gebhart/patrepeval huggingface dataset:
Characterization of Lawsonia intracellularis gen. nov., sp. nov., the Obligately Intracellular Bacterium of Porcine Proliferative Enteropathy (1995)

A novel obligately intracellular bacterium, ileal symbiont intracellularis, which was obtained from the intestines of pigs with proliferative enteropathy disease, was grown in pure cocultures with tissue cultures of rat cells. An examination of the 16S ribosomal DNA gene sequence revealed that the isolates which we obtained are members of the delta subdivision of the Proteobacteria and that the sequences of these organisms exhibit a level of similarly of 91% with the sequence of Desulfovibrio desulfuricans ATCC 27774. These isolates were homogeneous and differed in cellular morphology, acid fastness, phenotype, electrophoretic protein profile, and habitat from Desulfovibrio species. On the basis of the results of an integrated study of the phenotype and genotype of a consistent morphological entity found in particular porcine cells and associated with a well-defined clinical condition, we concluded that these bacteria belong to a previously undescribed genus and species, for which we propose the name Lawsonia intracellularis gen. nov., sp. nov. A species-specific recombinant DNA probe was cloned previously, and this probe was used to identify the bacterium in tissue culture cells and in the ileal epithelia of pigs with proliferative enteropathy disease. Coculture of the organism with a rat enterocyte cell line allowed us to designate strain NCTC 12656 the type strain and to describe the new genus and species. The organism which we cultured is pathogenic for pigs and causes proliferative enteropathy lesions in their ilea and colons, and Koch's postulates were fulfilled for this organism.
Cryosurgical ablation of the A-V node-His bundle: a new method for producing A-V block. (1977)

A cryosurgical instrument was used to ablate atrioventricular conduction. The procedure was carried out in 20 dogs and subsequently in three patients with drug resistant, life-threatening supraventricular tachycardias. In patients, the cryosurgical unit lowered the temperature of the His bundle area to 0 degrees C, effecting complete but reversible heart block. Rewarming resulted in resumption of normal atrioventricular conduction. The His bundle region then was cooled to -60 degrees C; complete heart block was produced with two or more 90-120 second freezes. Postoperative evaluations revealed persistent atrioventricular conduction block. The lesion showed no tendency to rupture, form aneurysm, or interfere with valvular function. In the clinical cases, postoperative studies demonstrated a stable pacemaker arising proximal to the branching portion of the His bundle. A potential application of the cryosurgical technique might be ablation of sites of dysrhythmia (i.e., ectopic foci, re-entry circuits, accessory pathways).
A Modified and Improved Method for Bisulphite Based Cytosine Methylation Analysis (1996)

Sequencing of bisulphite modified genomic DNA is the most powerful method to determine methylation patterns in chromosomal DNA. In many experimental systems, the amount of material available for analysis is very small which makes it necessary to perform experiments at extreme levels of sensitivity and reproducibility. In this communication, we present an improved modification of the bisulphite based sequencing method. Our strategy is to perform the bisulphite treatment and subsequent PCR steps on material embedded into agarose beads. This prevents loss of DNA during the experimental procedure and ensures an optimal bisulphite reactivity by maintaining the DNA in the single stranded form. The modification improves previously published protocols in that it facilitates the handling of probes and reproducibly reaches a very high level of sensitivity.
How useful are non-blocking loads, stream buffers and speculative execution in multiple issue processors? (2002)

We investigate the relative performance impact of non-blocking loads, stream buffers, and speculative execution both used individually and in conjunction with each other. We have simulated the SPEC92 benchmarks on a statically scheduled quad-issue processor model, running code from the Multiflow compiler. Non-blocking loads and stream buffers both provide a significant performance advantage, and their combination performs significantly better than either alone. For example, with a 64-byte, 2-way set associative cache with 32 cycle fetch latency, non-blocking loads reduce the run-time by 21% while stream-buffers reduce it by 26%, and the combined use of the two yields a 47% reduction. The addition of speculative execution further improves the performance of the systems that we have simulated, with or without non-blocking loads and stream buffers, by an additional 20% to 4O%. We expect that the use of all three of these techniques will be important in future generations of microprocessors.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Initiation of Hepatitis C Virus Infection Is Dependent on Cholesterol and Cooperativity between CD81 and Scavenger Receptor B Type I (2006)

