gebhart/patrepeval huggingface dataset:
Keratinocytes stimulate fibroblast hyaluronan synthesis through the release of stratifin: A possible role in the suppression of scar tissue formation (2011)

Scar tissue formation during healing of extensive skin wounds may be related to delayed reepithelialization, while elevated levels of hyaluronan may suppress scar tissue formation. This study investigates the expression of hyaluronan by human skin fibroblasts in response to keratinocyte-conditioned medium (KCM), and attempts to identify any active factors within the conditioned medium. Serum-free KCM was assessed for its ability to stimulate the incorporation of (3) H-glucosamine into fibroblast glycosaminoglycans, and hyaluronan synthesis. Conditioned medium was concentrated with an ultrafiltration membrane with a 30 kDa cutoff. Stratifin was assessed for its ability to stimulate hyaluronan synthesis and its role in KCM. KCM stimulated fibroblast glycosaminoglycan synthesis up to a 3.3-fold increase and a 6.5-fold increase in hyaluronan synthesis compared with serum-free controls. Preliminary characterization of the active factors showed that they are retained by a >30 kDa ultrafiltration membrane, and are protease sensitive and heat resistant. Emmprin and stratifin were shown to stimulate fibroblast hyaluronan synthesis, and the hyaluronan-stimulating activity of KCM was removed following stratifin depletion and to a lesser extent by emmprin depletion. Keratinocytes release soluble factors, including stratifin, that stimulate fibroblast hyaluronan synthesis, and this stimulation of fibroblast hyaluronan may contribute to the suppression of scar tissue formation.
RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome (2011)

RSEM is an accurate and user-friendly software tool for quantifying transcript abundances from RNA-Seq data. As it does not rely on the existence of a reference genome, it is particularly useful for quantification with de novo transcriptome assemblies. In addition, RSEM has enabled valuable guidance for cost-efficient design of quantification experiments with RNA-Seq, which is currently relatively expensive.
Mapping Spatial Pattern in Biodiversity for Regional Conservation Planning: Where to from Here? (2002)

Vast gaps in available information on the spatial distribution of biodiversity pose a major challenge for regional conservation planning in many parts of the world. This problem is often addressed by basing such planning on various biodiversity surrogates. In some situations, distributional data for selected taxa may be used as surrogates for biodiversity as a whole. However, this approach is less effective in data-poor regions, where there may be little choice but to base conservation planning on some form of remote environmental mapping, derived, for example, from interpretation of satellite imagery or from numerical classification of abiotic environmental layers. Although this alternative approach confers obvious benefits in terms of cost-effectiveness and rapidity of application, problems may arise if congruence is poor between mapped land-classes and actual biological distributions. I propose three strategies for making more effective use of available biological data and knowledge to alleviate such problems by (1) more closely integrating biological and environmental data through predictive modeling, with increased emphasis on modeling collective properties of biodiversity rather than individual entities; (2) making more rigorous use of remotely mapped surrogates in conservation planning by incorporating knowledge of heterogeneity within land-classes, and of varying levels of distinctiveness between classes, into measures of conservation priority and achievement; and (3) using relatively data-rich regions as test-beds for evaluating the performance of surrogates that can be readily applied across data-poor regions.
Self-regulation of 70-kilodalton heat shock proteins in Saccharomyces cerevisiae. (1990)

To determine whether the 70-kilodalton heat shock proteins of Saccharomyces cerevisiae play a role in regulating their own synthesis, we studied the effect of overexpressing the SSA1 protein on the activity of the SSA1 5'-regulatory region. The constitutive level of Ssa1p was increased by fusing the SSA1 structural gene to the GAL1 promoter. A reporter vector consisting of an SSA1-lacZ translational fusion was used to assess SSA1 promoter activity. In a strain producing approximately 10-fold the normal heat shock level of Ssa1p, induction of beta-galactosidase activity by heat shock was almost entirely blocked. Expression of a transcriptional fusion vector in which the CYC1 upstream activating sequence of a CYC1-lacZ chimera was replaced by a sequence containing a heat shock upstream activating sequence (heat shock element 2) from the 5'-regulatory region of SSA1 was inhibited by excess Ssa1p. The repression of an SSA1 upstream activating sequence by the SSA1 protein indicates that SSA1 self-regulation is at least partially mediated at the transcriptional level. The expression of another transcriptional fusion vector, containing heat shock element 2 and a lesser amount of flanking sequence, is not inhibited when Ssa1p is overexpressed. This suggests the existence of an element, proximal to or overlapping heat shock element 2, that confers sensitivity to the SSA1 protein.
Biochemical characterization of Candida albicans epitopes that can elicit protective and nonprotective antibodies (1997)

