transfer to salivary glands (1994)

Gene transfer to the salivary glands holds the potential for the therapy of salivary gland disorders and for delivery of therapeutic proteins to the mouth and upper gastrointestinal tract. Administration of the recombinant adenovirus vectors Ad.RSV beta gal [coding for the intracellular protein beta-galactosidase (beta-Gal)] and Ad alpha 1AT [coding for human alpha 1-antitrypsin (alpha 1-AT), a secreted protein] to salivary gland cell lines in vitro demonstrated exogenous gene expression. Retrograde ductal injection of the Ad.RSV beta gal vector to rat salivary glands in vivo resulted in beta-Gal expression in acinar and ductal cells. Exposure of submandibular glands in vivo to Ad alpha 1AT resulted in expression of alpha 1-AT mRNA transcripts, de novo synthesis of alpha 1-AT, and secretion in the saliva. To evaluate the feasibility of adenovirus-mediated gene transfer to human glands, human minor salivary glands were infected ex vivo with Ad.RSV beta gal, and implanted into severe combined immunodeficient mice. Evaluation of the human tissue demonstrated beta-Gal activity. These observations demonstrate that adenovirus vectors are capable of direct delivery of genes to the salivary glands, suggesting a variety of possible gene therapy applications.
CD24 affects CXCR4 function in pre-B lymphocytes and breast carcinoma cells (2006)

CD24 is a small, heavily glycosylated cell-surface protein which is linked to the membrane via a glycosyl-phosphatidylinositol (GPI-) anchor and therefore localizes in lipid rafts. CD24 is widely used as a cell-lineage marker for hematopoietic cells. CD24 is also expressed on a variety of human carcinomas, including epithelial ovarian, breast, prostate, colon and lung cancer and has been linked to poor prognosis. Except for its role as a ligand for P-selectin on carcinoma and myeloid cells, a specific function for CD24 has not been determined. Here we show that CD24 affects the function of the chemokine receptor CXCR4. Using isolated CD19-positive bone marrow B cells from CD24-knockout mice and CD24-/- pre-B lymphocytic cell lines, we demonstrate that CD24 expression reduces SDF-1-mediated cell migration and signalling via CXCR4. We observed that the loss of CD24 augmented cellular cholesterol levels and enhanced CXCR4 lipid raft association. Altered chemotactic migration and raft residence was also observed in MDA-MB-231 breast cancer cells expressing high and low levels of CD24 and CXCR4 receptor. MDA-MB-231 cells expressing low levels of CD24 also showed enhanced tumour formation in NOD/SCID mice compared with cells overexpressing CD24. These results demonstrate a novel role for CD24 as a regulator of CXCR4 function that could be relevant for breast cancer growth and metastasis.
Anti-KIR antibody enhancement of anti-lymphoma activity of natural killer cells as monotherapy and in combination with anti-CD20 antibodies (2013)

Natural killer (NK) cells mediate antilymphoma activity by spontaneous cytotoxicity and antibody-dependent cell-mediated cytotoxicity (ADCC) when triggered by rituximab, an anti-CD20 monoclonal antibody (mAb) used to treat patients with B-cell lymphomas. The balance of inhibitory and activating signals determines the magnitude of the efficacy of NK cells by spontaneous cytotoxicity. Here, using a killer-cell immunoglobulin-like receptor (KIR) transgenic murine model, we show that blockade of the interface of inhibitory KIRs with major histocompatibility complex (MHC) class I antigens on lymphoma cells by anti-KIR antibodies prevents a tolerogenic interaction and augments NK-cell spontaneous cytotoxicity. In combination with anti-CD20 mAbs, anti-KIR treatment induces enhanced NK-cell-mediated, rituximab-dependent cytotoxicity against lymphoma in vitro and in vivo in KIR transgenic and syngeneic murine lymphoma models. These results support a therapeutic strategy of combination rituximab and KIR blockade through lirilumab, illustrating the potential efficacy of combining a tumor-targeting therapy with an NK-cell agonist, thus stimulating the postrituximab antilymphoma immune response.
Plasma-assisted Grafting of Polyethylene Glycol (PEG) to Solid Substrates (2007)

