gebhart/patrepeval huggingface dataset:
Association between COX-2 polymorphisms and non-small cell lung cancer susceptibility. (2015)

Aim: To explore the association between COX-2 polymorphisms and non-small cell lung cancer (NSCLC) susceptibility. Methods: We collected fasting peripheral venous blood from 60 cases with NSCLC and 62 healthy controls through physical examinations, and applied PCR-RFLP to analyze COX-2 polymorphisms of two groups. Results: With respect to detecting COX-2 rs689466 and rs5275 polymorphisms, the distribution frequency of mutant genotype AA of COX-2 rs689466 in case group was higher than that in control group, which possessed significant difference between two groups (P < 0.05). Carriers with AA genotype were 4.05 times at risk of NSCLC than those with GG genotype (P = 0.04, OR=4.05, 95% CI = 1.14-14.43). The distribution of mutant genotype CC of COX-2 rs5275 was different between two groups, and carriers with genotype CC were at 5.70 times higher risk of NSCLC than those with genotype TT. After corrected by sex, gender, smoking and drinking factors, AA genotype of COX-2 rs689466 and CC genotype of COX-2 rs5275 still contributed to increased risk of NSCLC (OR=4.22, 95% CI=1.10-16.17, OR=6.95, 95% CI=1.27-38.11). After analyzed of linkage disequilibrium (LD) and haplotypes of alleles in two SNPs, the distribution frequency of A-C haplotype in case group was higher than that in control group, with significant difference between two groups (P < 0.05). After corrected by sex, gender, smoking and drinking factors, statistical difference was still found in the total distribution of A-C haplotype between two groups (P = 0.03, OR=6.11, 95% CI=1.16-32.2). Conclusions: COX-2 rs689466 and rs5275 polymorphisms may be related to NSCLC susceptibility. And A-C haplotype might be a susceptibility haplotype for NSCLC.
Proxy compilation of dynamically loaded Java classes with MoJo (2002)

Interest in Java implementations for resource-constrained environments such as embedded systems has been tempered by concerns regarding its efficiency. Current native compilers for Java offer dramatic increases in efficiency, but have poor support for dynamically-loaded classes, which are typically served by slow interpreters or JIT compilers, the code-size of this latter utterly mismatching the resource constraints of the system.After a brief survey of Ahead-of-Time compilers for Java, we present MoJo --- a new native compiler and the testbed for our proxy compilation scheme, which allows embedded clients to connect to servers and delegate compilation of Java class packages to native code libraries.We also present initial results from experimental testing using MoJo in a resource-constrained, mobile computing environment. We show that MoJo is faster than all surveyed Java implementations for the test platform executing our initial test application. Our proxy compilation scheme results in a 94% speed increase over the fastest tested interpreter system and a 20% speed increase over the fastest tested JIT system.The MoJo-generated binaries for the application are also shown to be 45 times smaller than those required by its nearest iPAQ JRE competitor and 275 times smaller than the Sun JRE v1.3.1 for iPAQ as a direct result of our incremental, on-demand transfer of API classes to the client.
Mouse models of chronic lung infection with Pseudomonas Aeruginosa: Models for the study of cystic fibrosis (2000)