We previously reported that the immunoglobulin M (IgM) monoclonal antibody (MAb) B6.1 protects mice against disseminated candidiasis, whereas the IgM MAb B6 does not. Both MAbs are specific for an adhesin fraction isolated from the cell surface of Candida albicans, but their epitope specificities differ. In the present study, we examined the surface locations of both epitopes and obtained structural information regarding the B6.1 epitope. Immunofluorescence confocal microscopic analysis of C. albicans yeast forms showed that epitope B6.1 is displayed rather homogeneously over the entire cell surface, whereas epitope B6 appears to have a patchy distribution. Both antibodies were essentially nonreactive with the surfaces of mycelial forms of the fungus, indicating that neither epitope is expressed on the surfaces of these forms. For isolation of the B6.1 epitope, the adhesin fraction consisting of cell surface phosphomannan was subjected to mildly acidic (10 mM HCl) hydrolysis and was fractionated into acid-labile and acid-stable portions by size exclusion chromatography. Antibody blocking experiments showed that the B6.1 epitope is an acid-labile moiety of the phosphomannan and that the B6 epitope is located in the acid-stable fraction. The B6 epitope appeared to be mannan because it was stable to heat (boiling) and protease treatments but was destroyed by alpha-mannosidase digestion. The B6.1 epitope eluted from the size exclusion column in two fractions. Mass spectroscopic analyses showed that one fraction contained material with the size of a mannotriose and that the other was a mixture of mannotriose- and mannotetraose-size substances. Dose response inhibition tests of the fractions indicated that the B6.1 epitope is associated with the mannotriose. Nuclear magnetic resonance (NMR) spectroscopic analysis of the epitope yielded data consistent with a beta-(1-->2)-linked mannotriose. The fine structure of the B6 epitope is under investigation. Information derived from these investigations will be useful both in understanding protective versus nonprotective antibody responses to C. albicans and in improving anti-Candida vaccine formulations.
Contemporary role of prostate cancer gene 3 in the management of prostate cancer (2011)

The PCA3 test is not capable of replacing the PSA test in clinical practice and an appropriate cut-off level with acceptable performance characteristics is hard to define. Its value as a first-line diagnostic test is limited. The addition of PCA3 to risk assessment tools leads to an increase in predictive capability. Data relating to the accuracy of PCA3 on prostate cancer staging are contradictory and PCA3 as prognostic test should be subject of future studies.
Primary structure of the succinyl-CoA synthetase of Escherichia coli (1985)

The primary structure of the succinyl-CoA synthetase of Escherichia coli has been deduced from the nucleotide sequence of a 2451-base-pair segment of DNA containing the corresponding sucC (beta subunit) and sucD (alpha subunit) genes. The genes are located at one end of a gene cluster that encodes several citric acid cycle enzymes: gltA-sdhCDAB-sucABCD; gltA, citrate synthase; sdh, succinate dehydrogenase; sucA and sucB, the dehydrogenase (E1) and succinyltransferase (E2) components of the 2-oxoglutarate dehydrogenase complex. The sucC and sucD genes are separated from the sucA and sucB genes by a 273-base-pair segment containing four palindromic units, but they appear to be expressed from a sucABCD read-through transcript that extends from the suc promoter to a potential rho-independent terminator at the distal end of sucD. The stop codon of the sucC gene overlaps the sucD initiation codon by a single nucleotide, indicating close translational coupling of the sucC and sucD genes. The sucC gene comprises 1161 base pairs (388 codons, excluding the stop codon), and it encodes a polypeptide of Mr 41 390 corresponding to the beta subunit of succinyl-CoA synthetase. The sucD gene comprises 864 base pairs (288 codons, excluding the start and stop codons), and it encodes a product of Mr 29 644, corresponding to the alpha subunit of succinyl-CoA synthetase. The alpha subunit contains a 12-residue amino acid sequence that is identical with the histidine peptide previously isolated from the phosphoenzyme. This sequence forms part of one of the two potential nucleotide binding sites detected in the alpha subunit.
Phase I Combination Trial of Lenalidomide and Azacitidine in Patients With Higher-Risk Myelodysplastic Syndromes (2010)

