gebhart/patrepeval huggingface dataset:
A quick search method for audio and video signals based on histogram pruning (2003)

This paper proposes a quick method of similarity-based signal searching to detect and locate a specific audio or video signal given as a query in a stored long audio or video signal. With existing techniques, similarity-based searching may become impractical in terms of computing time in the case of searching through long-running (several-days' worth of) signals. The proposed algorithm, which is referred to as time-series active search, offers significantly faster search with sufficient accuracy. The key to the acceleration is an effective pruning algorithm introduced in the histogram matching stage. Through the pruning, the actual number of matching calculations can be reduced by 200 to 500 times compared with exhaustive search while guaranteeing exactly the same search result. Experiments show that the proposed method can correctly detect and locate a 15-s signal in a 48-h recording of TV broadcasts within 1 s, once the feature vectors are calculated and quantized. As extentions of the basic algorithm, efficient AND/OR search methods for searching for multiple query signals and a feature dithering method for coping with signal distortion are also discussed.
Tree inference for single-cell data (2016)

Understanding the mutational heterogeneity within tumors is a keystone for the development of efficient cancer therapies. Here, we present SCITE, a stochastic search algorithm to identify the evolutionary history of a tumor from noisy and incomplete mutation profiles of single cells. SCITE comprises a flexible Markov chain Monte Carlo sampling scheme that allows the user to compute the maximum-likelihood mutation history, to sample from the posterior probability distribution, and to estimate the error rates of the underlying sequencing experiments. Evaluation on real cancer data and on simulation studies shows the scalability of SCITE to present-day single-cell sequencing data and improved reconstruction accuracy compared to existing approaches.
Random projection-based multiplicative data perturbation for privacy preserving distributed data mining (2006)

This paper explores the possibility of using multiplicative random projection matrices for privacy preserving distributed data mining. It specifically considers the problem of computing statistical aggregates like the inner product matrix, correlation coefficient matrix, and Euclidean distance matrix from distributed privacy sensitive data possibly owned by multiple parties. This class of problems is directly related to many other data-mining problems such as clustering, principal component analysis, and classification. This paper makes primary contributions on two different grounds. First, it explores independent component analysis as a possible tool for breaching privacy in deterministic multiplicative perturbation-based models such as random orthogonal transformation and random rotation. Then, it proposes an approximate random projection-based technique to improve the level of privacy protection while still preserving certain statistical characteristics of the data. The paper presents extensive theoretical analysis and experimental results. Experiments demonstrate that the proposed technique is effective and can be successfully used for different types of privacy-preserving data mining applications.
IB1, a JIP-1-related Nuclear Protein Present in Insulin-secreting Cells (1998)

JIP-1 is a cytoplasmic inhibitor of the c-Jun amino-terminal kinase activated pathway recently cloned from a mouse brain cDNA library. We report herein the expression cloning of a rat cDNA encoding a JIP-1-related nuclear protein from a pancreatic beta-cell cDNA library that we named IB1 for Islet-Brain 1. IB1 was isolated by its ability to bind to GTII, a cis-regulatory element of the GLUT2 promoter. The IB1 cDNA encodes a 714-amino acid protein, which differs from JIP-1 by the insertion of 47 amino acids in the carboxyl-terminal part of the protein. The remaining 667 amino acids are 97% identical to JIP-1. The 47-amino acid insertion contains a truncated phosphotyrosine interaction domain and a putative helix-loop-helix motif. Recombinant IB1 (amino acids 1-714 and 280-714) was shown to bind in vitro to GTII. Functionally IB1 transactivated the GLUT2 gene. IB1 was localized within the cytoplasm and the nucleus of insulin-secreting cells or COS-7 cells transfected with an expression vector encoding IB1. Using a heterologous GAL4 system, we localized an activation domain of IB1 within the first 280 amino acids of the protein. These data demonstrate that IB1 is a DNA-binding protein related to JIP-1, which is highly expressed in pancreatic beta-cells where it functions as a transactivator of the GLUT2 gene.
cis-trans Isomerization of Olefins by Intramolecular Energy Transfer (1965)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTcis-trans Isomerization of Olefins by Intramolecular Energy TransferHarry MorrisonCite this: J. Am. Chem. Soc. 1965, 87, 4, 932Publication Date (Print):February 1, 1965Publication History Published online1 May 2002Published inissue 1 February 1965https://pubs.acs.org/doi/10.1021/ja01082a055https://doi.org/10.1021/ja01082a055research-articleACS PublicationsRequest reuse permissionsArticle Views245Altmetric-Citations39LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Cancer Stem Cells (2009)

