gebhart/patrepeval huggingface dataset:
Hashing practice: analysis of hashing and universal hashing (1988)

Much of the literature on hashing deals with overflow handling (collision resolution) techniques and its analysis. What does all the analytical results mean in practice and how can they be achieved with practical files? This paper considers the problem of achieving analytical performance of hashing techniques in practice with reference to successful search lengths, unsuccessful search lengths and the expected worst case performance (expected length of the longest probe sequence). There has been no previous attempt to explicitly link the analytical results to performance of real life files. Also, the previously reported experimental results deal mostly with successful search lengths. We show why the well known division method performs “well” under a specific model of selecting the test file. We formulate and justify an hypothesis that by choosing functions from a particular class of hashing functions, the analytical performance can be obtained in practice on real life files. Experimental results presented strongly support our hypothesis. Several interesting problems arising are mentioned in conclusion.
Notch receptor expression in adult human liver: A possible role in bile duct formation and hepatic neovascularization (2001)

Notch signaling is an evolutionarily conserved mechanism, used to regulate cell fate decisions. Four Notch receptors have been identified in man (Notch-1 to -4). In this study, semiquantitative reverse transcription polymerase chain reaction (RT-PCR) and immunohistochemistry were used to examine the expression pattern of Notch receptor genes in whole adult human liver and isolated liver cell preparations. All 4 receptors were expressed in the adult liver, with no significant differences in the levels of Notch-1, -2, and -4 messenger RNA (mRNA) between normal and diseased liver. However, Notch-3 expression appeared to be increased in diseased tissue. The distribution of Notch-1 and -4 in normal tissue was similar, with Notch-1 also detectable at low levels in the sinusoidal endothelium. Notch-2 expression was more widely distributed, and detectable in hepatocytes, medium-sized bile ducts, and the sinusoidal endothelium. Notch-3 expression was seen on hepatocytes, with weaker expression detectable in portal veins, hepatic arteries, and the sinusoids. In normal liver tissue Notch-1, -2, and -3 were found to be coexpressed on bile duct epithelium; however, with the exception of Notch-3 in primary sclerosing cholangitis (PSC) livers, expression was absent on proliferating ductules in all disease states examined. Interestingly, the expression of Notch-2 and -3 was associated with numerous small vessels within the portal tract septa of diseased tissue. The absence of Notch receptor expression on proliferating bile ductules and its presence on neovessels suggests that Notch signaling may be important for normal bile duct formation and the aberrant neovascularization seen in diseased liver tissue.
A chloroplast transgenic approach to hyper‐express and purify Human Serum Albumin, a protein highly susceptible to proteolytic degradation (2003)

Human Serum Albumin (HSA) accounts for 60% of the total protein in blood serum and it is the most widely used intravenous protein in a number of human therapies. HSA, however, is currently extracted only from blood because of a lack of commercially feasible recombinant expression systems. HSA is highly susceptible to proteolytic degradation in recombinant systems and is expensive to purify. Expression of HSA in transgenic chloroplasts using Shine-Dalgarno sequence (SD), which usually facilitates hyper-expression of transgenes, resulted only in 0.02% HSA in total protein (tp). Modification of HSA regulatory sequences using chloroplast untranslated regions (UTRs) resulted in hyper-expression of HSA (up to 11.1% tp), compensating for excessive proteolytic degradation. This is the highest expression of a pharmaceutical protein in transgenic plants and 500-fold greater than previous reports on HSA expression in transgenic leaves. Electron micrographs of immunogold labelled transgenic chloroplasts revealed HSA inclusion bodies, which provided a simple method for purification from other cellular proteins. HSA inclusion bodies could be readily solubilized to obtain a monomeric form using appropriate reagents. The regulatory elements used in this study should serve as a model system for enhancing expression of foreign proteins that are highly susceptible to proteolytic degradation and provide advantages in purification, when inclusion bodies are formed.
Management of hypertriglyceridemia. (2007)

