gebhart/patrepeval huggingface dataset:
EXPO2009: structure solution by powder data in direct and reciprocal space (2009)

The program EXPO2009 is the evolution of EXPO2004 [Altomare, Caliandro, Camalli, Cuocci, Giacovazzo, Moliterni &amp; Rizzi (2004). J. Appl. Cryst . 37 , 1025–1028]. EXPO2009 performs all the steps of ab initio structure solution by powder data: indexing, space-group determination, estimation of the reflection integrated intensities, structure solution by direct/Patterson methods and/or by a direct-space/hybrid approach, and model refinement by the Rietveld technique. New procedures have been introduced in EXPO2009 for enhancing the structure solution process, particularly in the case of low-resolution data and/or organic compounds, when traditional approaches like direct methods may fail. The EXPO2009 graphical interface has been optimized and made very user friendly.
Transgenic expression of CYP7A1 in LDL receptor-deficient mice blocks diet-induced hypercholesterolemia (2006)

Constitutive expression of a cholesterol-7alpha-hydroxylase (CYP7A1) transgene in LDL receptor-deficient mice blocked the ability of a cholesterol-enriched diet to increase plasma levels of apolipoprotein B-containing lipoproteins. LDL receptor-deficient mice expressing the CYP7A1 transgene exhibited complete resistance to diet-induced hypercholesterolemia and to the accumulation of cholesterol in the liver. Hepatic mRNA expression of liver X receptor-inducible ABCG5 and ABCG8 was decreased in CYP7A1 transgenic, LDL receptor-deficient mice fed a cholesterol-enriched diet. Thus, increased biliary cholesterol excretion could not account for the maintenance of cholesterol homeostasis. CYP7A1 transgenic, LDL receptor-deficient mice fed the cholesterol-enriched diet exhibited decreased jejunal Niemann-Pick C1-Like 1 protein (NPC1L1) mRNA expression, an important mediator of intestinal cholesterol absorption. A taurocholate-enriched diet also decreased NPC1L1 mRNA expression in a farnesoid X receptor-independent manner. Reduced expression of NPC1L1 mRNA was associated with decreased cholesterol absorption ( approximately 20%; P < 0.05) exhibited by CYP7A1 transgenic LDL receptor-deficient mice fed the cholesterol-enriched diet. The combined data show that enhanced expression of CYP7A1 is an effective means to prevent the accumulation of cholesterol in the liver and of atherogenic apolipoprotein B-containing lipoproteins in plasma.
Covalent Layer-by-Layer Assembly of Water-Permeable and Water-Impermeable Polymer Multilayers on Highly Water-Soluble and Water-Sensitive Substrates (2012)

Aqueous methods for the layer-by-layer (LbL) assembly of polyelectrolyte multilayers (PEMs) are not, by their nature, well suited for the fabrication of thin films on substrates that are highly water-soluble or composed of water-sensitive materials. Here, we demonstrate that organic solvent-based processes for covalent (or “reactive”) LbL assembly can be used to fabricate multilayers directly on the surfaces of model water-soluble, water-reactive, and water-sensitive substrates that are either difficult or impossible to coat effectively using aqueous-based LbL methods. Our approach is based on methods for the reactive assembly of multilayers using poly(ethyleneimine) (PEI) and an amine-reactive polymer containing azlactone functionality (PVMDA) in polar-aprotic solvents. The amine-reactive nature of the resulting PEI/PVDMA films facilitated subsequent modification of film-coated surfaces by reaction with primary amine-based nucleophiles. Functionalization of films with the hydrophobic small-molecule amine n-decylamine resulted in the prolonged dissolution and release of underlying water-soluble substrates, and could be used to tune interfacial properties (e.g., to render these water-permeable films more hydrophobic). Fabrication of thicker PEI/PVDMA films resulted in coatings with superhydrophobic properties (e.g., water contact angles of ∼160°) that resisted the penetration of water and enhanced considerably the stabilities of water-sensitive substrates. This approach can, therefore, also be used, in various ways, and to varying extents, to design barriers that protect, enhance the stabilities of, or control/pattern the responses of water-soluble/reactive substrates when they are exposed to aqueous environments. Finally, our results demonstrate that the solubility of PEI and PVDMA in a range of different polar-aprotic solvents can provide flexibility with respect to coating water-soluble/sensitive materials that may also be soluble in some other polar organic solvents. The versatility of this approach could prove useful for modifying the interfacial properties of water-soluble and water-sensitive materials of interest in biotechnology, catalysis, and many other fundamental and applied contexts.
Is There Appetite after GLP‐1 and PACAP? (1998)