Cancer is a devastating disease that affects millions of people in the world. Our the- pies for tumors have mostly been based on classical chemotherapy and antiproliferative treatments. More recently,
A Genetic Pathway Conferring Life Extension and Resistance to UV Stress in Caenorhabditis elegans (1996)

A variety of mechanisms have been proposed to explain the extension of adult life span (Age) seen in several mutants in Caenorhabditis elegans (age-1: an altered aging rate; daf-2 and daf-23: activation of a dauer-specific longevity program; spe-26: reduced fertility; clk-1: an altered biological clock). Using an assay for ultraviolet (UV) resistance in young adult hermaphrodites (survival after UV irradiation), we observed that all these Age mutants show increased resistance to UV. Moreover, mutations in daf-16 suppressed the UV resistance as well as the increased longevity of all the Age mutants. In contrast to the multiple mechanisms initially proposed, these results suggest that a single, daf-16-dependent pathway, specifies both extended life span and increased UV resistance. The mutations in daf-16 did not alter the reduced fertility of spe-26 and interestingly a daf-16 mutant is more fertile than wild type. We propose that life span and some aspects of stress resistance are jointly negatively regulated by a set of gerontogenes (genes whose alteration causes life extension) in C. elegans.
Human α-Defensins Inhibit Hemolysis Mediated by Cholesterol-Dependent Cytolysins (2009)

Many pathogenic gram-positive bacteria release exotoxins that belong to the family of cholesterol-dependent cytolysins. Here, we report that human alpha-defensins HNP-1 to HNP-3 acted in a concentration-dependent manner to protect human red blood cells from the lytic effects of three of these exotoxins: anthrolysin O (ALO), listeriolysin O, and pneumolysin. HD-5 was very effective against listeriolysin O but less effective against the other toxins. Human alpha-defensins HNP-4 and HD-6 and human beta-defensin-1, -2, and -3 lacked protective ability. HNP-1 required intact disulfide bonds to prevent toxin-mediated hemolysis. A fully linearized analog, in which all six cysteines were replaced by aminobutyric acid (Abu) residues, showed greatly reduced binding and protection. A partially unfolded HNP-1 analog, in which only cysteines 9 and 29 were replaced by Abu residues, showed intact ALO binding but was 10-fold less potent in preventing hemolysis. Surface plasmon resonance assays revealed that HNP-1 to HNP-3 bound all three toxins at multiple sites and also that solution-phase HNP molecules could bind immobilized HNP molecules. Defensin concentrations that inhibited hemolysis by ALO and listeriolysin did not prevent these toxins from binding either to red blood cells or to cholesterol. Others have shown that HNP-1 to HNP-3 inhibit lethal toxin of Bacillus anthracis, toxin B of Clostridium difficile, diphtheria toxin, and exotoxin A of Pseudomonas aeruginosa; however, this is the first time these defensins have been shown to inhibit pore-forming toxins. An "ABCDE mechanism" that can account for the ability of HNP-1 to HNP-3 to inhibit so many different exotoxins is proposed.
The Histone Demethylase JMJD2B Is Regulated by Estrogen Receptor α and Hypoxia, and Is a Key Mediator of Estrogen Induced Growth (2010)

Estrogen receptor alpha (ERalpha) plays an important role in breast cancer. Upregulation of HIF-1alpha in ER(alpha)-positive cancers suggests that HIF-1alpha may cooperate with ERalpha to promote breast cancer progression and consequently affect breast cancer treatment. Here, we show the histone demethylase JMJD2B is regulated by both ERalpha and HIF-1alpha, drives breast cancer cell proliferation in normoxia and hypoxia, and epigenetically regulates the expression of cell cycle genes such as CCND1, CCNA1, and WEE1. We also show that JMJD2B and the hypoxia marker CA9 together stratify a subclass of breast cancer patients and predict a worse outcome of these breast cancers. Our findings provide a biological rationale to support the therapeutic targeting of histone demethylases in breast cancer patients.
Specific, High Affinity Binding of Tissue Inhibitor of Metalloproteinases-4 (TIMP-4) to the COOH-terminal Hemopexin-like Domain of Human Gelatinase A (1997)