Summary form only given. In this work inductively coupled argon plasma facilitates grafting of polyethylene glycol (PEG) to solid substrates. A plasma-polymerized primer coat was followed by a dip-coating procedure in a PEG/water solution. The primer coat was fabricated from a di (ethylene glycol) vinyl ether (EO2V) monomer vapor fed directly into the argon plasma. The primer/PEG composite film was studied with profilometer, visible-light microscope, scanning electron microscope (SEM), and impedance spectroscopy (IS). A "tape test" was used to evaluate film adhesion. Response of the PEG composite film to an AC electric perturbation was studied as a function of hydration state using IS. Withdrawing the primed substrate from the PEG solution at a prescribed and controlled speed contributed to uniformity of the deposited composite film. Most substrates were type 316 stainless steel; however preliminary work was completed on glass as well. Profilometer measurements show that the full composite film had a thickness of 850 nm, 200 nm of which was the primer. Optical micrographs of the film before and after a "tape test'" revealed effective adhesion of the primer/PEG composite film to polished SS substrate. Stability of processed coupons with primer/PEG coating was evaluated by immersing the coupons half way into a salt solution at room temperature for 48 hours. Samples were analyzed before and after immersion by optical microscopy, profilometry and SEM. Prospective applications include coatings on orthopedic implants and food processing equipment. The effectiveness of this composite film at reducing bacterial adhesion will be investigated.
Analysis of Sphingosine 1-Phosphate, Ceramides, and Other Bioactive Sphingolipids by High-Performance Liquid Chromatography-Tandem Mass Spectrometry (2001)

The lipid backbones of sphingolipids and their metabolites are highly bioactive compounds that affect diverse cellular functions. The metabolites that have been most extensively studied with respect to their effects on cell behavior are ceramides, sphingosine (and other sphingoid bases), and sphingosine 1-phosphate. Additionally, there is interest in other naturally occurring species such as lysosphingolipids (sphingosine, phosphorylcholine, and psychosines) and N-methyl (di- and tri-methyl)-sphingosines. In many cases, studies of cell signaling mediated by these compounds have focused on a single category (such as ceramides or sphingosine 1-phosphate) because of the technical difficulty of more comprehensive analyses. One obstacle in such studies is that most of these compounds are metabolically interconvertable, so it is difficult to assign a conclusive relationship. In this article, we describe the analytical methods for extraction, identification, and quantitation of sphingolipids using state-of-the-art tandem mass spectrometry (MS/MS). Precursor ion scans are used to distinguish various species of sphingolipids in crude extracts by their unique molecular decomposition products. Specific headgroup, sphingoid base, and fatty acid chain combinations can be readily determined. Quantitation is achieved by multiple reaction monitoring (MRM) in conjunction with high-pressure liquid chromatography (HPLC). Compared to precursor ion scans alone, MRM experiments yield greater sensitivity and lower limits of detection by monitoring a specific precursor and product ion pair. This sensitivity facilitates detection of dozens of individual molecular species under optimal ion formation and decomposition conditions for each species, eliminating any ambiguity that may arise from differences in the kinetics of dissociation.
Optimization of sampling pattern and the design of Fourier ptychographic illuminator (2015)

Fourier ptychography (FP) is a recently developed imaging approach that facilitates high-resolution imaging beyond the cutoff frequency of the employed optics. In the original FP approach, a periodic LED array is used for sample illumination, and therefore, the scanning pattern is a uniform grid in the Fourier space. Such a uniform sampling scheme leads to 3 major problems for FP, namely: 1) it requires a large number of raw images, 2) it introduces the raster grid artefacts in the reconstruction process, and 3) it requires a high-dynamic-range detector. Here, we investigate scanning sequences and sampling patterns to optimize the FP approach. For most biological samples, signal energy is concentrated at low-frequency region, and as such, we can perform non-uniform Fourier sampling in FP by considering the signal structure. In contrast, conventional ptychography perform uniform sampling over the entire real space. To implement the non-uniform Fourier sampling scheme in FP, we have designed and built an illuminator using LEDs mounted on a 3D-printed plastic case. The advantages of this illuminator are threefold in that: 1) it reduces the number of image acquisitions by at least 50% (68 raw images versus 137 in the original FP setup), 2) it departs from the translational symmetry of sampling to solve the raster grid artifact problem, and 3) it reduces the dynamic range of the captured images 6 fold. The results reported in this paper significantly shortened acquisition time and improved quality of FP reconstructions. It may provide new insights for developing Fourier ptychographic imaging platforms and find important applications in digital pathology.
Preparation of highly active enterogastrone (1969)

By using a 10% pure preparation of cholecystokinin–pancreozymin (CCK–PZ) a fraction was obtained which was inhibitory for H + secretion, pepsin secretion, and motor activity in antral and fundic pouches. This material possessed no significant CCK–PZ activity or secretin-like activity.
Human CD8+ herpes simplex virus-specific cytotoxic T-lymphocyte clones recognize diverse virion protein antigens (1992)