In the past several years, a number of cellular proteins have been identified as candidate entry receptors for hepatitis C virus (HCV) by using surrogate models of HCV infection. Among these, the tetraspanin CD81 and scavenger receptor B type I (SR-BI), both of which localize to specialized plasma membrane domains enriched in cholesterol, have been suggested to be key players in HCV entry. In the current study, we used a recently developed in vitro HCV infection system to demonstrate that both CD81 and SR-BI are required for authentic HCV infection in vitro, that they function cooperatively to initiate HCV infection, and that CD81-mediated HCV entry is, in part, dependent on membrane cholesterol.
Antiproliferative and immunomodulatory actions of beta-interferon and double-stranded RNA, individually and in combination, on human bladder tumor xenografts in nude mice. (1985)

A cell line, RT4, derived from a human transitional cell carcinoma of the bladder, was grown as a xenograft in athymic mice. The growth of the xenografts was inhibited by beta-interferon (IFN-beta), polyriboinosinic acid.polyribocytidilic acid, the mismatched double-stranded RNA analogue r(I)n . r(C12,U)n, and to a lesser extent recombinant IFN-beta, when treatment was initiated at the time of tumor inoculation. In contrast, the growth rate of established tumors, approximately 6 mm in diameter at the initiation of therapy, was inhibited by both double-stranded RNAs, but not natural IFN-beta, indicating a possible tumor size dependence on the effectiveness of IFN-beta. Combinations of natural or recombinant IFN-beta with either polyriboinosinic acid.polyribocytidilic acid or r(I)n.r(C12,U)n gave an antagonistic effect regardless of tumor mass at the initiation of treatment. This antagonism could be overcome by alternating r(I)n. r(C12,U)n and natural IFN-beta treatment. Natural killer cell activity against RT4 cells in culture was augmented in the spleens of mice treated with r(I)n.r(C12,U)n, but not in those treated with natural IFN-beta. RT4 cells treated in culture with IFN-beta, however, were significantly less efficient as targets for natural killer cells from r(I)n.r(C12,U)n-treated and control spleens. These results indicate that: the effectiveness of IFN-beta may be related to the tumor mass; double-stranded RNAs appear to work, at least partially, in an indirect, immunomodulatory manner; combination therapy can yield an antagonistic rather than an additive or synergistic antitumor effect; and strategic scheduling can overcome the antagonistic effect of combination therapy.
Detection of Genetic Loss in Tumors by Representational Difference Analysis (1994)

A variety of genetic lesions are found in tumors, including DNA losses, point mutations, gene amplifications, and rearrangements (Lasko et al. 1991; Salomon et al. 1991). Frequent losses of both alleles at a given locus or losses of one allele with functional inactivation of the other have been detected in many tumor types. These genetic lesions, manifesting themselves as loss of heterozygosity (LOH) and hemizygous and homozygous deletions, have been found to be the hallmarks of the presence of tumor suppressor genes. Many approaches have been taken in the past to identify these genes, but recently we have developed a new method that is both general and efficient (Lisitsyn et al. 1993, 1995). The method, called representational difference analysis, or RDA, is designed for analyzing the differences between complex but highly related genomes and combines three elements: representation, subtractive enrichment, and kinetic enrichment.
Migratory and proliferative effect of platelet‐derived growth factor in rabbit retinal endothelial cells: Evidence of an autocrine pathway of platelet‐derived growth factor (1994)

Angiogenesis is a crucial event in the progression of diabetic retinopathy. Migration and proliferation of endothelial cells (EC) are important steps in angiogenesis and are caused by angiogenic factors such as basic fibroblast growth factor (bFGF). In this work, capillary EC were isolated from rabbit retinal tissues and rabbit retinal EC (RREC) were found to secrete a migration factor for RREC in conditioned medium (CM). The activity was inhibited by an anti-platelet-derived growth factor (PDGF) antibody, but not by an anti-bFGF antibody. We also found that RREC showed a migratory response to PDGF. The response was induced by PDGF-BB and PDGF-AB dose dependently, but not by PDGF-AA, indicating that it was mediated by PDGF-beta receptor-dependent pathways, and that the PDGF-like factor was PDGF-BB or -AB. In addition, PDGF-BB induced the proliferation of RREC as well as bFGF. These data indicate that RREC have an autocrine pathway of PDGF by the secretion of and the response to PDGF. PDGF may play significant parts in angiogenesis in the progression of diabetic retinopathy.
The tumor suppressor gene WT1 inhibits ras-mediated transformation. (1995)

