gebhart/patrepeval huggingface dataset:
US Findings after Irreversible Electroporation Ablation: Radiologic-Pathologic Correlation (2011)

US findings in the acute period after IRE are dynamic and evolve. The ablation zone can be best predicted by measuring the external hyperechoic rim that forms 90-120 minutes after ablation. This rim is possibly attributable to evolving hemorrhagic infiltration via widened sinusoids.
Human telomerase reverse transcriptase promoter regulation in normal and malignant human ovarian epithelial cells. (2001)

The telomerase RNA-protein complex responsible for maintenance of telomeric DNA at chromosome ends, is usually inactive in most primary somatic human cells, but is specifically activated with in vitro immortalization and during tumorigenesis. Although expression of the RNA component of telomerase appears to be constitutive, the expression pattern of human telomerase reverse transcriptase (hTERT), the catalytic subunit of telomerase, is correlated with measured enzyme activity. In particular, a >80% concordance has been reported between telomerase activity and hTERT mRNA expression in ovarian tumors. Accordingly, to learn more about the mechanism regulating hTERT gene expression in ovarian carcinoma, we have performed a detailed analysis of the 5'-flanking promoter region of the hTERT gene. We have reported previously the isolation and analysis of a 5.8-kb genomic fragment containing the human hTERT gene promoter (M. Tzukerman et al., Mol. Biol. Cell, 11: 4381-4391, 2000). Deletion analysis of this promoter was carried out using transient transfection of promoter-reporter constructs in four different telomerase-expressing, ovarian carcinoma-derived cell lines, the tumorigenic properties of which have been characterized, and was compared with telomerase-negative primary human fibroblasts and nontransformed ovarian epithelial cells. These assays have shown that the hTERT promoter is inactive in telomerase-negative cells and is active in telomerase-positive cell lines. A core promoter of 283 bp upstream of the transcription initiation site (TI) was found to be sufficient for maximum promoter activity, suggesting the presence of inhibitory elements within the larger promoter sequence. Gel shift analysis of the core promoter using nuclear extracts from the ovarian and control cell lines revealed specific transcription factor binding using extracts from telomerase-positive cells. Among the binding elements, we identified two E-boxes (CACGTG) as well as a novel element (MT-box), which we identified recently in a number of differentiation systems. Site-directed mutagenesis was used to introduce mutations into this novel transcription factor binding element. These mutations significantly affect the transcriptional activity of hTERT promoter in a cell type-specific manner and suggest that the transcription factors that bind to the E-box and the novel element cooperatively function as major determinants of hTERT expression and telomerase activity in ovarian cancer. Further comparison of promoter activity, telomerase activity, and telomere length among the different ovarian cancer cells indicated that a threshold level of telomerase activity is apparently sufficient to protect telomere integrity and permit the immortal state of the different ovarian cancer cell lines.
Passive fire protection measures for concrete tunnels (1999)

executed or in the process of designing; worth mentioning are the Western Scheld tunnel (approximately 2x6.5 km), the tunnels in the Betuwe railway and the tunnels in the HSL (high velocity train) railway. The most prominent of these tunnels will be executed as bored tunnels. The Directorate-General of Public Works and Water Management (Rijkswaterstaat, denoted hereafter as RWS) requires that the structural integrity of the tunnels in highways should remain intact in the case of a -specific type of hydro-carbon- fire. Implicitly it is assumed the hazardous goods will be transported through these tunnels. With a view to protect the concrete (prevent the concrete from spalling and heating up of the reinforcement) when exposed to hydro-carbon fires, this normally results in the application of passive fire protection. Rijkswaterstaat and TNO jointly wrote a test procedure for the evaluation of such passive fire protection for concrete tunnels. The paper describes the test procedures and evaluation methods (section 1). Furthermore, results of recent research into the fire behaviour of the concrete tunnel segments for the Western Scheld tunnel will be presented (section 2).
High-density lipoprotein cholesterol and cardiovascular disease. Four prospective American studies. (1989)