Hypertriglyceridemia is associated with an increased risk of cardiovascular events and acute pancreatitis. Along with lowering low-density lipoprotein cholesterol levels and raising high-density lipoprotein cholesterol levels, lowering triglyceride levels in high-risk patients (e.g., those with cardiovascular disease or diabetes) has been associated with decreased cardiovascular morbidity and mortality. Although the management of mixed dyslipidemia is controversial, treatment should focus primarily on lowering low-density lipoprotein cholesterol levels. Secondary goals should include lowering non-high-density lipoprotein cholesterol levels (calculated by subtracting high-density lipoprotein cholesterol from total cholesterol). If serum triglyceride levels are high, lowering these levels can be effective at reaching non-high-density lipoprotein cholesterol goals. Initially, patients with hypertriglyceridemia should be counseled about therapeutic lifestyle changes (e.g., healthy diet, regular exercise, tobacco-use cessation). Patients also should be screened for metabolic syndrome and other acquired or secondary causes. Patients with borderline-high serum triglyceride levels (i.e., 150 to 199 mg per dL [1.70 to 2.25 mmol per L]) and high serum triglyceride levels (i.e., 200 to 499 mg per dL [2.26 to 5.64 mmol per L]) require an overall cardiac risk assessment. Treatment of very high triglyceride levels (i.e., 500 mg per dL [5.65 mmol per L] or higher) is aimed at reducing the risk of acute pancreatitis. Statins, fibrates, niacin, and fish oil (alone or in various combinations) are effective when pharmacotherapy is indicated.
Naphthalene Combretastatin Analogues — Synthesis, Cytotoxicity and Antitubulin Activity (2005)

Abstract For Abstract see ChemInform Abstract in Full Text.
Myc-Transformed Epithelial Cells Down-Regulate Clusterin, Which Inhibits Their Growth in Vitro and Carcinogenesis in Vivo (2004)

Effective treatment of malignant carcinomas requires identification of proteins regulating epithelial cell proliferation. To this end, we compared gene expression profiles in murine colonocytes and their c-Myc-transformed counterparts, which possess enhanced proliferative potential. A surprisingly short list of deregulated genes included the cDNA for clusterin, an extracellular glycoprotein without a firmly established function. We had previously demonstrated that in organs such as skin, clusterin expression is restricted to differentiating but not proliferating cell layers, suggesting a possible negative role in cell division. Indeed, its transient overexpression in Myc-transduced colonocytes decreased cell accumulation. Furthermore, clusterin was down-regulated in rapidly dividing human keratinocytes infected with a Myc-encoding adenovirus. Its knockdown via antisense RNA in neoplastic epidermoid cells enhanced proliferation. Finally, recombinant human clusterin suppressed, in a dose-dependent manner, DNA replication in keratinocytes and other cells of epithelial origin. Thus, clusterin appears to be an inhibitor of epithelial cell proliferation in vitro. To determine whether it also affects neoplastic growth in vivo, we compared wild-type and clusterin-null mice with respect to their sensitivity to 7, 12-dimethylbenz(a)anthracene /12-Otetradecanoylphorbol-13-acetate (DMBA/TPA)-induced skin carcinogenesis. We observed that the mean number of papillomas/mouse was higher in clusterin-null animals. Moreover, these papillomas did not regress as readily as in wild-type mice and persisted beyond week 35. The rate of progression toward squamous cell carcinoma was not altered, although those developing in clusterin-null mice were on average better differentiated. These data suggest that clusterin not only suppresses epithelial cell proliferation in vitro but also interferes with the promotion stage of skin carcinogenesis.
CPP1, a DNA-binding protein involved in the expression of a soybean leghemoglobin c3 gene (2000)

Nodulin genes are specifically expressed in the nitrogen-fixing root nodules. We have identified a novel type of DNA-binding protein (CPP1) interacting with the promoter of the soybean leghemoglobin gene Gmlbc3. The DNA-binding domain of CPP1 contains two similar Cys-rich domains with 9 and 10 Cys, respectively. Genes encoding similar domains have been identified in Arabidopsis thaliana, Caenorhabditis elegans, the mouse, and human. The domains also have some homology to a Cys-rich region present in some polycomb proteins. The cpp1 gene is induced late in nodule development and the expression is confined to the distal part of the central infected tissue of the nodule. A constitutively expressed cpp1 gene reduces the expression of a Gmlbc3 promoter-gusA reporter construct in Vicia hirsuta roots. These data therefore suggest that CPP1 might be involved in the regulation of the leghemoglobin genes in the symbiotic root nodule.
EEG Signal Processing (2007)