The binding properties of the newly described tissue inhibitor of metalloproteinases-4 (TIMP-4) to progelatinase A and to the COOH-terminal hemopexin-like domain (C domain) of the enzyme were examined. We present evidence for the first time of a specific, high affinity interaction between TIMP-4 and the C domain of human gelatinase A and show that TIMP-4 binds both progelatinase A and the C domain in a similar manner to that of TIMP-2. Saturable binding of recombinant C domain to TIMP-4 and to TIMP-2 but not to TIMP-1 was demonstrated using a microwell protein binding assay. The recombinant collagen binding domain of gelatinase A, comprised of the three fibronectin type II-like repeats, did not bind to TIMP-4, indicating that binding is mediated selectively by the C domain. Binding to TIMP-4 was of high affinity with an apparent Kd of 1.7 x 10(-7) M but slightly weaker than that to TIMP-2 (apparent Kd of 0.66 x 10(-7) M). Affinity chromatography confirmed the TIMP-4-C domain interaction and also showed that the complex could not be disrupted by 1 M NaCl or 10% dimethyl sulfoxide, thereby further demonstrating the tight binding. To verify the biological significance of this interaction, binding of full-length progelatinase A to TIMP-4 was investigated. TIMP-4 and TIMP-2 but not TIMP-1 bound specifically to purified TIMP-2-free human recombinant full-length progelatinase A and to full-length rat proenzyme from the conditioned culture medium of ROS 17/2.8 cells. Preincubation of the C domain with TIMP-2 was found to reduce subsequent binding to TIMP-4 in a concentration-dependent manner. Competition between TIMP-2 and TIMP-4 for a common or overlapping binding sites on the gelatinase A C domain may occur; alternatively TIMP-2 may prevent the binding of TIMP-4 by steric hindrance or induction of a conformational change in the C domain. We propose that the binding of progelatinase A to TIMP-4 represents a third TIMP-progelatinase interaction in addition to that of progelatinase A with TIMP-2 and progelatinase B with TIMP-1 described previously. This new phenomenon may be of important physiological significance in modulating the cell surface activation of progelatinase A.
Handbook of Interventional Radiologic Procedures (2001)

Handbook of Interventional Radiologic Procedures, 4ed - Libros de Medicina - Radiologia General - 55,00
Human papillomavirus type 16 is an important infectious factor in the high incidence of esophageal cancer in Anyang area of China (2001)

To investigate the potential role of human papillomavirus (HPV) infection in the pathogenesis of esophageal carcinomas in the Anyang area of China, we have evaluated specimens collected by balloon cytology examination from volunteers in two regions with significantly different incidences of esophageal carcinoma. 138 donors were from a village in a county with an esophageal carcinoma (EC) age-adjusted mortality rate of 132x10(5), the remaining 68 were resident in a second village from another county with an EC mortality rate of 52x10(5). Specimens were evaluated using both polymerase chain reaction (PCR) amplification and in situ hybridization (ISH) protocols. PCR results showed that the prevalence of the human papillomavirus type 16 (HPV-16) E6 gene in the high incidence area was 1.9-fold higher than that of the low incidence area (72 and 37%, respectively, P < 0.01). Moreover, the positive rate corresponded with pathology grade. Similar results were obtained with the HPV-16 E7 gene. As the cells undergoing cytopathological progress, the HPV-16 E6 positive rate was increased, in both villages. In contrast to HPV-16 E6 and E7, detection of the HPV L1 gene was consistently lower, and its prevalence decreased with increasing dysplasia grades (P < 0.05). By ISH analyses, the expression rate of HPV-16 E6 in the specimens collected from the high incidence area was 2.2-fold higher than those from the low incidence area (49 versus 22%, respectively; P < 0.05), and transcription of the E6 gene paralleled cytopathology. HPV-18 was also detected in 17 and 15% of the specimens from the high and low incidence areas, respectively, but most of these samples were also simultaneously HVP-16 positive. These results suggest that HVP-16 plays a causative role in the high incidence of esophageal cancer in the Anyang region of CHINA:
Abstract 1957: The Carboxyterminal Telopeptide of Procollagen type I and Procollagen type III Aminoterminal Peptide (PIIINP) are Strong Predictors of Cardiovascular Morbidity and Mortality in the Elderly; The Cardiovascular Health Study (2007)