The combination of lenalidomide and azacitidine is well tolerated with encouraging clinical activity. The go-forward dose is azacitidine 75 mg/m(2) on days 1 through 5 and lenalidomide 10 mg on days 1 through 21.
Determining the cause of anemia (1991)

In the vast majority of cases, the cause of microcytic hypochromic anemia is clearly suggested by the patient history, physical examination results, red cell indexes, and peripheral blood smear. Thus, further diagnostic testing, if necessary, can be very selective. When the underlying cause of anemia is obscure, the serum ferritin concentration should be measured first. If it is normal or increased, serum iron and free erythrocyte protoporphyrin levels can be determined. The serum iron level is low in anemias caused by iron deficiency and chronic disease but normal or elevated in those resulting from the thalassemias, hemoglobin E disorders, and lead toxicity. The free erythrocyte protoporphyrin level is elevated with iron deficiency, the anemia of chronic disease, and lead toxicity but normal with thalassemias and hemoglobin E disorders. Results of these two test indicate which of the more specific tests is most likely to yield the correct diagnosis.
Preimplantation genetic diagnosis for β‐thalassaemia: the Sardinian experience (2004)

Our study shows that PGD for beta-thalassaemia is an available procedure for couples who wish to avoid termination of pregnancy, except in cases where the IVF cycle efficiency is very poor.
Functional genomics: Probing plant gene function and expression with transposons (1998)

Transposable elements provide a convenient and flexible means to disrupt plant genes, so allowing their function to be assessed. By engineering transposons to carry reporter genes and regulatory signals, the expression of target genes can be monitored and to some extent manipulated. Two strategies for using transposons to assess gene function are outlined here: First, the PCR can be used to identify plants that carry insertions into specific genes from among pools of heavily mutagenized individuals (site-selected transposon mutagenesis). This method requires that high copy transposons be used and that a relatively large number of reactions be performed to identify insertions into genes of interest. Second, a large library of plants, each carrying a unique insertion, can be generated. Each insertion site then can be amplified and sequenced systematically. These two methods have been demonstrated in maize, Arabidopsis , and other plant species, and the relative merits of each are discussed in the context of plant genome research.
An approach for the higher efficiency in the HIT cells (2005)

The highest conversion efficiency to date of 21.5% (confirmed by AIST) with a size of 100.3 cm/sup 2/ has been achieved in an HIT cell. Because of this high efficiency and the cell's superior temperature characteristics, HIT cells are highly regarded by consumers. Sanyo will increase the production volume of cells and modules to meet the demand both inside and outside of Japan. We have been investigating suitable materials based on Sanyo's technology for fabricating high-quality a-Si solar cells to obtain higher build-in potential and control the junction properties, and have been studying how to treat the surface to create a good interface without introducing any damage. We will continue our efforts to obtain even higher levels of conversion efficiency by using the high potential that this structure has.
Confined Compression of Canine Annulus Fibrosus Under Chemical and Mechanical Loading (1995)

Uniaxial confined compression and swelling experiments on cylindrical specimens taken either in an axial or in a radial direction from a canine lumbar annulus fibrosus are presented. The loading protocol consisted of a combination of stepwise mechanical and chemical loading. Swelling and consolidation curves of normalized displacement versus square root of normalized time did not show a dependence on site or orientation of the specimen. All stages in which height increases, namely, conditioning, swelling, and desolidation show only slight differences in these normalized curves. Consolidation is initially faster, and later slower. The transport coefficient for axial specimens is higher than for radial specimens, for consolidation e.g., 3.14 +/- 1.56 10(-10) m2s(-1) and 1.11 +/- 0.33 10(-10) m2s(-1) respectively, the biphasic aggregate moduli are 1.01 +/- 0.31 MPa and 0.66 +/- 0.30 MPa, respectively.
A clustering method using the strength of citation (1990)