Electroencephalograms (EEGs) are becoming increasingly important measurements of brain activity and they have great potential for the diagnosis and treatment of mental and brain diseases and abnormalities. With appropriate interpretation methods they are emerging as a key methodology to satisfy the increasing global demand for more affordable and effective clinical and healthcare services. Developing and understanding advanced signal processing techniques for the analysis of EEG signals is crucial in the area of biomedical research. This book focuses on these techniques, providing expansive coverage of algorithms and tools from the field of digital signal processing. It discusses their applications to medical data, using graphs and topographic images to show simulation results that assess the efficacy of the methods. Additionally, expect to find: explanations of the significance of EEG signal analysis and processing (with examples) and a useful theoretical and mathematical background for the analysis and processing of EEG signals; an exploration of normal and abnormal EEGs, neurological symptoms and diagnostic information, and representations of the EEGs; reviews of theoretical approaches in EEG modelling, such as restoration, enhancement, segmentation, and the removal of different internal and external artefacts from the EEG and ERP (event-related potential) signals; coverage of major abnormalities such as seizure, and mental illnesses such as dementia, schizophrenia, and Alzheimer's disease, together with their mathematical interpretations from the EEG and ERP signals and sleep phenomenon; descriptions of nonlinear and adaptive digital signal processing techniques for abnormality detection, source localization and brain-computer interfacing using multi-channel EEG data with emphasis on non-invasive techniques, together with future topics for research in the area of EEG signal processing. © 2007 by John Wiley &amp; Sons Ltd,. All Rights Reserved.
Cytokeratin 20 and guanylyl cyclase C mRNA is largely present in lymph node and liver specimens of colorectal cancer patients (2003)

The aim of our prospective study was to detect circulating epithelial cells (CEC) indicating the presence of disseminated tumor cells (DTC) in tissues affected by lymphatic and hematogenic colorectal cancer metastasis. DTC were tracked in lymph node, liver or bone marrow samples of 245 colorectal cancer patients using 2 independent RT-PCR assays for cytokeratin 20 (CK20) and guanylylcyclase C (GCC) that demonstrated a sensitivity of 1 colorectal cancer cell in 10(6) nucleated hematopoietic cells. CK20 mRNA was detected in 79% of lymph nodes, 35% of both liver lobes and 11% of bone marrow samples. GCC mRNA was found in 68% of lymph nodes, 60% of both liver lobes and 6% of bone marrow specimens. Both markers were recorded in 63% of lymph nodes, 45% of at least 1 liver lobe and 1% of bone marrow samples. There was no significant difference when comparing lymph node samples tested positive for both markers in patients with (N1/2; 65%) and without (N0; 56%) nodal involvement. The same was true when comparing the percentages of patients with and without clinically overt distant metastasis who were positive for both markers in at least 1 liver lobe (62% vs. 41%) or in bone marrow (4% vs. 0%). A score denoting the cumulative sum of tests indicating presence of CK20 and GCC mRNA in the liver was significantly related with UICC classification (p = 0.039). However, addition of lymph node results to this score decreased the correlation. The high incidence of clinically inconspicuous lymph node and liver samples tested positive for both markers emphasizes the function of these organs as primary filters for epithelial cells possibly shed from colorectal carcinomas. The potential prognostic significance of these findings warrants verification, especially regarding the importance of CEC or DTC resident in the liver of colorectal cancer patients.
The Limitations of Deep Learning in Adversarial Settings (2016)

Deep learning takes advantage of large datasets and computationally efficient training algorithms to outperform other approaches at various machine learning tasks. However, imperfections in the training phase of deep neural networks make them vulnerable to adversarial samples: inputs crafted by adversaries with the intent of causing deep neural networks to misclassify. In this work, we formalize the space of adversaries against deep neural networks (DNNs) and introduce a novel class of algorithms to craft adversarial samples based on a precise understanding of the mapping between inputs and outputs of DNNs. In an application to computer vision, we show that our algorithms can reliably produce samples correctly classified by human subjects but misclassified in specific targets by a DNN with a 97% adversarial success rate while only modifying on average 4.02% of the input features per sample. We then evaluate the vulnerability of different sample classes to adversarial perturbations by defining a hardness measure. Finally, we describe preliminary work outlining defenses against adversarial samples by defining a predictive measure of distance between a benign input and a target classification.
Integrated Micro/Nano Fluidics for Mass-spectrometry Protein Analysis (2002)