Background: The fibrillar myocardial extracellular matrix is mainly composed of type I and III fibrillar collagen and their turnover are reflected in the serum level of carboxyl-terminal propeptide type I (PIP) and procollagen type III aminoterminal peptide (PIIINP). The prognostic value of these biomarkers in elderly individuals with heart failure (HF) or other cardiovascular disease (CVD) and in healthy subjects is largely unknown. Aim: To determine the predictive value of PIP, its degradation metabolite, carboxyterminal telopeptide of procollagen type I (CTIP), and PIIINP serum level for the incident CV morbidity and mortality in a nested case control study of community-dwelling elderly individuals enrolled in the Cardiovascular Health Study (CHS). Methods: In 880 participants (ppts) enrolled in the CHS (mean age 77 ± 6 yrs, 52 % males, 79 % white), 310 with HF, 287 controls (no HF but other CVD) and 283 healthy ppts, serum levels of PIIINP, PIP and CTIP were measured by radioimmunoassay. The number of incident CV disease and death were recorded. Wilcoxon rank sum test, Kruskal-Wallis test, and Cox proportional hazards regression were used as appropriate. Results: Age, gender and race and fully adjusted analyses are presented in the table : Conclusions: In this large elderly cohort, there is a strong association between CTIP, PIIINP and incident CVD and death. Elevated CTIP level increases the risk of death more than 50% and of symptomatic PVD by almost two-fold. Whereas PIIINP has a lower predictive power than CTIP, PIP was not associated with incident CVD or death. Serum CTIP and PIIINP have a good prognostic value for both incident CVD and death in elderly individuals with or without known CV disease.
Hybrid MPI/OpenMP Parallel Programming on Clusters of Multi-Core SMP Nodes (2009)

Today most systems in high-performance computing (HPC) feature a hierarchical hardware design: Shared memory nodes with several multi-core CPUs are connected via a network infrastructure. Parallel programming must combine distributed memory parallelization on the node interconnect with shared memory parallelization inside each node. We describe potentials and challenges of the dominant programming models on hierarchically structured hardware: Pure MPI (Message Passing Interface), pure OpenMP (with distributed shared memory extensions) and hybrid MPI+OpenMP in several flavors. We pinpoint cases where a hybrid programming model can indeed be the superior solution because of reduced communication needs and memory consumption, or improved load balance. Furthermore we show that machine topology has a significant impact on performance for all parallelization strategies and that topology awareness should be built into all applications in the future. Finally we give an outlook on possible standardization goals and extensions that could make hybrid programming easier to do with performance in mind.
Limitations Arising from Optical Saturation in Fluorescence and Thermal Lens Spectrometries Using Pulsed Laser Excitation: Application to the Determination of the Fluorescence Quantum Yield of Rhodamine 6G (1996)

The high incident irradiances available with pulsed lasers can lead to a significant depletion of the ground-state population of the chromophore and to optical saturation effects. As a result, the optical absorption coefficient decreases as a function of the excitation energy and, because the amount of energy released by radiative and nonradiative relaxation processes depends on the amount of energy absorbed, nonlinear energy-dependent signals are obtained. Therefore, large errors can be introduced when fluorescence and photothermal data are used to determine fluorescence quantum yields. This work provides experimental results describing the effects of optical saturation on fluorescence and thermal lens measurements for rhodamine 6G in various media and over a wide energy range. It is shown that, when optical saturation is avoided, the photothermal method gives accurate absolute values of Φ f ranging from 0.93 to 0.95, depending on the solvent. On the contrary, fluorescence measurements seem to be sensitive to additional experimental artifacts that are more difficult to characterize and to eliminate. Index Headings: Optical saturation; Thermal lens spectrometry; Fluorescence; Rhodamine 6G; Fluorescence quantum yield.
Dependence of the Gold Nanorod Aspect Ratio on the Nature of the Directing Surfactant in Aqueous Solution (2003)

