gebhart/patrepeval huggingface dataset:
Assembly factors as a new class of disease genes for mitochondrial complex I deficiency: cause, pathology and treatment options (2011)

Complex I deficiency is the most frequent cause of oxidative phosphorylation disorders. The disease features a large diversity of clinical symptoms often leading to progressive encephalomyopathies with a fatal outcome. There is currently no cure, and although disease-causing mutations have been found in the genes encoding complex I subunits, half of the cases remain unexplained. However, in the past 5 years a new class of complex I disease genes has emerged with the finding of specific assembly factors. So far nine such genes have been described and it is believed that in the near future more will be found. In this review, we will address whether the functions of these chaperones point towards a general molecular mechanism of disease and whether this enables us to design a treatment for complex I deficiency.
No Evidence for Mouse Pancreatic β-Cell Epithelial-Mesenchymal Transition In Vitro (2007)

We used cre/loxP-based genetic lineage tracing analysis to test a previously proposed hypothesis that in vitro cultured adult pancreatic beta-cells undergo epithelial-mesenchymal transition (EMT) to generate a highly proliferative, differentiation-competent population of mesenchymal islet "progenitor" cells. Our results in the mouse that are likely to be directly relevant to the human system show that adult mouse beta-cells do not undergo EMT in vitro and that the mesenchymal cells that arise in cultures of adult pancreas are not derived from beta-cells. We argue that these cells most likely originate from expansion of mesenchymal cells integral to the heterogeneous pancreatic islet preparations. As such, these mesenchymal "progenitors" might not represent the best possible source for generation of physiologically competent beta-cells for treatment of diabetes.
Determination of hepatitis C virus genotypes in the United States by cleavase fragment length polymorphism analysis (1997)

We describe the application of a new DNA-scanning method, which has been termed Cleavase Fragment Length Polymorphism (CFLP; Third Wave Technologies, Inc., Madison, Wis.), for the determination of the genotype of hepatitis C virus (HCV). CFLP analysis results in the generation of structural fingerprints that allow discrimination of different DNA sequences. We analyzed 251-bp cDNA products generated by reverse transcription-PCR of the well-conserved 5'-noncoding region of HCV. We determined the genotypes of 87 samples by DNA sequencing and found isolates representing 98% of the types typically encountered in the United States, i.e., types 1a, 1b, 2a/c, 2b, 3a, and 4. Blinded CFLP analysis of these samples was 100% concordant with DNA sequencing results, such that closely related genotypes yielded patterns with strong familial resemblance whereas more divergent sequences yielded patterns with pronounced dissimilarities. In each case, the aggregate pattern was indicative of genotypic grouping, while finer changes suggested subgenotypic differences. We also assessed the reproducibility of CFLP analysis in HCV genotyping by analyzing three distinct isolates belonging to a single subtype. These three isolates yielded indistinguishable CFLP patterns, as did replicate analysis of a single isolate. This study demonstrates the suitability of this technology for HCV genotyping and suggests that it may provide a low-cost, high-throughput alternative to DNA sequencing or other, more costly or cumbersome genotyping approaches.
Numerical Simulation of the Impact of Flow-Induced Geomechanical Response on the Productivity of Stress-Sensitive Reservoirs (1999)

Abstract Fluid production from oil/gas reservoirs perturbs the local stress state, both through variations in pore pressure and also changes in the local total stress. In stress sensitive reservoirs, these changes in the stress state cause deformation in the solid part of the rock which, in turn, affects the fluid-flow properties and, consequently, the reservoir productivity. Different reservoir conditions and production scenarios yield different degrees of reservoir productivity reduction. Therefore, a model that can be applied to study the effect of fluid flow/ deformation processes on the productivity of stress-sensitive reservoirs is essential for optimum reservoir management. This paper presents a 3D finite difference, fully implicit model to simulate the physical phenomena occurring during the production from reservoirs with stress-sensitive mechanical and fluid-flow properties. The model considers two different physical domains: (i) an inner porous domain representing the reservoir, where fluid-flow and rock deformation occurs, and (ii) a surrounding domain representing the extended stress-disturbed region caused by the reservoir depletion. The inclusion of the surrounding domain leads to a more realistic modeling of the actual reservoir geomechanical boundary conditions. The reservoir is treated as a poro-elastic system consisting of a deforming solid skeleton and a moving compressible fluid. Nonlinear elastic deformation is assumed for both domains. The model has been applied to illustrate the effect that rock deformation has on reservoir productivity. Results show that for stress-sensitive reservoirs, calculated flow rates obtained from conventional fluid-flow models can be significantly different from flow rates calculated from coupled fluid-flow/geomechanics models. Also, production rates calculated from fully coupled, single-domain models may differ from flow rates calculated from fully coupled, two-domain models.
Observation on development of haemocytes in Boleophthalmus pectinirostris (2001)