Article Integrated Micro/Nano Fluidics for Mass-spectrometry Protein Analysis was published on December 1, 2002 in the journal International Journal of Nonlinear Sciences and Numerical Simulation (volume 3, issue 3-4).
Crystallographic Investigation and Selective Inhibition of Mutant Isocitrate Dehydrogenase (2013)

Mutations in isocitrate dehydrogenase (IDH), a key enzyme in the tricarboxylic acid cycle, have recently been found in ~75% glioma and ~20% acute myeloid leukemia. Different from the wild-type enzyme, mutant IDH1 catalyzes the reduction of α-ketoglutaric acid to <i>D</i>-2-hydroxyglutaric acid. Strong evidence has shown mutant IDH1 represents a novel target for this type of cancer. We found two 1-hydroxypyridin-2-one compounds that are potent inhibitors of R132H and R132C IDH1 mutants with K<sub>i</sub> values as low as 120 nM. These compounds exhibit >60-fold selectivity against wild-type IDH1 and can inhibit the production of <i>D</i>-2-hydroxyglutaric acid in IDH1 mutated cells, representing novel chemical probes for cancer biology studies. We also report the first inhibitor-bound crystal structures of IDH1(R132H), showing these inhibitors have H-bond, electrostatic and hydrophobic interactions with the mutant enzyme. Comparison with the substrate-bound IDH1 structures revealed the structural basis for the high enzyme selectivity of these compounds.
Two regions of homozygosity on chromosome 3p in squamous cell carcinoma of the head and neck: Comparison with cytogenetic analysis (1996)

These experiments support cytogenetic data that indicate two regions of 3p loss in SCCHN tumors. The 3p regions that show a high frequency of homozygosity may contain tumor suppressor genes involved in the development and/or progression of squamous cancer. The region surrounding D3S32 may contain an essential gene that is conserved in two copies even when much of 3p is lost.
Sequence context outside the target region influences the effectiveness of miR-223 target sites in the RhoB 3′UTR (2009)

MicroRNAs (miRNAs) are 21-22 nucleotide regulatory small RNAs that repress message translation via base-pairing with complementary sequences in the 3' untranslated region (3'UTR) of targeted transcripts. To date, it is still difficult to find a true miRNA target due to lack of a clear understanding of how miRNAs functionally interact with their targeted transcripts for efficient repression. Previous studies have shown that nucleotides 2 to 7 at the 5'-end of a mature miRNA, the 'seed sequence', can nucleate miRNA/target interactions. In the current study, we have validated that the RhoB mRNA is a bona fide miR-223 target. We have analyzed the functional activities of two miR223-binding sites within the RhoB 3'UTR. We find that the two miR-223 target sites in the RhoB 3'UTR contribute differentially to the total repression of RhoB translation. Moreover, we demonstrate that some AU-rich motifs located upstream of the distal miRNA-binding site enhance miRNA function, independent of the miRNA target sequences being tested. We also demonstrate that the AU-rich sequence elements are polar, and do not affect the activities of miRNAs whose sites lie upstream of these elements. These studies provide further support for the role of sequences outside of miRNA target region influencing miRNA function.
Growing Group of Extended-Spectrum β-Lactamases: the CTX-M Enzymes (2003)

The production of β-lactamases is the predominant cause of resistance to β-lactam antibiotics in gram-negative bacteria. These enzymes cleave the amide bond in the β-lactam ring, rendering β-lactam antibiotics harmless to bacteria. They are classified according to the scheme of Ambler et al. (2) into four classes, designated classes A to D, on the basis of their amino acid sequences, with classes A and C being the most frequently occurring among bacteria. Oxyimino-cephalosporins such as cefotaxime and ceftazidime, which are inherently less susceptible to β-lactamases, were introduced in the early 1980s to treat infections caused by gram-negative bacilli that were resistant to established β-lactams and that produced class A, C, and D β-lactamases. Their repetitive and increased use induced the appearance of resistant strains, which overproduced class C enzymes (42, 72) and/or which produced extended-spectrum β-lactamases (ESBLs), mainly those of class A but also those of class D (19, 61).