A new method for modelling and clustering a relational graph produced from the citation relation among scientific articles is discussed. One article corresponds to a point and a citation link corresponds to a directed walk in the graph. This graph is a direct-citation graph and a total-citation graph is derived from it. There exist two types of directed citation graph; i.e., citing directed-graph and cited directed-graph. The former is considered in this paper. These graphs are repre sented in the form of similarity matnces which are asymmetric. The characteristics of these graphs are analyzed by clustering. For this study, a research database was designed and produced to acquire bibliographic information and obtain relations be tween articles in it. A modelling methodology of its relational structure is described in this article. Combinatonal clustering methods have been examined and a clustering method for an asymmetric similarity matrix is also proposed.
In vivo glyco‐engineered antibody with improved lytic potential produced by an innovative non‐mammalian expression system (2007)

Recent studies have demonstrated that the reduction of the core fucosylation on N-glycans of human IgGs is responsible for a clearly enhanced antibody-dependent cellular cytotoxicity (ADCC). This finding might give access to improved active therapeutic antibodies. Here, the expression of the tumor antigen-specific antibody IGN311 was performed in a glyco-optimized strain of the moss Physcomitrella patens. Removal of plant specific N-glycan structures in this plant expression host was achieved by targeted knockout of corresponding genes and included quantitative elimination of core fucosylation. Antibodies transiently expressed and secreted by such genetically modified moss protoplasts assembled correctly, showed an unaltered antigen-binding affinity and, in extensive tests, revealed an up to 40-fold enhanced ADCC. Thus, the glyco-engineered moss-based transient expression platform combines a rapid technology with the subsequent analysis of glycooptimized therapeutics with regard to advanced properties.
Selection of tumor-specific epitopes on target antigens for radioimmunotherapy of breast cancer. (1995)

Evidence is presented for two different breast epithelial antigens that some epitopes have greater tumor specificity and are more effective targets for radioimmunotherapy than others. The two antigens, which are major components of the human milk fat globule membrane, are breast mucin and a M(r) 46,000 glycoprotein (BA46). Of five monoclonal antibodies (Mc5, Mc1, BrE-1, BrE-2, and BrE-3) against breast mucin, all recognize overlapping amino acid epitopes on the tandem repeat domain. However, each have unique and different tissue and tumor specificities and unique epitope structures on the fully glycosylated breast mucin. In preclinical studies, radioimmunoconjugates of all five monoclonal antibodies inhibit growth of transplantable breast tumors in immunodeficient mice. In human clinical trials, radioiodinated Mc5 was very poor in localizing breast tumor metastases. On the other hand, 111In-labeled BrE-3 imaged almost 90% of breast tumors and showed promise in radioimmunotherapy when labeled with 90Y. The failure of Mc5 in clinical trials may be partly attributed to the high levels of its epitope on circulating mucin compared to the epitope of BrE-3. The Mc5 binding affinity increased significantly with glycosylation, while the BrE-3 epitope was masked by glycosylation. The BA46 glycoprotein is a breast tumor-associated membrane antigen containing an NH2-terminal, epidermal growth factor-like domain into which a cell adhesion sequence (RGD) is inserted and a COOH-terminal domain with homology to the phospholipid binding C1/C2 domain of coagulation factors V and VIII. It promotes cell attachment in an RGD-dependent manner. Monoclonal antibody Mc8, which binds to the C2-like domain, is only moderately effective in experimental radioimmunotherapy, while Mc3, which binds an epitope in the EGF-like RGD domain, was highly effective in destroying breast tumors in nude mice. With 90Y-labeled Mc3, 6 of 7 mice are cured of the tumors. These results indicate that by selecting appropriate monoclonal antibodies, a normal antigen can be used as a target for radioimmunotherapy.
Beneficial Effects of RheothRx Injection in Patients Receiving Thrombolytic Therapy for Acute Myocardial Infarction (1996)

Adjunctive therapy with poloxamer 188 resulted in substantial benefit in this randomized trial, including significantly smaller infarcts, greater myocardial salvage, better left ventricular function, and a lower incidence of in-hospital reinfarction. Although the mechanisms are unproven, poloxamer 188 treatment may accelerate thrombolysis, reduce reocclusion, and ameliorate reperfusion injury.
Interference of CD40L-Mediated Tumor Immunotherapy by Oncolytic Vesicular Stomatitis Virus (2009)