The discovery of the CFTR gene in 1989 has lead to rapid progress in understanding the molecular basis of cystic fibrosis (CF) and the biological properties of the cystic fibrosis transmembrane conductance regulator (CFTR) protein. However, more than 10 years later, recurrent lung infections with Pseudomonas aeruginosa, which lead to chronic lung disease and eventual respiratory failure, remain the major cause of morbidity and mortality among CF patients. A distinguishing feature of lung disease in CF is an exaggerated and persistent inflammatory response, characterized by the accumulation of excessive numbers of neutrophils and dysregulated cytokine production. The events leading to the establishment of lung infection with P. aeruginosa, especially the inflammatory and immunological events, and the relation between the CF defect and infection, remain largely undefined. Progress in this area has been hampered by the lack of a suitable animal model. An exciting achievement in the past few years has been the development of a number of variants of CFTR-deficient mice which exhibit defective cAMP-mediated Cl− conductance and have a range of clinical phenotypes from mild to severe. In parallel, a model of chronic P. aeruginosa lung infection has been established in genetically and immunologically well-defined inbred mouse strains which differ in susceptibility to this infection in the lung. BALB/c mice are resistant, while DBA/2 mice are extremely susceptible, with high mortality within 3 days of infection. C57BL/6 and A/J mice are relatively susceptible and experience low mortality. Furthermore, the bacterial load correlates with the magnitude and quality of the inflammatory response in the infected lungs of BALB/c and C57BL/6 mice. Although results of infection studies in CFTR-deficient mice have been variable, C57BL/6-Cftrm1UNC/Cftrm1UNC knockout mice compared to littermate control mice are highly susceptible to chronic P. aeruginosa infection in the lung. The availability of CFTR knockout mice and non-CF inbred mice differing in susceptibility to chronic P. aeruginosa infection offers useful tools for progress in understanding the genesis of chronic P. aeruginosa infection and the ensuing inflammation in the CF lung, as well as the relation between the CF defect and infection. Information generated from these studies will provide the rationale for the development of novel immunomodulatory measures capable of ameliorating or modulating the chronic inflammation associated with CF lung disease. Pediatr Pulmonol. 2000;30:413–424. © 2000 Wiley-Liss, Inc.
The human alpha 1(XV) collagen chain contains a large amino-terminal non-triple helical domain with a tandem repeat structure and homology to alpha 1(XVIII) collagen. (1994)

We have cloned and characterized cDNAs encoding the alpha 1 chain of type XV collagen from a human placenta library. Using primer extension cloning we extended the cDNAs to the 5' end of the mRNA and determined the complete deduced primary structure of the human alpha 1(XV) chain. The polypeptide chain contains nine triple helical domains separated by eight non-triple helical regions and flanked by large amino-terminal (555 amino acid residues) and carboxyl-terminal (256 amino acid residues) non-triple helical domains. Comparison of amino acid sequences of the human alpha 1(XV) chain with those of mouse alpha 1(XVIII) collagen showed remarkable similarity within both amino- and carboxyl-terminal non-triple helical domains. Within the carboxyl third of the amino-terminal domain a tandem repeat structure is found with an about 45-amino acid residue sequence repeated four times. This amino acid sequence has a strikingly high similarity to rat cartilage proteoglycan core protein. Northern blot analysis of human embryonic RNA revealed that alpha 1(XV) mRNA is expressed predominantly in internal organs such as the adrenal gland, kidney, and pancreas.
Zoledronic acid treatment impairs protein geranyl-geranylation for biological effects in prostatic cells (2006)

Although zoledronic acid is currently the most efficient bisphosphonate in metastatic prostate cancer management, its mechanism of action in prostatic cells remains unclear. We suggest in this work that although in first intention ZOL inhibits FPPsynthase its main biological actitivity is directed against protein Geranylgeranylation.
Glutamic Acid Decarboxylase Injection Into Lymph Nodes: Beta Cell Function and Immune Responses in Recent Onset Type 1 Diabetes Patients (2020)

clinicaltrials.gov, identifier NCT02352974.
Efficient in vivo manipulation of mouse genomic sequences at the zygote stage. (1996)

We describe a transgenic mouse line carrying the cre transgene under the control of the adenovirus EIIa promoter that targets expression of the Cre recombinase to the early mouse embryo. To assess the ability of this recombinase to excise loxP-flanked DNA sequences at early stages of development, we bred EIIa-cre transgenic mice to two different mouse lines carrying loxP-flanked target sequences: (i) a strain with a single gene-targeted neomycin resistance gene flanked by 1oxP sites and (ii) a transgenic line carrying multiple transgene copies with internal loxP sites. Mating either of these loxP-carrying mouse lines to EIIa-cre mice resulted in first generation progeny in which the loxP-flanked sequences had been efficiently deleted from all tissues tested, including the germ cells. Interbreeding of these first generation progeny resulted in efficient germ-line transmission of the deletion to subsequent generations. These results demonstrate a method by which loxP-flanked DNA sequences can be efficiently deleted in the early mouse embryo. Potential applications of this approach are discussed, including reduction of multicopy transgene loci to produce single-copy transgenic lines and introduction of a variety of subtle mutations into the line.
ISP: Using idle SMs in hardware-based prefetching (2013)