Wilms' tumor belongs to a small group of pediatric neoplasms that have served as paradigms of human cancers in which recessive mutations play a primary role in tumorigenesis. WT1 is a candidate tumor suppressor gene that is mutationally inactivated in a proportion of both familial and sporadic Wilms' tumors. Recent studies demonstrated that WT1 can partially suppress growth of a Wilms' tumor cell line in vitro and in vivo. We investigated the ability of WT1 to inhibit the expression of the transformed phenotype in non-Wilms' tumor cells. The expression of WT1 cDNA in ras-transformed NIH3T3 cells yielded large, flat cells that exhibited complete contact-inhibition. These morphologic changes were associated with decreased proliferation, suppression of clonogenicity in soft agar and inhibition of tumor growth in nude mice. Moreover, expression of WT1 in non-transformed NIH3T3 cells resulted in similar morphologic changes and profound resistance to transformation by an activated ras oncogene. These studies suggest that tumor inhibition by WT1 in these cells may be achieved by interference with the ras-mediated signalling pathway.
Hexamer Palindromic Oligonucleotides with 5′CG-3′ Motif(s) Induce Production of Interferon (1996)

We have shown previously that 30-mer oligonucleotides containing hexamer palindromic sequences with 5'-CG-3' motif(s) induce interferon (IFN), activate natural killer (NK) cells, and thus exhibit tumor-regressing activity. The present study showed that a hexamer palindromic oligonucleotide (5'-AACGTT-3') alone induced IFN from mouse spleen cells when added with cationic liposomes. Accordingly, 32 kinds of hexamer palindromic oligonucleotides were tested for their ability to induce IFN in the presence of cationic liposomes. The results show that oligonucleotides with NACGTN and NTCGAN sequences exhibited the strongest activity. ACGCGT and TCGCGA also possessed moderate but significant activity. In contrast, palindromes without CG motif(s) were devoid of the activity. No hexamer oligonucleotides showed the activity when liposomes were absent. A complete palindromic sequence was essential as any single base substitution resulted in diminished activity. Among variety of palindromic oligonucleotides of different sizes with an ACGT sequence at the center, the tetramer oligonucleotide was without activity, whereas the activity of hexamer and longer oligonucleotides was almost equally high. These results strongly suggest that the minimal essential structure required for IFN induction is the hexamer palindromic sequence with CG motif(s).
Preparation of Ultrafine Carbon Tubes in Nanochannels of an Anodic Aluminum Oxide Film (1996)

A template carbonization technique was applied to prepare carbon nanotubes and submicron-tubes in one dimensional channels. An anodic aluminum oxide film that has uniform and straight channels with a diameter at the nanometer level was used as a one-dimensional template. The pyrolytic carbon deposition on the channel wall was carried out by exposing the anodic oxide film to propylene at 800 °C. The carbon was then liberated from the anodic oxide film by HF washing. It was found that the resultant carbon is comprised only of uniform hollow tubes with open ends. The infiltration of poly(furfuryl alcohol) into the channels of the film followed by heat treatment led to the formation of bamboolike carbon tubes. For all the carbon tubes obtained here, the outer diameter (30 or 230 nm) and the length (60 or 75 μm) precisely reflect the channel diameter and the thickness of the template used, respectively. Furthermore, in the case of the carbon tubes from propylene, the wall thickness of the tubes was easily controllable by changing the carbon deposition period.
Studies on hypolipidemic agents. II Synthesis of 1-arenesulfonyloxy-2-alkanone derivatives as potent esterase inhibitors and hypolipidemic agents. (1986)