The role of the HLA class I-restricted, CD8+, herpes simplex virus (HSV)-specific cytotoxic T lymphocytes (CTL) in the control of human HSV infections is controversial because previous reports suggest that a substantial portion of the antigen-specific lytic response is mediated by CD4+ cells. To address this question directly, we isolated HSV-specific CD8+ CTL clones from a patient with recurrent genital herpes. These CTL were cloned by coculturing responder peripheral blood mononuclear cells (PBMC) with phytohemagglutinin-stimulated PBMC that had been infected with live HSV-2 and then irradiated prior to the addition of responder cells. After 1 week, CTL were cloned by limiting dilution using phytohemagglutinin stimulation and allogeneic feeder PBMC. Seven clones were isolated; all seven clones were CD8+ CD4- CD3+ DRbright, six lysed only HSV-2-infected targets, and one lysed both HSV-1- and HSV-2-infected targets. Antigen presentation was restricted by two to three different HLA class I loci. To determine the antigens recognized by these HSV-specific CTL, target cells were infected with HSV in the presence of acyclovir, 5,6-dichloro-1-beta-D-ribofuranosylbenzimidazole, or cycloheximide in a series of drug block/release protocols to limit the repertoire of viral gene expression to select transcriptional classes. Five of the clones exhibited a different pattern of cytotoxicity, suggesting that each recognized a distinct HSV antigen. One of the clones appears to be directed against an immediate-early antigen; six of the clones recognize virion proteins. Five of these clones recognized internal virion proteins that could be introduced into target cells by HSV infection in the absence of virus gene expression. Antigen specificity was further tested by using vaccinia virus vectors that express glycoproteins gD2 and gB2 or the tegument protein VP16. One clone lysed vaccinia virus/gD2-infected target cells; the remaining clones did not recognize any of these gene products. The diversity of the CD8+ response from a single individual indicated that several different antigens are recognized when presented in the context of a variety of class I HLA alleles, a pattern that markedly differs from that described for another human herpesvirus, cytomegalovirus.
Studies on matter production of taro plant (Colocasia esculenta Schott). II. Varietal differences of dry matter production and tuber growth. (1988)

サトイモの3つの型, 子イモ用品種(石川早生, 女早生), 親子イモ兼用品種(赤芽), 親イモ用品種(台湾芋)を圃場栽培し, 乾物生産およびイモ肥大特性を調査した. 1. 品種間で個体生長量に大差がみられた. イモ重の推移では, 子イモ用品種では, 子・孫イモの肥大が目立ち, 赤芽では親・子イモが, 台湾芋では親イモの肥大が生育末期まで続いた. 2. 乾物生産速度とイモ生産速度との関係は, 生育の前半と後半に分けられ, とくに, 赤芽と台湾芋では生育後半にイモ肥大によって乾物生産速度が高められた. 3. イモ生産速度と葉面積指数との関係は, 赤芽と台湾芋で葉面積指数が高くなることによってイモ生産速度が高まることが示唆された.
<title>Analyzing deep-UV lens aberrations using aerial image and latent image metrologies</title> (1994)

The technique of direct aerial image metrology (AIM) has been applied to characterize the performance of a microlithographic lens. AIM is potentially faster and more reproducible than measurements obtained by scanning electron microscopy. Direct measurement of the aerial image eliminates both the process variations associated with resist processing as well as the subjective nature of evaluating resist profiles. We have used AIM to evaluate some of the primary aberrations of a 248 nm stepper lens. We compare the results to those obtained with latent image scatterometry, a proven technique for measuring lens performance. We found that AIM, while providing qualitatively good results, contained some slight systematic errors that reduced the accuracy of the data. The sources of error and their remedies are discussed.
Eine vereinfachte Synthese von Methionin‐Enkephalin (1978)

A Convenient Synthesis of Methionin‐Enkephalin An efficient synthesis of methionin‐enkephalin has been developed by prolongation of the C‐terminal amino acid methylester using Boc‐Phe‐OH Nomenklatur und Abkürzungen nach den Regeln der IUPAC‐IUB‐Commission on Bichemical Nomenclature: Hoppe‐Seyler's Z. physiol. Chem. 348 , 256 (1967), J. Biol. Chem. 247 , 977 (1972); weitere Abkürzungen: DCC = Dicyclohexylcarbodiimid, HOBt = 1‐Hydroxybenzotriazol, DMF = Dimethylformamid. , Boc‐Gly‐Gly‐OH and Boc‐Tyr‐OH.