The Graphics Processing Unit (GPU) is the most promising candidate platform for faster rate of improvement in peak processing speed, low latency and high performance. The highly programmable and multithreaded nature of GPUs makes them a remarkable candidate for general purpose computing. However, supporting non-graphics computing on graphics processors requires addressing several architecture challenges. In this paper, we focus on improving performance by better hiding long waiting time to transfer data from the slow global memory. Thereupon study an effective light-overhead prefetching mechanism, which utilizes idle processing elements. Our results show that we can potentially improve Instruction per Cycle (IPC) up to 8%.
Successful Embolization of Persistent Endoleak from a Patent Inferior Mesenteric Artery (1997)

Purpose: To report the successful endovascular occlusion of a persistent endoleak owing to collateral perfusion in a 1-year-old bifurcated aortic endograft. Methods and Results: An 81-year-old man underwent endovascular repair of a 5.5-cm abdominal aortic aneurysm (AAA) with a bifurcated stent-graft in 1995; collateral perfusion of the excluded aneurysm by retrograde filling of the patent inferior mesenteric artery (IMA) was noted postoperatively. At his 1-year follow-up, the mid-sac endoleak persisted on contrast-enhanced computed tomography. Using the superior mesenteric artery for access, the stump of the IMA was successfully embolized with glue. Conclusions: This case, which highlights the importance of documenting a patent IMA prior to AAA endografting, illustrates one option for the management of persistent collateral perfusion of endovascularly excluded aneurysms.
LIV-1 enhances the aggressive phenotype through the induction of epithelial to mesenchymal transition in human pancreatic carcinoma cells (2009)

LIV-1 is a downstream target of STAT3 and is essential for the nuclear localization of Snail, a master regulator of epithelial to mesenchymal transition (EMT). Little is known about the association of LIV-1 with pancreatic carcinoma development, therefore, expression of LIV-1 mRNA was analyzed by real-time reverse transcriptase polymerase chain reaction (RT-PCR) in 9 cultured cell lines (8 carcinoma and 1 normal duct cell lines) and 24 pancreatic tissues (12 carcinoma and 12 normal tissues). Localization of this gene product was investigated by immunohistochemistry in 72 pancreatic carcinoma and the relation between its expression and clinicopathological findings was examined. To assess the function of LIV-1 in pancreatic carcinoma cells, stable siRNA expressing Panc-1 cells were generated. Higher expression of LIV-1 mRNA was found in both pancreatic carcinoma cell lines and pancreatic carcinoma tissues compared to normal duct cell line and histologically normal tissues, respectively. Immunohistochemical analysis revealed that LIV-1 expression was frequently found in 76.4% of pancreatic carcinoma tissues and its expression level was associated with tumor size and lymphatic infiltration. Down-regulated LIV-1 cells showed significant inhibition of anchorage-dependent or -independent proliferation and cell motility in vitro and reduction of tumor growth and metastasis in vivo. Furthermore, nuclear expression of Snail was decreased and E-cadherin expression was restored in LIV-1 siRNA expressing pancreatic carcinoma cells. These findings indicate that LIV-1 may be involved in acquisition of the aggressive phenotype of human pancreatic carcinoma cells through the induction of epithelial to mesenchymal transition.
THE SPECTROPHOTOMETRIC DETERMINATION OF AMINE, AMINO ACID AND PEPTIDE WITH 2,4,6- TRINITROBENZENE 1-SULFONIC ACID* (1960)

Journal Article THE SPECTROPHOTOMETRIC DETERMINATION OF AMINE, AMINO ACID AND PEPTIDE WITH 2,4,6- TRINITROBENZENE 1-SULFONIC ACID Get access KAZUO SATAKE, KAZUO SATAKE Faculty of Science From the Department of Chemistry, Tokyo Metropolitan UniversityTokyo Search for other works by this author on: Oxford Academic PubMed Google Scholar TSUNEO OKUYAMA, TSUNEO OKUYAMA Faculty of Science From the Department of Chemistry, Tokyo Metropolitan UniversityTokyo Search for other works by this author on: Oxford Academic PubMed Google Scholar MOCHIHIKO OHASHI, MOCHIHIKO OHASHI Faculty of Science From the Department of Chemistry, Tokyo Metropolitan UniversityTokyo Search for other works by this author on: Oxford Academic PubMed Google Scholar TOMOTAKA SHINODA TOMOTAKA SHINODA Faculty of Science From the Department of Chemistry, Tokyo Metropolitan UniversityTokyo Search for other works by this author on: Oxford Academic PubMed Google Scholar The Journal of Biochemistry, Volume 47, Issue 5, 25 May 1960, Pages 654–660, https://doi.org/10.1093/oxfordjournals.jbchem.a127107 Published: 25 May 1960 Article history Received: 16 November 1959 Published: 25 May 1960
Insulin-like Growth Factor I and Its Binding Proteins:  A Study of the Binding Interface Using B-Domain Analogues (1999)