Anitobesity drugs must increase the sensitivity of the hypothalamic satiety center towards leptin and antagonize the synthesis and action of NPY. The array of pharmacologic tools available is vast and presently ineffective. Among peptide analogs considered for evaluation [NPY-5 antagonists and CCK-A, bombesin, amylin and melanocyte-stimulating hormone-4 (or melanin-concentrating hormone?) agonists], is there a place for GLP-1 and PACAP? GLP-1 receptors present in ARC, PVN, VMN, and SON are the target for both central and blood-borne GLP-1 in those hypothalamic neurons endowed with GLUT-2 and glucokinase. GLP-1, hypersecreted by L-cells after a meal, is a potent insulinotropic agent and, together with glucose, reduces food intake and induces c-fos in the ARC. PACAP is present in the ARC, PVN, and SCH, and its hypothalamic type I receptor elevates cAMP and inositol triphosphate in the PVN, where it may perhaps antagonize NPY-induced food intake and hyperinsulinemia. However, irrelevant neuroendocrine, autonomic, and circadian functions are also activated by this peptide, making it a less than ideal base on which to build an obesity treatment.
Co-overexpression of geraniol-10-hydroxylase and strictosidine synthase improves anti-cancer drug camptothecin accumulation in Ophiorrhiza pumila (2015)

Camptothecin (CPT) belongs to a group of monoterpenoidindole alkaloids (TIAs) and its derivatives such as irinothecan and topothecan have been widely used worldwide for the treatment of cancer, giving rise to rapidly increasing market demands. Genes from Catharanthus roseus encoding strictosidine synthase (STR) and geraniol 10-hydroxylase (G10H), were separately and simultaneously introduced into Ophiorrhiza pumila hairy roots. Overexpression of individual G10H (G lines) significantly improved CPT production with respect to non-transgenic hairy root cultures (NC line) and single STR overexpressing lines (S lines), indicating that G10H plays a more important role in stimulating CPT accumulation than STR in O. pumila. Furthermore, co-overexpression of G10H and STR genes (SG Lines) caused a 56% increase on the yields of CPT compared to NC line and single gene transgenic lines, showed that simultaneous introduction of G10H and STR can produce a synergistic effect on CPT biosynthesis in O. pumila. The MTT assay results indicated that CPT extracted from different lines showed similar anti-tumor activity, suggesting that transgenic O. pumila hairy root lines could be an alternative approach to obtain CPT. To our knowledge, this is the first report on the enhancement of CPT production in O. pumila employing a metabolic engineering strategy.
Growth of Moraxella catarrhalis with human transferrin and lactoferrin: expression of iron-repressible proteins without siderophore production (1994)

Moraxella (Branhamella) catarrhalis, a mucosal pathogen closely related to Neisseria species, is a prominent cause of otitis media in young children and lower respiratory tract infections in adults. In this study, we investigated whether M. catarrhalis can compete for iron bound to human transferrin or human lactoferrin in a manner similar to that utilized by Neisseria meningitidis and Neisseria gonorrhoeae. Our studies demonstrated that M. catarrhalis obtains iron from these serum carrier proteins and also maintains growth with ferric nitrate in vitro. Furthermore, we report that when M. catarrhalis is grown under iron-limited conditions, the bacteria express new outer membrane proteins that are not detected in membranes of organisms cultured in an iron-rich environment. We have shown that these are iron-repressible proteins since they are not induced by other environmental stresses and the expression of these proteins is repressed when a source of iron is provided for iron-limited bacteria. The iron-repressible proteins are expressed in the absence of any detectable siderophore production. These iron-repressible proteins may be important for the acquisition and utilization of iron in vivo, which could allow M. catarrhalis to colonize and survive on human mucosal surfaces.
Characterization of the catalase antioxidant defense gene Cat1 of maize, and its developmentally regulated expression in transgenic tobacco (1993)