The blood, kidney and spleen of Boleophthalmeus pectinirostris were observed on stained smears. The results show that the development of B .pectinirostris haemocytes experiences 3 periods, which are primitive stage, immature stage and mature stage.The mother haemoblasts complete a process of maturation when flowing from the he matopoietic organs into the peripheral blood vessels.The morphological characters of the crythrocyte, neutrophil, lymphocyte and monocyte of B .pectinirostris are described at different development Stages.
Experimental Reproduction of Postweaning Multisystemic Wasting Syndrome in Pigs by Dual Infection with Mycoplasma hyopneumoniae and Porcine Circovirus Type 2 (2004)

The objectives of this study were to investigate the interactions between Mycoplasma hyopneumoniae and porcine circovirus type 2 (PCV2) and to establish a model for studying the pathogenesis of and testing intervention strategies for the control of PCV2-associated porcine respiratory disease complex (PRDC). Sixty-seven pigs were randomly assigned to four groups. Group 1 (n=17) pigs served as controls, group 2 (n=17) pigs were inoculated with M. hyopneumoniae, group 3 (n=17) pigs were dual infected with M. hyopneumoniae and PCV2, and group 4 (n=16) pigs were inoculated with PCV2. Pigs were inoculated intratracheally with M. hyopneumoniae at 4 weeks of age followed by intranasal inoculation with PCV2 at 6 weeks of age. Dual-infected pigs had moderate dyspnea, lethargy, and reduced weight gain. The overall severity of macroscopic lung lesions, PCV2-associated microscopic lesions in lung and lymphoid tissues, and the amount of PCV2-antigen associated with these lesions were significantly (P <0.05) higher in dual-infected pigs compared with all other groups. Four of 17 (23.5%) dual-infected pigs had decreased growth rate and severe lymphoid depletion and granulomatous lymphadenitis associated with high amounts of PCV2-antigen consistent with postweaning multisystemic wasting syndrome (PMWS). PCV2-antigen in lung tissue was most often associated with M. hyopneumoniae-induced peribronchial lymphoid hyperplasia, suggesting that this is an important site for PCV2 replication in the lung. This study indicates that M. hyopneumoniae potentiates the severity of PCV2-associated lung and lymphoid lesions, increases the amount and prolongs the presence of PCV2-antigen, and increases the incidence of PMWS in pigs.
Myelin basic protein and creatine kinase BB isoenzyme as CSF markers of intracranial tumors and stroke (1986)

ABSTRACT In patients with intracranial tumors (ICT) and acute cerebral infarctions (CI), both necrosis and reversible changes occur in central nervous system (CNS) tissue. The damaged CNS cells release specific substances into the cerebrospinal fluid (CFS). Radioimmunoassay (RIA)-determined myelin basic protein (MBP) and RIA-determined creatin kinase BB (CK-BB) are markers of damage to CNS specific structures. The elevated CSF level of MBP is considered a marker of myelin damage and the increased concentration of CSF CK-BB may be of combined neuronal and astrocytic origin. CSF was collected from 57 patients with the diagnosis of CI (n =30) and ICT (n =27) and the concentration of MBP and CK-BB were measured by RIA. Our study shows increased CSF levels of MBP and CK-BB in patients with CI and patients with ICT. We have also found a linear correlation between MBP and CK-BB in both CI and ICT, and for a given CK-BB level, MBP was significantly higher in patients with ICT than in patients with CI. These facts suggest that lesion markers behave differently in the different pathologic processes affecting the CNS.
133 Remodelling the oligosaccharide of human IgG antibodies: effects on biological activities (1997)