The biological activity of the insulin-like growth factors (IGF-I and IGF-II) is regulated by six IGF binding proteins (IGFBPs 1-6). To examine the surface of IGF-I that associates with the IGFBPs, we created a series of six IGF-I analogues, [His(4)]-, [Gln(9)]-, [Lys(9)]-, [Ser(16)]-, [Gln(9),Ser(16)]-, and [Lys(9),Ser(16)]IGF-I, that contained substitutions for residues Thr(4), Glu(9), or Phe(16). Substitution of Ser for Phe(16) did not affect secondary structure but significantly decreased the affinity for all IGFBPs by between 14-fold and >330-fold, indicating that Phe(16) is functionally important for IGFBP association. While His(4) or Gln(9) substitutions had little effect on IGFBP affinity, changing the negative charge of Glu(9) to a positive Lys(9) selectively decreased the affinities of IGFBP-2 and -6 by 140- and 30-fold, respectively. Furthermore, the effects of mutations to both residues 9 and 16 appear to be additive. The analogues are biologically active in rat L6 myoblasts and they retain native structure as assessed by their far-UV circular dichroism (CD) profiles. We propose that Phe(16) and adjacent hydrophobic residues (Leu(5) and Leu(54)) form a functional binding pocket for IGFBP association.
Application of NMR SHAPES Screening to an RNA Target (2003)

Several NMR screening techniques have been developed in recent years to aid in the identification of lead drug compounds. These NMR methods have traditionally been used for protein targets, and here we examine their applicability for an RNA target. We used the SHAPES compound library to test three different NMR screening methodologies: the saturation transfer difference (STD), the 2D trNOESY, and the WaterLOGSY experiments. We found that the WaterLOGSY experiment was the most sensitive method for our RNA target, the P4P6 domain of the Tetrahymena thermophila Group I intron. Using the WaterLOGSY experiment, we found that 23 of the 112 SHAPES compounds interact with P4P6. To identify which of these 23 hits bind through nonspecific interactions, we counterscreened with a linear duplex RNA control and identified one of the SHAPES compounds as interacting with P4P6 specifically. We thus demonstrated that the WaterLOGSY experiment in combination with the SHAPES compound library can be used to efficiently find RNA binding lead compounds.
Synthesis of Primary Amines:  First Homogeneously Catalyzed Reductive Amination with Ammonia (2002)

The synthesis of primary amines via reductive amination of the corresponding carbonyl compounds with aqueous ammonia is achieved for the first time with soluble transition metal complexes. Up to an 86% yield and a 97% selectivity for benzylamines were obtained in the case of various benzaldehydes by using a Rh-catalyst together with water-soluble phosphine and ammonium acetate. In the case of aliphatic aldehydes, a bimetallic catalyst based on Rh/Ir gave improved results.
Metabolic engineering of Escherichia coli for improved 6-deoxyerythronolide B production (2003)