A genomic clone containing the maize Cat1 gene has been isolated and its complete DNA sequence determined. The start of transcription has been mapped by primer extension. Six introns were identified in the Cat1 coding region. In order to determine the tissue-specific expression pattern of the Cat1 gene, promoter-reporter gene fusion constructs were made consisting of 2.5 kb and 0.8 kb of the 5' Cat1 sequence fused to the coding region of the beta-glucuronidase (GUS) gene. These fusion constructs were introduced into Nicotiana tabacum cv. Burley 21 and the expression of Cat1-GUS in various tissues was examined. In transgenic tobacco, the Cat1 promoter can drive GUS expression at relatively high levels in mature seeds. GUS activity starts to accumulate at about 10 days after flowering, reaching a maximum at about 22 days after flowering, and decreases thereafter, but persists until after seed desiccation through early germination. Low levels of GUS activity can be detected in pollen. This corresponds to the Cat1 expression pattern observed in maize.
Structure and function of lysosomal phospholipase A2: identification of the catalytic triad and the role of cysteine residues (2005)

Lysosomal phospholipase A2 (LPLA2) is an acidic phospholipase that is highly expressed in alveolar macrophages and that may play a role in the catabolism of pulmonary surfactant. The primary structure found in LCAT is conserved in LPLA2, including three amino acid residues potentially required for catalytic activity and four cysteine residues. LPLA2 activity was measured in COS-7 cells transfected with c-myc-conjugated mouse LPLA2 (mLPLA2) or mutated LPLA2. Single alanine substitutions in the catalytic triad resulted in the elimination of LPLA2 activity. Four cysteine residues (C65, C89, C330, and C371), conserved between LPLA2 and LCAT, were replaced with alanine. Quadruple mutations at C65, C89, C330, and C371, double mutations at C65 and C89, and a single mutation at C65 or C89 resulted in the elimination of activity. Double mutations at C330 and C371 and a single mutation at C330 or C371 resulted in a partial reduction of activity. Thus, the presence of a disulfide bond between C330 and C371 is not required for LPLA2 activity. We propose that one disulfide bond between C65 and C89 and free cysteine residues at C330 and C371 and the triad, serine-198, aspartic acid-360, and histidine-392, are required for the full expression of mLPLA2 activity.
A Block-sorting Lossless Data Compression Algorithm (1994)

We describe a block-sorting, lossless data compression algorithm, and our implementation of that algorithm. We compare the performance of our implementation with widely available data compressors running on the same hardware.&#13;\n&#13;\nThe algorithm works by applying a reversible transformation to a block of input text. The transformation does not itself compress the data, but reorders it to make it easy to compress with simple algorithms such as move-to-front coding. &#13;\n&#13;\nOur algorithm achieves speed comparable to algorithms based on the techniques of Lempel and Ziv, but obtains compression close to the best statistical modelling techniques. The size of the input block must be large (a few kilobytes) to achieve good compression.
Prostate cancer screening (1995)

Epidemiology of Prostate Cancer, Wael A. Sakr and Clara Ward. Natural History of Prostate Cancer, Peter C. Albertsen. Mathematical Issues: PSA Testing, Ruth Etzioni and David F. Penson. Evidence of Benefit of Screening in Other Cancers, Ismail Jatoi. The Role of Prostate Specific Antigen and Its Variants in Prostate Cancer Screening, Faiyaaz M. Jhaveri, Michael K. Brawer, and Eric A. Klein. The Digital Rectal Examination in Prostate Cancer Screening, Joseph Basler. Philosophical Reflections on PSA Screening: What Should We Now Think and Do? Paul H. Lange. Imaging in Prostate Cancer Screening, Aaron Sulman and Martin I. Resnick. Risk Factors for Prostate Cancer, David L. Shepherd. Transrectal Ultrasound and Artifical Neural Networks in the Diagnosis of Prostate Cancer, Tillmann Loch. Evidence of the Effectiveness of Prostate Cancer Screening, Chris Magee and Ian M. Thompson. Prostate Cancer Screening: A Note of Caution, Otis W. Brawley. Quality of Life and Health Behavior in Prostate Cancer Screening Populations, Mark S. Litwin and Kristen A. Reid. Prostate Cancer Screening Recommendations from Organized Medicine, Gregory T. Sweat. Informed Consent and Prostate Specific Antigen Screening: What Patients Ought to Know, Evelyn C. Y. Chan. Experience of Prostate Cancer Awareness Week, Zinelabidine Abouelfadel and E. David Crawford. The Laval University Screening Trial Results, Fernand Labrie, Bernard Candas, Lionel Cusan, and Jose-Luis Gomez. Cancer of the Prostate Risk Index Test and Software (CAPRI), Scott A. Optenberg, Atanacio C. Guillen, John P. Campbell, and Ian M. Thompson. The European Randomized Study of Screening for Prostate Cancer (ERSPC), Fritz H. Schroder and Ingrid van der Cruijsen-Koeter for the ERSPC Study Group. Index.
Reduction of the Accumulation of Advanced Glycation End Products by ACE Inhibition in Experimental Diabetic Nephropathy (2002)