Conference Article| November 01 1997 133 Remodelling the oligosaccharide of human IgG antibodies: effects on biological activities SHAHLA ABADEH; SHAHLA ABADEH 1Department of Immunology, The University of Birmingham, B15 2TT, UK Search for other works by this author on: This Site PubMed Google Scholar STEPHEN CHURCH; STEPHEN CHURCH 1Department of Immunology, The University of Birmingham, B15 2TT, UK Search for other works by this author on: This Site PubMed Google Scholar SUCAI DONG; SUCAI DONG 1Department of Immunology, The University of Birmingham, B15 2TT, UK Search for other works by this author on: This Site PubMed Google Scholar JOHN LUND; JOHN LUND 1Department of Immunology, The University of Birmingham, B15 2TT, UK Search for other works by this author on: This Site PubMed Google Scholar MARGARET GOODALL; MARGARET GOODALL 1Department of Immunology, The University of Birmingham, B15 2TT, UK Search for other works by this author on: This Site PubMed Google Scholar ROY JEFFERIS ROY JEFFERIS 1Department of Immunology, The University of Birmingham, B15 2TT, UK Search for other works by this author on: This Site PubMed Google Scholar Biochem Soc Trans (1997) 25 (4): S661. https://doi.org/10.1042/bst025s661 Views Icon Views Article contents Figures & tables Video Audio Supplementary Data Peer Review Share Icon Share Facebook Twitter LinkedIn Email Cite Icon Cite Get Permissions Citation SHAHLA ABADEH, STEPHEN CHURCH, SUCAI DONG, JOHN LUND, MARGARET GOODALL, ROY JEFFERIS; 133 Remodelling the oligosaccharide of human IgG antibodies: effects on biological activities. Biochem Soc Trans 1 November 1997; 25 (4): S661. doi: https://doi.org/10.1042/bst025s661 Download citation file: Ris (Zotero) Reference Manager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex toolbar search Search Dropdown Menu toolbar search search input Search input auto suggest filter your search All ContentAll JournalsBiochemical Society Transactions Search Advanced Search This content is only available as a PDF. © 1997 Biochemical Society1997 Article PDF first page preview Close Modal You do not currently have access to this content.
Inherited Genetic Variants Associated with Occurrence of Multiple Primary Melanoma (2015)

Recent studies, including genome-wide association studies, have identified several putative low-penetrance susceptibility loci for melanoma. We sought to determine their generalizability to genetic predisposition for multiple primary melanoma in the international population-based Genes, Environment, and Melanoma (GEM) Study. GEM is a case-control study of 1,206 incident cases of multiple primary melanoma and 2,469 incident first primary melanoma participants as the control group. We investigated the odds of developing multiple primary melanoma for 47 SNPs from 21 distinct genetic regions previously reported to be associated with melanoma. ORs and 95% confidence intervals were determined using logistic regression models adjusted for baseline features (age, sex, age by sex interaction, and study center). We investigated univariable models and built multivariable models to assess independent effects of SNPs. Eleven SNPs in 6 gene neighborhoods (TERT/CLPTM1L, TYRP1, MTAP, TYR, NCOA6, and MX2) and a PARP1 haplotype were associated with multiple primary melanoma. In a multivariable model that included only the most statistically significant findings from univariable modeling and adjusted for pigmentary phenotype, back nevi, and baseline features, we found TERT/CLPTM1L rs401681 (P = 0.004), TYRP1 rs2733832 (P = 0.006), MTAP rs1335510 (P = 0.0005), TYR rs10830253 (P = 0.003), and MX2 rs45430 (P = 0.008) to be significantly associated with multiple primary melanoma, while NCOA6 rs4911442 approached significance (P = 0.06). The GEM Study provides additional evidence for the relevance of these genetic regions to melanoma risk and estimates the magnitude of the observed genetic effect on development of subsequent primary melanoma.
Protective effect of liposome encapsulation on paclitaxel developmental toxicity in the rat (1997)