Escherichia coli is an attractive candidate as a host for polyketide production and has been engineered to produce the erythromycin precursor polyketide 6-deoxyerythronolide B (6dEB). In order to identify and optimize parameters that affect polyketide production in engineered E. coli, we first investigated the supply of the extender unit ( 2S)-methylmalonyl-CoA via three independent pathways. Expression of the Streptomyces coelicolor malonyl/methylmalonyl-CoA ligase ( matB) pathway in E. coli together with methylmalonate feeding resulted in the accumulation of intracellular methylmalonyl-CoA to as much as 90% of the acyl-CoA pool. Surprisingly, the methylmalonyl-CoA generated from the matB pathway was not converted into 6dEB. In strains expressing either the S. coelicolor propionyl-CoA carboxylase (PCC) pathway or the Propionibacteria shermanii methylmalonyl-CoA mutase/epimerase pathway, methylmalonyl-CoA accumulated up to 30% of the total acyl-CoA pools, and 6dEB was produced; titers were fivefold higher when strains contained the PCC pathway rather than the mutase pathway. When the PCC and mutase pathways were expressed simultaneously, the PCC pathway predominated, as indicated by greater flux of (13)C-propionate into 6dEB through the PCC pathway. To further optimize the E. coli production strain, we improved 6dEB titers by integrating the PCC and mutase pathways into the E. coli chromosome and by expressing the 6-deoxyerythronolide B synthase (DEBS) genes from a stable plasmid system.
New modulated structure in a Pb-doped Bi-Ca-Sr-Cu-O superconductor (1988)

A new modulated structure has been observed in a Pb-doped Bi-Ca-Sr-Cu-O superconductor (Tc,0=105 K) in addition to the incommensurate modulated structure reported by several researchers. This new modulation occurs in the b* direction and shows up as satellite spots to each of the original diffracted spots. Upon cooling to 88 K the diffraction spots due to the original modulation disappear, while the spots due to the new modulation remain. In the case of the undoped samples, the modulation does not disappear upon cooling to 30 K, which is below the Tc,0 of the sample (∼75 K).
Defective function of the cystic fibrosis-causing missense mutation G551D is recovered by genistein (1999)

The patch-clamp technique was used to investigate the effects of the isoflavone genistein on disease-causing mutations (G551D and DeltaF508) of the cystic fibrosis transmembrane conductance regulator (CFTR). In HeLa cells recombinantly expressing the trafficking-competent G551D-CFTR, the forskolin-stimulated Cl currents were small, and average open probability of G551D-CFTR was P(o) = 0.047 +/- 0.019. Addition of genistein activated Cl currents approximately 10-fold, and the P(o) of G551D-CFTR increased to 0.49 +/- 0.12, which is a P(o) similar to wild-type CFTR. In cystic fibrosis (CF) epithelial cells homozygous for the trafficking-impaired DeltaF508 mutation, forskolin and genistein activated Cl currents only after 4-phenylbutyrate treatment. These data suggested that genistein activated CFTR mutants that were present in the cell membrane. Therefore, we tested the effects of genistein in CF patients with the G551D mutation in nasal potential difference (PD) measurements in vivo. The perfusion of the nasal mucosa of G551D CF patients with isoproterenol had no effect; however, genistein stimulated Cl-dependent nasal PD by, on average, -2.4 +/- 0.6 mV, which corresponds to 16.9% of the responses (to beta-adrenergic stimulation) found in healthy subjects.
Tunable, all-reflective spatial heterodyne spectrometer for broadband spectral line studies in the visible and near-ultraviolet (2009)

A spatial heterodyne spectrometer (SHS) is an interferometric device that combines high resolving power and a large input acceptance angle in a compact format suitable for use at small telescope focal planes and spacecraft for observations of faint, angularly extended emission-line sources. The primary limitation of SHS instruments has come from the spatial sampling of their output interference pattern image, which limits their use to a narrow bandpass. We describe the first-light results from a broadband all-reflective SHS that can be mechanically aligned to any heterodyne wavelength from 300 to 700 nm. Such an instrument can be extremely useful for the near simultaneous study of the brightness and line shapes of major atomic and molecular diagnostic emissions from extended astrophysical targets such as comets or planetary atmospheres. We discuss the results of this validation program and the potential improvements that could be used to expand and/or improve the broadband spectral response of the instrument.
Bacteraemia caused by Anaerotruncus colihominis and emended description of the species (2006)

Although the source of the bacteraemia in the patient cannot be determined, this report suggests that A colihominis is of clinical significance. Spore formation is proposed as an emended description of A colihominis.
An Exploration of the Cantor Set (2010)

This paper is a summary of some interesting properties of the Cantor ternary set and a few investigations of other general Cantor sets. The ternary set is discussed in detail, followed by an explanation of three ways of creating general Cantor sets developed by the author. The focus is on the dimension of these sets, with a detailed explaination of Hausdor ¤ dimension included, and how they act as interesting examples of fractal sets.