The effect of ACE inhibition on the formation of advanced glycation end products (AGEs) and oxidative stress was explored. Streptozocin-induced diabetic animals were randomized to no treatment, the ACE inhibitor ramipril (3 mg/l), or the AGE formation inhibitor aminoguanidine (1 g/l) and followed for 12 weeks. Control groups were followed concurrently. Renal AGE accumulation, as determined by immunohistochemistry and both serum and renal fluorescence, were increased in diabetic animals. This was attenuated by both ramipril and aminoguanidine to a similar degree. Nitrotyrosine, a marker of protein oxidation, also followed a similar pattern. The receptor for AGEs, gene expression of the membrane-bound NADPH oxidase subunit gp91phox, and nuclear transcription factor-kappaB were all increased by diabetes but remained unaffected by either treatment regimen. Two other AGE receptors, AGE R2 and AGE R3, remained unchanged for the duration of the study. The present study has identified a relationship between the renin-angiotensin system and the accumulation of AGEs in experimental diabetic nephropathy that may be linked through oxidative stress
Site-Specific Incorporation of a Redox-Active Amino Acid into Proteins (2003)

The redox-active amino acid 3,4-dihydroxy-l-phenylalanine (DHP), which can undergo two-electron oxidation to a quinone, has been incorporated selectively and efficiently into proteins in Escherichia coli in response to a TAG codon. We have demonstrated that DHP can be oxidized electrochemically within the protein. The ability to incorporate a redox-active amino acid site specifically into proteins should facilitate the study of electron transfer in proteins, as well as enable the engineering of redox proteins with novel properties.
Barcode Readers using the Camera Device in Mobile Phones (2004)

This paper shows new algorithms and the implementations of image reorganization for EAN/QR barcodes in mobile phones. The mobile phone system used here consists of a camera, mobile application processor, digital signal processor (DSP), and display device, and the source image is captured by the embedded camera device. The introduced algorithm is based on the code area found by four corners detection for 2D barcode and spiral scanning for 1D barcode using the embedded DSP. This algorithm is robust for practical situations and the DSP has good enough performance for the real-time recognition of the codes. The performance of our image processing is 66.7 frames/sec for EAN code and 14.1 frames/sec for QR code image processing, and this is sufficient performance for practical use. The released mobile phone had performance of 5-10 frames/sec including OS and subsystem overheads.
CCR2+ Monocyte-Derived Dendritic Cells and Exudate Macrophages Produce Influenza-Induced Pulmonary Immune Pathology and Mortality (2008)

Infection with pathogenic influenza virus induces severe pulmonary immune pathology, but the specific cell types that cause this have not been determined. We characterized inflammatory cell types in mice that overexpress MCP-1 (CCL2) in the lungs, then examined those cells during influenza infection of wild-type (WT) mice. Lungs of both naive surfactant protein C-MCP mice and influenza-infected WT mice contain increased numbers of CCR2(+) monocytes, monocyte-derived DC (moDC), and exudate macrophages (exMACs). Adoptively transferred Gr-1(+) monocytes give rise to both moDC and exMACs in influenza-infected lungs. MoDC, the most common inflammatory cell type in infected lungs, induce robust naive T cell proliferation and produce NO synthase 2 (NOS2), whereas exMACs produce high levels of TNF-alpha and NOS2 and stimulate the proliferation of memory T cells. Relative to WT mice, influenza-infected CCR2-deficient mice display marked reductions in the accumulation of monocyte-derived inflammatory cells, cells producing NOS2, the expression of costimulatory molecules, markers of lung injury, weight loss, and mortality. We conclude that CCR2(+) monocyte-derived cells are the predominant cause of immune pathology during influenza infection and that such pathology is markedly abrogated in the absence of CCR2.
Microchip Encoded Combinatorial Libraries: Generation of a Spatially Encoded Library from a Pool Synthesis The Solid-Phase Synthesis of Complex Small Molecules (1996)