Paclitaxel is an anticancer drug that has demonstrated severe embryotoxicity in chicks. This embryotoxicity is reduced by liposome encapsulation of the drug. The current study was designed to evaluate the potential of liposome encapsulation for reducing paclitaxel embryotoxicity in rats. Wistar rats were treated with paclitaxel on day 8 of pregnancy (plug = day 0) at doses of 0.67, 2.0, or 10.0 mg/kg intravenously. The same doses of paclitaxel encapsulated in liposomes were administered intravenously to other groups of animals. Control animals were given blank liposomes. Free paclitaxel produced maternal and embryotoxicity at 10.0 mg/kg with three of seven dams dying and resorption of all embryos in surviving dams. Liposome encapsulation at 10.0 mg/kg was not associated with maternal death and there were live fetuses on evaluation at term, although litter size was reduced and malformations occurred in surviving fetuses. At 2.0 mg/kg free paclitaxel, fetal weight was decreased and resorptions increased. Liposome encapsulation at 2.0 mg/kg produced litter results similar to those obtained in control animals given empty liposomes. Malformations were prominent at 2.0 mg/kg free paclitaxel and at 10.0 mg/kg paclitaxel in liposomes and included exencephaly/anencephaly, ventral wall defects, facial clefts, anophthalmia, diaphragmatic hernia, and defects of the kidney, cardiovascular system, and tail. Liposome encapsulation appeared to shift the developmental response to paclitaxel such that 10 mg/kg encapsulated drug produced effects similar to 2.0 mg/kg free drug. These results may have implications for drug delivery of therapeutic agents used during human pregnancy.
Catheter modification of the atrioventricular junction with radiofrequency energy for control of atrioventricular nodal reentry tachycardia. (1991)

Radiofrequency ablation of the perinodal right atrium appears to be safe and effective for treatment of typical AVNRT:
Significance analysis of functional categories in gene expression studies: a structured permutation approach (2005)

http://www.bios.unc.edu/~fwright/SAFE.
In vitro selection and affinity maturation of antibodies from a naive combinatorial immunoglobulin library. (1992)

We have used a combinatorial immunoglobulin library approach to obtain monoclonal antibodies from nonimmune adult mice, thereby establishing the principles of (i) accessing naive combinatorial antibody libraries for predetermined specificities and (ii) increasing the affinity of the selected antibody binding sites by random mutagenesis. A combinatorial Fab library expressing immunoglobulin mu and kappa light-chain fragments on the surface of filamentous phage was prepared from bone marrow of nonimmunized, adult BALB/c mice with the multivalent display vector pComb8. Phage displaying low affinity Fabs (binding constants, 10(4)-10(5) M-1) binding to a progesterone-bovine serum albumin conjugate were isolated from the library. Random mutagenesis of the heavy- and light-chain variable regions expressed in the mono-valent phage display vector pComb3 was performed by error-prone PCR, and subsequently clones with improved affinity for the hapten conjugate were selected. We demonstrate that antibodies with desirable characteristics from a nonimmune source may be selected and affinity maturation may be achieved by using the twin vectors pComb8 and pComb3, thus opening the route to obtaining specific antibodies from a generic library and bypassing immunization.
A new human B-cell non-Hodgkin's lymphoma cell line (Karpas 422) exhibiting both t (14;18) and t(4;11) chromosomal translocations (1990)

Abstract A unique B-cell non-Hodgkin's lymphoma (NHL) cell line (Karpas 422), bearing both t(14;18) and t(4;11) chromosomal translocations as well as several other chromosomal abnormalities, has been established from the pleural effusion of a patient with chemotherapy-resistant NHL. This cell line has the same karyotypic features as malignant cells from the patient. The major cell clone is characterized chromosomally by 46,XX t(2;10)(p23;q22.1), t(4;11)(q21.3; q23.1), t(14;18)(q32.1;q21.3), t(4;16)(q21.3;p13.1). Both phenotypically and genotypically, the cell line has features of a mature B-cell neoplasm with no evidence for commitment to other lineages. Rearrangements of the C-ETS-1 oncogene and N-CAM-1 and CD3 genes that map to 11q23 were not detected by conventional Southern analysis. BCL-2 was rearranged within the major breakpoint cluster. The K422 cell line has a unique karyotype; this is the first occasion that the t(4;11) translocation has been described in a t(14;18) lymphoma. The cell line will be of value in determining the molecular nature of the t(4;11) translocation.
Hierarchical scheduling of DSP programs onto multiprocessors for maximum throughput (2003)

A multiprocessor scheduling algorithm that simultaneously considers pipelining, retiming, parallel execution and hierarchical node decomposition to maximize performance throughput is presented. The algorithm is able to take into account interprocessor communication delays, and memory and processor availability constraints. The results on a set of benchmarks demonstrate the algorithm's ability to achieve near optimal speedups across a wide range of applications of various types of concurrency, with good scalability with respect to processor count.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Inhibitors of arachidonoyl ethanolamide hydrolysis. (1994)