The British Regional Heart Study (BRHS) reported in 1986 that much of the inverse relation of high-density lipoprotein cholesterol (HDLC) and incidence of coronary heart disease was eliminated by covariance adjustment. Using the proportional hazards model and adjusting for age, blood pressure, smoking, body mass index, and low-density lipoprotein cholesterol, we analyzed this relation separately in the Framingham Heart Study (FHS), Lipid Research Clinics Prevalence Mortality Follow-up Study (LRCF) and Coronary Primary Prevention Trial (CPPT), and Multiple Risk Factor Intervention Trial (MRFIT). In CPPT and MRFIT (both randomized trials in middle-age high-risk men), only the control groups were analyzed. A 1-mg/dl (0.026 mM) increment in HDLC was associated with a significant coronary heart disease risk decrement of 2% in men (FHS, CPPT, and MRFIT) and 3% in women (FHS). In LRCF, where only fatal outcomes were documented, a 1-mg/dl increment in HDLC was associated with significant 3.7% (men) and 4.7% (women) decrements in cardiovascular disease mortality rates. The 95% confidence intervals for these decrements in coronary heart and cardiovascular disease risk in the four studies overlapped considerably, and all contained the range 1.9-2.9%. HDLC levels were essentially unrelated to non-cardiovascular disease mortality. When differences in analytic methodology were eliminated, a consistent inverse relation of HDLC levels and coronary heart disease event rates was apparent in BRHS as well as in the four American studies.
Logical performance of 9 qubit compass codes in ion traps with crosstalk errors (2020)

Abstract We simulate four quantum error correcting codes under error models inspired by realistic noise sources in near-term ion trap quantum computers: T 2 dephasing, gate overrotation, and crosstalk. We use this data to find preferred codes for given error parameters along with logical error biases and a pseudothreshold which compares the physical and logical gate failure rates for a CNOT gate. Using these results we conclude that Bacon–Shor-13 is the most promising near term candidate as long as the impact of crosstalk can be mitigated through other means.
RETRACTED: 5-Aza-Deoxycytidine Induces Selective Degradation of DNA Methyltransferase 1 by a Proteasomal Pathway That Requires the KEN Box, Bromo-Adjacent Homology Domain, and Nuclear Localization Signal (2005)

5-Azacytidine- and 5-aza-deoxycytidine (5-aza-CdR)-mediated reactivation of tumor suppressor genes silenced by promoter methylation has provided an alternate approach in cancer therapy. Despite the importance of epigenetic therapy, the mechanism of action of DNA-hypomethylating agents in vivo has not been completely elucidated. Here we report that among three functional DNA methyltransferases (DNMT1, DNMT3A, and DNMT3B), the maintenance methyltransferase, DNMT1, was rapidly degraded by the proteasomal pathway upon treatment of cells with these drugs. The 5-aza-CdR-induced degradation, which occurs in the nucleus, could be blocked by proteasomal inhibitors and required a functional ubiquitin-activating enzyme. The drug-induced degradation occurred even in the absence of DNA replication. Treatment of cells with other nucleoside analogs modified at C-5, 5-fluorodeoxyuridine and 5-fluorocytidine, did not induce the degradation of DNMT1. Mutation of cysteine at the catalytic site of Dnmt1 (involved in the formation of a covalent intermediate with cytidine in DNA) to serine (CS) did not impede 5-aza-CdR-induced degradation. Neither the wild type nor the catalytic site mutant of Dnmt3a or Dnmt3b was sensitive to 5-aza-CdR-mediated degradation. These results indicate that covalent bond formation between the enzyme and 5-aza-CdR-incorporated DNA is not essential for enzyme degradation. Mutation of the conserved KEN box, a targeting signal for proteasomal degradation, to AAA increased the basal level of Dnmt1 and blocked its degradation by 5-aza-CdR. Deletion of the catalytic domain increased the expression of Dnmt1 but did not confer resistance to 5-aza-CdR-induced degradation. Both the nuclear localization signal and the bromo-adjacent homology domain were essential for nuclear localization and for the 5-aza-CdR-mediated degradation of Dnmt1. Polyubiquitination of Dnmt1 in vivo and its stabilization upon treatment of cells with a proteasomal inhibitor indicate that the level of Dnmt1 is controlled by ubiquitin-dependent proteasomal degradation. Overexpression of the substrate recognition component, Cdh1 but not Cdc20, of APC (anaphase-promoting complex)/cyclosome ubiquitin ligase reduced the level of Dnmt1 in both untreated and 5-aza-CdR-treated cells. In contrast, the depletion of Cdh1 with small interfering RNA increased the basal level of DNMT1 that blocked 5-aza-CdR-induced degradation. Dnmt1 interacted with Cdh1 and colocalized in the nucleus at discrete foci. Both Dnmt1 and Cdh1 were phosphorylated in vivo, but only Cdh1 was significantly dephosphorylated upon 5-aza-CdR treatment, suggesting its involvement in initiating the proteasomal degradation of DNMT1. These results demonstrate a unique mechanism for the selective degradation of DNMT1, the maintenance DNA methyltransferase, by well-known DNA-hypomethylating agents.
Regulation of Adipogenesis by Natural and Synthetic REV-ERB Ligands (2010)