An encoding method which provides ready access to the structure of individual compounds in a combinatorial library of small organic molecules has been developed. Glass-encased microchips each of which contain a unique binary encoded ID which can be scanned and recorded using radiofrequency (RF) were added to indi vidual tea bags containing polystyrene polymer functionalized with a Wang linker. The tea bags were subjected to a three-step synthesis. At each stage of the synthesis, the microchips were RF-scanned and the unique ID's were recorded. After the synthesis was complete, each tea bag was introduced to individual wells of a microtiter plate and the products were deblocked from the polymer. The histogram of the ID for each well was then used to assign the structure of every product in the library. A library of 64 compounds was thus synthesized using a pooled compound strategy, affording a positionally encoded discrete library.
The Size of the Cochlea and Predictions of Insertion Depth Angles for Cochlear Implant Electrodes (2006)

The cochlear size measure distance A was repeatable to within the resolution of the high-resolution computed tomography image data. The basal turn of the normally formed cochlea is variable in size. These variations in size would produce >5.0 mm variation in the length of the lateral wall to the point consistent with an insertion depth angle of 360 degrees . Cochlear size influenced final insertion depth angles obtained for the perimodiolar Nucleus 24 Contour Advance electrode.
Tumorigenicity of Human Malignant Lymphoblasts: Comparative Study With Unmanipulated Nude Mice, Antilymphocyte Serum-Treated Nude Mice, and X-Irradiated Nude Mice23 (1980)

The ability of unmanipulated, antilymphocyte serum (ALS)-treated, and X-irradiated nude BALB/c female mice (in their 13th backcross generation) to serve as hosts for 10 human lymphoblastoid cell lines as well as for peripheral blood lymphocytes from healthy humans was compared. The 10 lymphoma lines included 7 previously characterized and reported in the literature. Significant differences with respect to both latency period for tumor appearance and success rate for tumor transplantation were detected among the 3 experimental groups. The unmanipulated mice were poor recipients for lymphoma heterotranplants, and tumors were produced in only two instances. In contrast, 6 tumor lines were successfully transplanted in mice inoculated with ALS, and all 10 lines were successfully transplanted in X-irradiated recipients. Although tumors were readily produced in ALS-treated and X-irradiated mice, no gross or histologic evidence of focal or distant metastases was apparent. Human lymphoblastoid cells were recultured, essentially unchanged, from the heterotransplants from 6 of 7 tumors tested. Although the tumor line HT 1460, originally from a human lymphoma, was successfully transplanted in all 3 groups, only mouse cells were recultured. The use of X-irradiation, rather than ALS, to immunosuppress nude mice offers a more standardized method for heterotransplanting human tumor cell lines and permits ready comparisons between laboratories. Furthermore X-radiation permits transplantation and subsequent study of lymphoblastoid tumors that are otherwise difficult to successfully transplant in nude mice.
A Natural Kinase-Deficient Variant of Fibroblast Growth Factor Receptor 1 (1996)

A fibroblast growth factor receptor 1 variant missing 37 amino acids from the carboxy-terminal tyrosine kinase catalytic domain was discovered in human lung fibroblasts and several other human cell lines. The receptor variant binds specifically to acidic fibroblast growth factor but has no tyrosine kinase activity. It was found that cellular transfectants expressing the fibroblast growth factor receptor 1 variant are mitogenically inactive and ligand binding to the receptor causes neither receptor autophosphorylation nor phospholipase C-gamma transphosphorylation. The fibroblast growth factor receptor 1 variant therefore represents an inactive receptor for acidic fibroblast growth factor. Since both kinase and kinase-deficient receptor forms are expressed in cells, it is conceivable that the kinase-deficient receptor plays an important role in regulating cellular responses elicited by acidic fibroblast growth factor stimulation.
Characterization of somatostatin transactivating factor-1, a novel homeobox factor that stimulates somatostatin expression in pancreatic islet cells. (1993)

The endocrine pancreas consists of several differentiated cell types that are distinguished by their selective expression of peptide hormones such as insulin, glucagon, and somatostatin. Although a number of homeobox-type factors have been proposed as key regulators of individual peptide genes in the pancreas, their cellular distribution and relative abundance remain uncharacterized. Also, their overlapping DNA binding specificities have further obscured the regulatory functions these factors perform during development. In this report we characterize a novel homeobox-type somatostatin transactivating factor termed STF-1, which is uniformly expressed in cells of the endocrine pancreas and small intestine. The 283-amino acid STF-1 protein binds to tissue-specific elements within the somatostatin promoter and stimulates somatostatin gene expression both in vivo and in vitro. Remarkably, STF-1 comprises the predominant tissue-specific element-binding activity in nuclear extracts from somatostatin-producing pancreatic islet cells, suggesting that this protein may have a primary role in regulating peptide hormone expression and specifying endocrine cell lineage in the developing gut.