Oncolytic virotherapy can be achieved in two ways: (1) by exploiting an innate ability of certain viruses to selectively replicate in tumor tissues, and (2) by using viruses to deliver toxic or immunostimulatory genes to tumors. Vesicular stomatitis virus (VSV) selectively replicates in tumors lacking adequate type I interferon response. The efficacy of oncolytic virotherapy using VSV against B16 melanomas in C57BL/6 mice is dependent on CD8(+) T and natural killer cells. Because immunotherapies that prime specific CD8(+) T cells against melanocyte/melanoma antigens can generate significant therapeutic responses, we hypothesized that engineering VSV to express the potent T cell costimulatory molecule CD40 ligand (VSV-CD40L) would enhance virotherapy with concomitant priming of melanoma-specific T cells. However, we observed no difference in antitumor efficacy between the parental VSV-GFP and VSV-CD40L. In contrast, intratumoral injection of a replication-defective adenovirus expressing CD40L (Ad-CD40L) consistently produced significantly greater therapy than either replication-competent VSV-GFP or VSV-CD40L. The Ad-CD40L-mediated tumor regressions were associated with specific T cell responses against tumor-associated antigens (TAAs), which took several days to develop, whereas VSV-CD40L rapidly induced high levels of T cell activation without specificity for TAAs. These data suggest that the high levels of VSV-associated immunogenicity distracted immune responses away from priming of tumor-specific T cells, even in the presence of potent costimulatory signals. In contrast, a replication-defective Ad-CD40L allowed significant priming of T cells directed against TAAs. These observations suggest that an efficiently primed antitumor T cell response can produce similar, if not better, therapy against an established melanoma compared with intratumoral injection of a replication-competent oncolytic virus.
Role of Nanochemical Environments in Porous TiO2 in Photocurrent Efficiency and Degradation in Dye Sensitized Solar Cells (2005)

Elongated dye sensitized solar cells with a thickness gradient of the nanoporous TiO2 front electrode were used to assess the impact of the layer thickness on photocurrent and degradation. The photocurrent efficiency passes through a maximum (in our case at about 12 microm). Interestingly, the degradation rate also strongly depends on the layer thickness and is about 3 times faster for a 15-microm cell (in comparison with a 1-microm cell). To explain these nonanticipated results, a model to describe the I3(-)/I- concentration within a typical dye sensitized solar cell under steady-state conditions was derived. It includes the nanoporous TiO2 layer and a bulk solution with their different mobilities for the electrolyte species. Using typical parameters from the literature, it turned out that, despite the fact that the initial I- concentration is about 1 order of magnitude larger and the assumed diffusion coefficient is 1.3 times higher, the depletion of the I- concentration at the TiO2/FTO front contact happens to be in the same range as the depletion of the I3(-) concentration at the back contact. This stresses the importance of iodide in nanoporous environments for both the maximum attainable photocurrent and its role in the regeneration of the oxidized dye. Enhanced degradation rates might be related to poor iodide supply, since the oxidized state cannot be regenerated efficiently.
Substantially Complete Removal of the 34kDa Allergenic Soybean Protein,Gly mBd 30 K, from Soy Milk of a Mutant Lacking theα- andα′-Subunits of Conglycinin (1996)

Substantially complete removal (99.78%) of the allergenic soybean protein, Gly m Bd 30 K, was attained by applying simple centrifugation at 10,000 x g and at pH 4.5 in the presence of Na2SO4 to defatted soy milk from a genetically mutated soybean cultivar (Tohoku 124) which lacked the alpha- and alpha'-subunits of conglycinin. The removal rate was ten times higher than that (97.44%) from a normal soybean cultivar of I.O.M. grade.
Methyl 12-chlorodehydroabietate (2006)

The structure of the title compound (systematic name: methyl 6-chloro-7-isopropyl-1,4a-dimethyl-1,2,3,4,4a,9,10,10a-octahydro­phenanthrene-1-carboxyl­ate), C21H29ClO2, has been determined by X-ray diffraction and is compared with the structures of methyl 12-acetyl­dehydro­abietate and methyl dehydro­abietate.