The nuclear hormone receptor, REV-ERB, plays an essential role in adipogenesis. Rev-erbalpha expression is induced in 3T3-L1 cells during adipogenesis, and overexpression of this receptor leads to expression of adipogenic genes. We recently demonstrated that the porphyrin heme functions as a ligand for REV-ERB, and binding of heme is required for the receptor's activity. We therefore hypothesized that REV-ERB ligands may play a role in regulation of adipogenesis. We detected an increase intracellular heme levels during 3T3-L1 adipogenesis that correlated with induction of aminolevulinic acid synthase 1 (Alas1) expression, the rate-limiting enzyme in heme biosynthesis. If the increase in Alas1 expression was blocked, adipogenesis was severely attenuated, indicating that induction of expression of Alas1 and the increase in heme synthesis is critical for differentiation. Inhibition of heme synthesis during adipogenesis leads to decreased recruitment of nuclear receptor corepressor to the promoter of a REV-ERB target gene, suggesting alteration of REV-ERB activity. Treatment of 3T3-L1 cells with a synthetic REV-ERB ligand, SR6452, resulted in induction of adipocyte differentiation to a similar extent as treatment with the peroxisomal proliferator-activated receptor-gamma agonist, rosiglitazone. Combination of SR6452 and rosiglitazone had an additive effect on stimulation of adipocyte differentiation. These results suggest that heme, functioning as a REV-ERB ligand, is an important signaling molecule for induction of adipogenesis. Moreover, synthetic small molecule ligands for REV-ERB are effective modulators of adipogenesis and may be useful for treatment of metabolic diseases.
Beta-tricalcium phosphate (beta-TCP) graft combined with bone marrow stromal cells (MSCs) for posterolateral spine fusion. (2005)

Macaque lumber posterolateral spine fusion (PLF) was performed by using beta-TCP graft combined with bone marrow derived stromal cells (MSCs), to evaluate whether a beta-TCP/MSCs hybrid can be used for PLF instead of autogenous bone graft. Nine crab-eating macaque underwent bilateral PLF at L4-L5. The implants were divided into three groups: 1) beta-TCP/MSCs hybrid, 2) autogenous bone, and 3) beta-TCP. Six monkeys were sacrified at 12 weeks and three monkeys were sacrificed at 24 weeks after implantation. Manual palpation, radiography, micro computed tomography, peripheral quantitative computed tomography (pQCT), and histology were used to assess bone formation. Manual palpation and X-ray showed that 83.3% of hybrid groups and 66.7% of autogenous groups achieved solid spine fusion, whereas none of other groups fused. Histological analysis showed that all of the hybrid groups achieved massive bone formation. Bone mineral density (BMD) evaluated with pQCT in the hybrid groups increased by additional new bone. Beta-TCP/MSCs hybrid can be used for PLF instead of autogenous bone graft. Thus it can be hypothesized that the monkey PLF can simulate human PLF.
Nuclear Polarization inHe3Gas Induced by Optical Pumping and Dipolar Exchange (1960)

Received 26 September 1960DOI:https://doi.org/10.1103/PhysRevLett.5.373©1960 American Physical Society
Molecular Electronics with Carbon Nanotubes (2003)

Abstract For Abstract see ChemInform Abstract in Full Text.
Nanopore Detector based analysis of single-molecule conformational kinetics and binding interactions (2006)