Many 2-oxoalkyl arenesulfonate derivatives having straight or branched alkyl chains of different lengths, 2-oxoalkyl bis-arenesulfonate derivatives, and alkyl arenesulfonate derivatives having a ketal moiety at the 2-position on the alkyl chain were synthesized, and their esterase-inhibitory activities, as well as hypolipidemic activities, were evaluated.Among these compounds, 1-(2, 4, 6-trimethylbenzenesulfonyloxy)-2-dodecanone (III-1u), and 1-(2, 3, 4, 6-tetramethylbenzenesulfonyloxy)-2-hexanone (III-1w), -2-octanone (III-1x) and -2-decanone (III-1y) exhibited potent esterase-inhibitory activities (IC50=3×10-10, 2×10-10, 2×10<-10> and 3×<-11>M, respectively). However, the sulfonate (XV) having a ketal moiety on the alkyl chain and the bis-sulfonate (XVI) exhibited low inhibitory activities toward esterase in comparison with III and XII. Most of the compounds III and some of the compounds XII exhibited potent hypolipidemic activities corresponding to more than 50% lipid-lowering effect (plasma triglyceride and cholesterol ester) in vivo. The structure-activity relatioinships of these compounds are discussed.
Statistical machine learning makes automatic control practical for internet datacenters (2009)

Horizontally-scalable Internet services on clusters of commodity computers appear to be a great fit for automatic control: there is a target output (service-level agreement), observed output (actual latency), and gain controller (adjusting the number of servers). Yet few datacenters are automated this way in practice, due in part to well-founded skepticism about whether the simple models often used in the research literature can capture complex real-life workload/performance relationships and keep up with changing conditions that might invalidate the models. We argue that these shortcomings can be fixed by importing modeling, control, and analysis techniques from statistics and machine learning. In particular, we apply rich statistical models of the application’s performance, simulation-based methods for finding an optimal control policy, and change-point methods to find abrupt changes in performance. Preliminary results running a Web 2.0 benchmark application driven by real workload traces on Amazon’s EC2 cloud show that our method can effectively control the number of servers, even in the face of performance anomalies. 1
A Randomized Controlled Trial of the Effect of Real-Time Telemedicine Support on Glycemic Control in Young Adults With Type 1 Diabetes (ISRCTN 46889446) (2005)

Real-time telemedicine transmission and feedback of information about blood glucose results with nurse support is feasible and acceptable to patients, but to significantly improve glycemic control, access to real-time decision support for medication dosing and changes in diet and exercise may be required.
Anti-GD2 monoclonal antibody 3F8 plus granulocyte-macrophage colony-stimulating factor (GM-CSF) for primary refractory neuroblastoma (NB) in bone marrow (BM) (2007)

9502 Background: Despite high-dose chemotherapy, NB in BM often persists and forebodes death. Methods: 3F8/GM- CSF was used in 63 patients (pts) with NB in BM by morphology and/or metaiodobenzylguanidine (MIBG) scan, no prior progressive disease or immunotherapy, and no soft tissue NB; 35 (56%) of the pts had received second-line therapy and 24 (38%) were post-transplant. Treatment was repeated if human anti-mouse antibody (HAMA) titer was low. Results: Of 30 pts with NB in BM but normal MIBG scans (Group 1), 25 (83%) had complete response (CR) after cycle 1 (n=17), cycle 2 (n=5), or cycle 3, 6, or 7 (one pt each), including 13/16 post-transplant pts. Among 15 pts with NB in BM and abnormal MIBG scans (Group 2), 12 (80%) had CR in BM after cycle 1 (n=5), cycle 2 (n=4), cycle 4 (n=2), or cycle 9 (n=1); MIBG scans normalized in 5/11 pts who had multiple abnormal MIBG(+) sites and in 4/4 pts who had one abnormal MIBG(+) site (irradiated in three pts). Of 18 pts who had abnormal MIBG scans but no NB seen in BM tests (Group 3), 14 (78%) had CR or near CR, including eight whose MIBG(+) sites were irradiated. Early HAMA limited treatment in 19 pts, but was prevented by high-dose cyclophosphamide. CR continues in 12 pts (five never transplanted) with long follow-up (20+ -to- 146+ months) and in 10 pts with short follow-up. The only common toxicities of this outpatient treatment were pain and hives; there were no long-term toxicities. Conclusions: 3F8/GM-CSF is well tolerated, achieves a high CR rate against primary refractory NB in BM (including post-transplant), and may prolong disease control in non- transplanted pts. Further experience will show whether it ought to be used for consolidative therapy in place of myeloablative cytoreduction. No significant financial relationships to disclose.
A new peripherally implanted subcutaneous permanent central venous access device for patients requiring chemotherapy. (1993)