Arachidonoyl ethanolamide (anandamide) is a naturally occurring brain constituent that binds to a specific brain cannabinoid receptor (CBR1). An amidase activity (anandamide amidase) in membrane fractions of brain and in cultured neuroblastoma cells rapidly degrades anandamide to arachidonic acid (Deutsch, D. G., and Chin, S. (1993) Biochem. Pharmacol. 46, 791-796). In the current study, analogs of anandamide representing three classes of putative transition-state inhibitor (trifluoromethyl ketones, alpha-keto esters, and alpha-keto amides) were synthesized and tested as inhibitors of anandamide hydrolysis in vitro and as ligands for CBR1. The trifluoromethyl ketones and alpha-keto esters showed nearly 100% inhibition of anandamide hydrolysis in vitro at 7.5 microM inhibitor and 27.7 microM anandamide. Arachidonyl trifluoromethyl ketone was the only synthetic compound in the series of fatty acid derivatives able to displace [3H]CP-55940 binding to CBR1 with a Ki of 0.65 microM. It was also the most effective inhibitor in intact neuroblastoma cells, leading to a 12-fold increase of cellular anandamide levels at 12 microM. From the action of these inhibitors on this hydrolytic enzyme, it seems likely that anandamide is cleaved by a mechanism that involves an active-site serine hydroxyl group. These inhibitors may serve as useful tools to elucidate the role anandamide plays in vivo.
Comparative Serum Glycoproteomics Using Lectin Selected Sialic Acid Glycoproteins with Mass Spectrometric Analysis:  Application to Pancreatic Cancer Serum (2006)

A strategy is developed in this study for identifying sialylated glycoprotein markers in human cancer serum. This method consists of three steps: lectin affinity selection, a liquid separation and characterization of the glycoprotein markers using mass spectrometry. In this work, we use three different lectins (Wheat Germ Agglutinin, (WGA) Elderberry lectin,(SNA), Maackia amurensis lectin, (MAL)) to extract sialylated glycoproteins from normal and cancer serum. Twelve highly abundant proteins are depleted from the serum using an IgY-12 antibody column. The use of the different lectin columns allows one to monitor the distribution of alpha(2,3) and alpha(2,6) linkage type sialylation in cancer serum vs that in normal samples. Extracted glycoproteins are fractionated using NPS-RP-HPLC followed by SDS-PAGE. Target glycoproteins are characterized further using mass spectrometry to elucidate the carbohydrate structure and glycosylation site. We applied this approach to the analysis of sialylated glycoproteins in pancreatic cancer serum. Approximately 130 sialylated glycoproteins are identified using microLC-MS/MS. Sialylated plasma protease C1 inhibitor is identified to be down-regulated in cancer serum. Changes in glycosylation sites in cancer serum are also observed by glycopeptide mapping using microLC-ESI-TOF-MS where the N83 glycosylation of alpha1-antitrypsin is down regulated. In addition, the glycan structures of the altered proteins are assigned using MALDI-QIT-MS. This strategy offers the ability to quantitatively analyze changes in glycoprotein abundance and detect the extent of glycosylation alteration as well as the carbohydrate structure that correlate with cancer.
Quantum accuracy threshold for concatenated distance-3 codes (2005)

We prove a new version of the quantum threshold theorem that applies to concatenation of a quantum code that corrects only one error, and we use this theorem to derive a rigorous lower bound on the quantum accuracy threshold epsilon_0. Our proof also applies to concatenation of higher-distance codes, and to noise models that allow faults to be correlated in space and in time. The proof uses new criteria for assessing the accuracy of fault-tolerant circuits, which are particularly conducive to the inductive analysis of recursive simulations. Our lower bound on the threshold, epsilon_0 &gt; 2.73 \times 10^{-5} for an adversarial independent stochastic noise model, is derived from a computer-assisted combinatorial analysis; it is the best lower bound that has been rigorously proven so far.
Soy Protein Based Biodegradable Flexible Polyurethane Foam (2010)

Soy protein based biodegradable polyurethane (PU) foams were prepared by incorporating soy protein isolate (SPI) into flexible PU foam. The effects SPI content and isocyanate index on the density, resilience, compression set, and biodegradability of the soy protein based PU foams were investigated. The results showed that, soy protein enhanced the compression set, resilience, and biodegradability of PU foams, but increased the density. Furthermore, soy protein can increase open cell proportion in the soy protein based flexible PU foams, and then regulate their properties. The density and compression set value of the soy protein based PU foams decreased with increase in isocyanate index, while the resilience increased. The biodegradability of soy protein based flexible PU foam makes it a prospective material for disposable usage.