In essence, the heart of chemistry is now accessible to a new, single-molecule, observation method that can track both external molecular binding states, and internal conformation states.
celA from Bacillus lautus PL236 encodes a novel cellulose-binding endo-beta-1,4-glucanase (1992)

celA from the cellulolytic bacterium Bacillus lautus PL236 encodes EG-A, an endo-beta-1,4-glucanase. An open reading frame of 2,100 bp preceded by a ribosome-binding site encodes a protein with a molecular mass of 76,863 Da with a typical signal sequence. The NH2-terminal active domain of EG-A is not homologous to any reported cellulase or xylanase and may represent a new family of such enzymes. A 150-amino-acid COOH-terminal peptide is homologous to noncatalytic domains in several other cellulases (A. Meinke, N.R. Gilkes, D.G. Kilburn, R.C. Miller, Jr., and R.A.J. Warren, J. Bacteriol. 173:7126-7135, 1991). Upstream of celA, a partial open reading frame encodes a 145-amino-acid peptide which also belongs to the family mentioned. Zymogram analysis of extracts from Escherichia coli and supernatants of Bacillus subtilis and B. megaterium, including protease-deficient mutants thereof, which express celA, revealed two active proteins, EG-A-L and EG-A-S, with Mrs of 74,000 and 57,000, respectively. The proportion of EG-A-L to EG-A-S depends on the extracellular proteolytic activity of the host organism, indicating that EG-A-S arises from posttranslational proteolytic modification of EG-A-L. Since EG-A-S has an NH2 terminus corresponding to the predicted NH2-terminal sequence of EG-A, processing appears to take place between the catalytic and noncatalytic domains described. EG-A-L and EG-A-S were purified to homogeneity and shown to have almost identical characteristics with respect to activity against soluble substrates and pH and temperature dependency. EG-A-L binds strongly to cellulose, in contrast to EG-A-S, and has higher activity against insoluble substrates than the latter. We conclude that the COOH-terminal 17,000-Mr peptide of EG-A-L constitutes a cellulose-binding domain.
Simplified method to estimate salivary buffer capacity (1989)

A new and simplified method to estimate the salivary buffer capacity was tested. The method, Dentobuff Strip, consists of a pH indicator paper that has been impregnated with acid. A small volume of saliva is added to the strip and after 5 min the color of the strip is compared with a chart. The colors have been chosen to indicate low, medium, or good buffer capacity. The buffer capacity of stimulated saliva samples from 62 subjects was measured with the new method and compared with two commonly used clinical methods, Dentobuff, and an electrometric method. The three methods correlated well, and patients with a low salivary buffer capacity (final pH less than or equal to 4), according to the electrometric method, were readily identified with the new Dentobuff Strip method.
A New Group of Phage Anti-CRISPR Genes Inhibits the Type I-E CRISPR-Cas System of Pseudomonas aeruginosa (2014)

ABSTRACT CRISPR-Cas systems are one of the most widespread phage resistance mechanisms in prokaryotes. Our lab recently identified the first examples of phage-borne anti-CRISPR genes that encode protein inhibitors of the type I-F CRISPR-Cas system of Pseudomonas aeruginosa . A key question arising from this work was whether there are other types of anti-CRISPR genes. In the current work, we address this question by demonstrating that some of the same phages carrying type I-F anti-CRISPR genes also possess genes that mediate inhibition of the type I-E CRISPR-Cas system of P. aeruginosa . We have discovered four distinct families of these type I-E anti-CRISPR genes. These genes do not inhibit the type I-F CRISPR-Cas system of P. aeruginosa or the type I-E system of Escherichia coli . Type I-E and I-F anti-CRISPR genes are located at the same position in the genomes of a large group of related P. aeruginosa phages, yet they are found in a variety of combinations and arrangements. We have also identified functional anti-CRISPR genes within nonprophage Pseudomonas genomic regions that are likely mobile genetic elements. This work emphasizes the potential importance of anti-CRISPR genes in phage evolution and lateral gene transfer and supports the hypothesis that more undiscovered families of anti-CRISPR genes exist. Finally, we provide the first demonstration that the type I-E CRISPR-Cas system of P. aeruginosa is naturally active without genetic manipulation, which contrasts with E. coli and other previously characterized I-E systems. IMPORTANCE The CRISPR-Cas system is an adaptive immune system possessed by the majority of prokaryotic organisms to combat potentially harmful foreign genetic elements. This study reports the discovery of bacteriophage-encoded anti-CRISPR genes that mediate inhibition of a well-studied subtype of CRISPR-Cas system. The four families of anti-CRISPR genes described here, which comprise only the second group of anti-CRISPR genes to be identified, encode small proteins that bear no sequence similarity to previously studied phage or bacterial proteins. Anti-CRISPR genes represent a newly discovered and intriguing facet of the ongoing evolutionary competition between phages and their bacterial hosts.
A Dynamic MapReduce Scheduler for Heterogeneous Workloads (2009)