Class A ESBLs hydrolyze oxyimino-cephalosporins and aztreonam but not 7-α-substituted β-lactams. They are generally susceptible to β-lactamase inhibitors (clavulanate, sulbactam, tazobactam). According to the functional classification scheme of Bush et al. (23), class A ESBLs are therefore clustered in group 2be, which can be subdivided on the basis of their activities against ceftazidime and cefotaxime as ceftazidimases (higher levels of hydrolytic activity against ceftazidime than against cefotaxime) and cefotaximases (higher levels of hydrolytic activity against cefotaxime than against ceftazidime), respectively (48).

However, class A ESBLs form a heterogeneous molecular cluster comprising β-lactamases sharing 20 to >99% identity. The earliest class A ESBLs, which were reported from 1985 to 1987, differed from widespread plasmid-mediated TEM-1/2 and SHV-1 penicillinases by one to four point mutations, which extend their hydrolytic spectra (51, 90, 91). TEM and SVH ESBLs now comprise at least 130 members and have a worldwide distribution. Most of them are ceftazidimases, and only a few are cefotaximases.

More recently, non-TEM and non-SHV plasmid-mediated class A ESBLs have been reported: ceftazidimases of the PER, VEB, TLA-1, and GES/IBC types and cefotaximases of the SFO-1, BES-1, and CTX-M types (8, 12, 13, 16, 31, 58, 62, 75, 76, 79, 81, 88, 96). The CTX-M β-lactamases are the most widespread enzymes. They were initially reported in the second half of the 1980s, and their rate of dissemination among bacteria and in most parts of the world has increased dramatically since 1995. This review focuses on the origin, epidemiology, clinical impact, enzymatic properties, and structural relationships of the CTX-M-type ESBLs.
Introduction to the Dossier Report (2005)

Maintaining the perspective of being a reference point for the international scientifi c community in the journalism research and related areas and for the public that reads works of researchers from Brazil and other countries, number 2 of the Brazilian Journalism Research presents the second part of the Dossier Report on journalism research in Brazil.We should keep in mind that the Dossier´s purpose is to present regularly articles that off er panoramic readings which, validated by strict methodological procedures, deal with varied aspects of studies of the press or of journalism research, always from a historical perspective, so that the very sequence of the Dossiers represents, as time goes by, a kind of living fi le of scientifi c journalism research conducted by Brazilian research institutions, as well as by those in other countries, focusing on the intention of the contextual reading.
Modulation of gene expression rather than monoamine oxidase inhibition (1996)

(-)-Deprenyl has been used to irreversibly inhibit monoamine oxidase B (MAO-B) in Parkinson's disease (PD) and Alzheimer's disease (AD) as a possible means of improving dopaminergic neurotransmission or of reducing neuronal necrosis caused by oxidative radical damage. Recent research in tissue culture and animal models has shown that (-)-deprenyl can reduce neuronal apoptosis caused by a variety of agents, in a variety of neuronal subtypes through a mechanism(s) that does not require MAO-B inhibition. Studies using general P450 blockers have shown that one of the principal metabolites of (-)-deprenyl, (-)-desmethyldeprenyl, mediates the antiapoptotic action. Other research has shown that (-)-deprenyl can induce altered expression of a number of genes in preapoptotic neurons both in vitro and in vivo, including the genes for superoxide dismutase (SOD) 1 and 2, BCL-2 and BCL-XL, nitric oxide synthase, c-JUN, and nicotinamide adenine dinucleotide dehydrogenase. Antiapoptosis by (-)-deprenyl is associated with a prevention of a progressive reduction of mitochondrial membrane potential in preapoptotic neurons, which has been shown to occur early in apoptosis and is likely an initiating factor. The above changes in gene expression appear to reduce oxidative radical damage to mitochondria and maintain mitochondrial permeability, thereby blocking mitochondrial "signals" that initiate apoptosis. In situ evidence suggests that apoptosis contributes to neuronal death in a number of neurodegenerative diseases. If apoptosis is critical to the progression of one or more human neurodegenerative diseases, then transcriptionally active agents such as (-)-desmethyldeprenyl may be of value in treating the diseases. The kinetics of (-)-deprenyl metabolism, however, and its biodistribution after oral administration, make it unlikely that the antiapoptotic action has played a major role in benefits found for the drug in PD and AD to date.