This device provides a highly acceptable, additional method of implantable, permanent central venous access for chemotherapy patients with a low complication rate. The successful use of the Cath-Finder and minor extent of the procedure may allow this device to be inserted in a clinic procedure room without sedation and fluoroscopy.
Mechanical stress modeling for silicon fabrication processes (2002)

Two finite element methods are implemented to investigate localized mechanical stress fields generated during multiple stages of silicon IC fabrication. The boundary loading method (BL) uses the oxide interface stresses as a boundary condition for the substrate solution. In the fully integrated method (FI), the strains in substrate are calculated along with the oxide stress computation. Both of the methods can be used to couple stresses generated by oxidation volume expansion to strains present from other sources such as thermal expansion, dopants, and intrinsic film stresses. They are then evaluated on computational intensiveness and in stress solution variation. It is found that the BL method computes nearly the same oxide solution as the FI method and the oxide solution corresponds very well in the oxide and surface films for a LOCOS process.
A Herpes Simplex Virus Type 1 γ34.5 Second-Site Suppressor Mutant That Exhibits Enhanced Growth in Cultured Glioblastoma Cells Is Severely Attenuated in Animals (2001)

We describe here the neurovirulence properties of a herpes simplex virus type 1 gamma34.5 second-site suppressor mutant. gamma34.5 mutants are nonneurovirulent in animals and fail to grow in a variety of cultured cells due to a block at the level of protein synthesis. Extragenic suppressors with restored capacity to replicate in cells that normally do not support the growth of the parental gamma34.5 deletion mutant have been isolated. Although the suppressor virus reacquires the ability to grow in nonpermissive cultured cells, it remains severely attenuated in mice and is indistinguishable from the mutant gamma34.5 parent virus at the doses investigated. Repairing the gamma34.5 mutation in the suppressor mutant restores neurovirulence to wild-type levels. These studies illustrate that (i) the protein synthesis and neurovirulence defects observed in gamma34.5 mutant viruses can be genetically separated by an extragenic mutation at another site in the viral chromosome; (ii) the extragenic suppressor mutation does not affect neurovirulence; and (iii) the attenuated gamma34.5 mutant, which replicates poorly in many cell types, can be modified by genetic selection to generate a nonpathogenic variant that regains the ability to grow robustly in a nonpermissive glioblastoma cell line. As this gamma34.5 second-site suppressor variant is attenuated and replicates vigorously in neoplastic cells, it may have potential as a replication-competent, viral antitumor agent.
Identification of a novel interleukin-15 (IL-15) transcript isoform generated by alternative splicing in human small cell lung cancer cell lines. (1996)

IL-15 is a cytokine promoting growth and differentiation of T, B and NK lymphocytes. By RT-PCR analysis, using primers allowing amplification of the entire IL-15 mRNA coding region, 9/11 small cell lung cancer (SCLC) cell lines displayed detectable IL-15 gene expression. In addition to the expected band sizing 524 bp, a larger band was also observed. Cloning and sequence analysis of the larger cDNA from two SCLC cell lines revealed a size of 643 hp due to the presence of additional 119 hp within the previously reported IL-15 cDNA sequence. The 119 hp sequence matched with an IL-15 genomic sequence downstream the IL-15 second coding exon and may represent a previously unreported alternative exon (exon A). The SCLC-associated IL-15 mRNA isoform has a shorter open reading frame (ORF) due to stop codons in exon A, followed by a new AUG codon. The predicted IL-15 precursor protein displays a shorter signal peptide but shares the same aminoacidic composition of mature IL-15 protein. A possible functional role of IL-15, different from 'IL-2-like' activity, in human tumours, is suggested.