MapReduce is an important programming model for building data centers containing ten of thousands of nodes. In a practical data center of that scale, it is a common case that I/O-bound jobs and CPU-bound jobs, which demand different resources, run simultaneously in the same cluster. In the MapReduce framework, parallelization of these two kinds of job has not been concerned. In this paper, we give a new view of the MapReduce model, and classify the MapReduce workloads into three categories based on their CPU and I/O utilization. With workload classification, we design a new dynamic MapReduce workload predict mechanism, MR-Predict, which detects the workload type on the fly. We propose a Triple-Queue Scheduler based on the MR-Predict mechanism. The Triple-Queue scheduler could improve the usage of both CPU and disk I/O resources under heterogeneous workloads. And it could improve the Hadoop throughput by about 30% under heterogeneous workloads.
Hand Detection and Pose Estimation using Convolutional Neural Networks (2015)

This thesis examines how convolutional neural networks can applied to the problem of hand detection and hand pose estimation. Two families of convolutional neural networks are trained, aimed at performing the task of classification or regression. The networks are trained on specialized data generated from publicly available datasets. The algorithms used to generate the specialized data are also disclosed. The main focus has been to investigate the different structural properties of convolutional neural networks, not building optimized hand detection, or hand pose estimation, systems. Experiments revealed, that classifier networks featuring a relatively high number of convolutions offers the highest performance on external validation data. Additionally, shallow classifier networks featuring a relatively low number of convolutions, yields a high classification accuracy on training and testing data, but a very low accuracy on the validation set. This effect uncovers one of the fundamental difficulties in building a hand detection system: The asymmetric classification problem. In further investigation, it is also remarked, that relatively shallow classifier networks probably becomes color sensitive. Furthermore, regressor networks featuring multiscale inputs typically yielded the lowest error, when tasked with computing key-point locations directly from data. It is also revealed, that color data implicitly contain more information, making it easier to compute key-point locations, especially in the image space. However, to be able to derive the color invariant features, deeper regressor networks are required.
Lymphokine-independent induction of macrophage membrane IL-1 by autoreactive T cells recognizing either class I or class II MHC determinants. (1988)

Here we report that autoreactive T cell clones and T cell hybridomas that recognize class I or class II MHC determinants can induce IL-1 expression on cultured macrophages in an MHC-restricted manner. This genetic restriction of membrane IL-1 (mIL-1) induction is not absolute, however; it is manifest only in macrophages that have been cultured for several days before stimulation. Macrophages that are evaluated within 24 h after adherence display a basal level of mIL-1, and the T cell-induced augmentation of basal mIL-1 expression is not MHC-restricted. It appears that T cells of both Th1 and Th2 type have the capacity to induce mIL-1, suggesting that this function is not limited to the T cell subset (Th2) that is able to use IL-1. Most importantly, the ability of T cells to induce IL-1 on macrophages seems to occur by virtue of direct cellular interactions, and is independent of lymphokine secretion. The induction event is rapid enough (2 to 4 h) to allow T cells to interact with both antigen and IL-1 during the initial T cell/macrophage contact. These findings thus reveal an efficient mechanism for the induction of IL-1 during Ag presentation to T cells.
Streptococcal Pyrogenic Exotoxin A Release, Distribution, and Role in a Murine Model of Fasciitis and Multiorgan Failure Due to Streptococcus pyogenes (1996)

The role of streptococcal pyrogenic exotoxin A (SPEA) was evaluated in a murine model of fasciitis and multiorgan failure due to a toxigenic strain of Streptococcus pyogenes. Increased serum levels of SPEA at 15 and 21 h were associated with a survival time of <24 h. Levels of SPEA correlated with interleukin-6 levels. Immunostaining showed SPEA localized to renal and hepatic cells. Neutralizing rabbit antibody to SPEA was administered to mice challenged with S. pyogenes, but no effect on survival was observed. Vaccination of mice with recombinant SPEA enhanced mortality due to streptococcal infection, despite the development of neutralizing immunity to the toxin prior to infection. Hence, SPEA is produced systemically during S. pyogenes soft-tissue infection, and increased levels are associated with reduced survival. In this model, however, SPEA did not appear to play a dominant role in pathogenesis; passive immunization against SPEA was not protective, and active immunization enhanced mortality.