A three-step seed-mediated growth method was used to make gold nanoparticles. Different surfactants, alkyltrimethylammonium bromides (CnTAB, n = 10, 12, 14, 16, and 18) and cetylpyridinium chloride (C16PC), were chosen as stabilizers. In general, it was found that as the length of the surfactant chain increased, the resulting gold nanoparticles' aspect ratio increased: the aspect ratio was 1 (for C10TAB), 5 ± 2 (C12TAB), 17 ± 3 (C14TAB), and 23 ± 4 (C16TAB). The plasmon absorption maxima for the gold nanoparticles varied as a function of the shape, from 520 nm (spheres) to beyond 2000 nm (high aspect ratio nanorods). We propose that the surfactant binds as a bilayer to the growing nanoparticle and assists in nanoparticle elongation via a “zipping” mechanism.
An Unusual Cause of Low-Flow, Low-Gradient Severe Aortic Stenosis: Left-to-Right Shunt due to Atrial Septal Defect (2008)

Paradoxical low-flow, low-gradient severe aortic valve stenosis (AVS) may occur despite preserved left-ventricular (LV) ejection fraction in older females with marked LV concentric remodeling and small LV cavity size or in patients with coexisting severe mitral regurgitation. This report illustrates the case of a paradoxical low-flow, low-gradient severe AVS despite preserved LV function related to an ostium secundum atrial septal defect (ASD) in a patient presenting with congestive heart failure. Left-to-right shunt ASD that lowers forward LV stroke volume translating into lower transvalvular gradients is an underrecognized cause of paradoxical low-flow, low-gradient severe AVS. In addition, if not detected before open-heart surgery, ASD may result in cardiopulmonary bypass life-threatening complications.
[Expression and characterization of Huwentoxin-XI (HWTX-XI) and its mutants]. (2011)

Huwentoxin-XI (HWTX-XI) is a protein isolated from the crude venom of spider Ornithoctonus huwena. It has 55 amino acid residues containing 6 cysteine residues forming 3 disulfide bonds. It shows potent inhibitory effect on trypsin and voltage-gated potassium channels in rat dorsal root ganglion cells. According to the structure-function relationship of HWTX-XI, we designed two mutants through mutation of potassium channel inhibition related amino acid residues (R5I, R10T,R25A and R5I,R25A) and then expressed them with high purity by using the vector pVT102U on Saccharamyces cerevisiae strain S78; The two mutants had the same trypsin inhibition activity as HWTX-XI, whereas their potassium channel inhibition activity and animal toxicity were much lower than those of HWTX-XI. This study is helpful for designing drugs of trypsin related diseases based on HWTX-XI.
Overexpression of CXC Chemokines by an Adrenocortical Carcinoma: A Novel Clinical Syndrome (2001)

A patient with adrenocortical carcinoma presented with fever, leukocytosis, and increased acute phase reactants. The tumor was infiltrated with neutrophils. Immunohistochemical staining of the tumor showed positive signal for epithelial neutrophil-activating protein-78, an angiogenic and chemotactic CXC chemokine. Conditioned medium from tumor-derived cells (RL-251) showed high concentration of IL-8, epithelial neutrophil-activating protein-78, Gro alpha, and Gro gamma, angiogenic CXC chemokines with a potential role in tumorigenesis. An adrenal cancer/severe combined immunodeficiency mouse chimera was developed. Mice grew tumors rapidly, and circulating levels of IL-8 and epithelial neutrophil-activating protein-78 were detected. In contrast, animals transplanted with NCI-H295 cells, a nonchemokine-secreting cell line, grew tumors more slowly and did not have detectable chemokine levels. Similar to the patient, mice with RL-251 tumors developed marked leukocytosis and neutrophilia, and their tumors were infiltrated with neutrophils. Mice were passively immunized with epithelial neutrophil-activating protein-78 antisera. A marked decrease in tumor growth was observed. Potential for chemokine production by other adrenocortical tumors was investigated by RT-PCR in archival material. Six of seven adrenal carcinomas and one of three adenomas had cDNA for IL-8; six of seven carcinomas and the three adenomas had cDNA for epithelial neutrophil-activating protein-78. We concluded that the clinical presentation of this case resulted from increased tumor production of chemotactic chemokines. Through their angiogenic and chemotactic properties these chemokines may play an important role in adrenal tumorigenesis.