gebhart/patrepeval huggingface dataset:
Highly Parallel SNP Genotyping (2003)

The genetic factors underlying common disease arelargely unknown. Discovery of disease-causing genes willtransform our knowledge of the genetic contribution tohuman disease, lead to new genetic screens, and underpinresearch into new cures and improved lifestyles. The sequencing of the human genome has catalyzed efforts tosearch for disease genes by the strategy of associating sequence variants with measurable phenotypes. In particular, the Human Genome Project and follow-on efforts tocharacterize genetic variation have resulted in the discovery of millions of single-nucleotide polymorphisms(SNPs) (Patil et al. 2001; Sachidanandam et al. 2001;Reich et al. 2003). This represents a significant fraction ofcommon genetic variation in the human genome and creates an unprecedented opportunity to associate genes withphenotypes via large-scale SNP genotyping studies...
Randomizing Social Networks: a Spectrum Preserving Approach (2008)

Understanding the general properties of real social networks has gained much attention due to the proliferation of networked data. The nodes in the network are the individuals and the links among them denote their relationships. Many applications of networks such as anonymous Web browsing require relationship anonymity due to the sensitive, stigmatizing, or confidential nature of the relationship. One general approach for this problem is to randomize the edges in true networks, and only disclose the randomized networks. In this paper, we investigate how various properties of networks may be affected due to randomization. Specifically, we focus on the spectrum since the eigenvalues of a network are intimately connected to many important topological features. We also conduct theoretical analysis on the extent to which edge anonymity can be achieved. A spectrum preserving graph randomization method, which can better preserve network properties while protecting edge anonymity, is then presented and empirically evaluated.
The Combi-Targeting Concept:  Chemical Dissection of the Dual Targeting Properties of a Series of “Combi-Triazenes” (2003)

The combi-targeting concept postulates that a molecule termed a "combi-molecule" designed to interact with an oncoreceptor on its own and allowed to further degrade to another more stable inhibitor of the latter receptor + a DNA-damaging species should be more potent than the individual combination of the same inhibitor with a DNA-damaging agent in cells expressing the targeted receptor. Recently, using the epidermal growth factor receptor (EGFR) as a target, we demonstrated the feasibility of combi-molecules with dual EGFR/DNA-targeting properties and with the ability to degrade to another potent inhibitor of EGFR. However, despite a clear demonstration of their superior potency when compared with classical combinations in EGFR-expressing cells, the true contribution of each fragment of the combi-molecules to their overall antiproliferative activity remained elusive. Here, we report a structure-function approach whereby a series of quinazoline-based "combi-triazenes" were altered to either abrogate the affinity of the EGFR-targeting quinazoline head or to suppress the DNA-damaging property of the triazene tail. The results showed that (a) inactivation of the quinazoline head by appending an N-methylaniline group to its 4-position reduced EGFR tyrosine kinase (TK) inhibitory activity by ca. 200-fold and decreased the ability of the combi-molecule to block serum-induced growth stimulation in c-erbB2 transfected NIH3T3 cells by ca. 10-fold, (b) abrogation of the alkylating activity or the DNA-damaging potential of the triazene tail by forming 3,3-dimethyltriazenes did not suppress EGFR TK inhibitory affinity but decreased the antiproliferative activity in basal growth assays, and (c) the antiproliferative activities of the monoalkyltriazenes that possessed binary EGFR TK inhibitory and alkylating activities were superior to those of their monotargeted counterparts. The results in toto suggest that each component of the dual targeting property of combi-triazenes plays a critical role in their overall antiproliferative activity.
Life after the White Paper (1989)

This paper reviews the contents of the White Paper — the NHS Review, ‘Working for Patients’ published in January 1989’ — and the initial reactions to it. It is easy to fault the White Paper for its unevenness and incompleteness. On the other hand, just because it leaves so many loose‐ends and is non‐prescriptive in detail, there is scope to fashion what happens next in an experimental, evolutionary way. The author seeks to move the debate on from analysis of the document's strengths and weaknesses to consideration of what those who care about the British National Health Service can do to shape the future that the White Paper has begun to create.
Cloning of a novel alpha 2,3-sialyltransferase that sialylates glycoprotein and glycolipid carbohydrate groups. (1994)

Sialyltransferases are a family of 10-12 enzymes that catalyze the transfer of sialic acid to carbohydrate groups of glycoproteins and glycolipids. Three sialyltransferase cDNAs have been cloned, revealing a highly conserved sialylmotif in the catalytic domain of these enzymes. Using a polymerase chain reaction-based approach, we cloned a 150-base pair fragment of a new sialymotif from human placenta mRNA, which was then used as a probe to clone the complete coding sequence of the corresponding gene from a cDNA library. Like the other members of the sialyltransferase gene family cloned to date, the new cDNA coded for a protein predicted to have an NH2-terminal signal-anchor sequence and had the sialylmotif located in the center of the molecule. Comparison with the three other cloned sialyltransferases revealed extensive sequence homology that was not recognized earlier. Expression of a soluble recombinant form of the protein in COS-1 cells produced an active sialyltransferase, which used oligosaccharide, glycoprotein, and glycolipid acceptor substrates with terminal galactose in the Gal beta 1,3GalNAc and Gal beta 1, 4GlcNAc sequences but not the Gal beta 1,3GlcNAc sequence. The sialylated products were sensitive to digestion with the Newcastle disease virus sialidase, which is specific for sialic acid-galactose linkages in the alpha 2,3 linkage. The results suggest that this new member of the sialyltransferase gene family is the enzyme previously described as a glycolipid sialyltransferase activity (SAT-3), which forms the terminal sequences NeuAc alpha-2,3Gal beta 1,3GalNAc-R and NeuAc alpha 2,3Gal beta 1, 4GlcNAc-R.
Comparative efficiency of forming m4T.cntdot.G versus m4T.cntdot.A base pairs at a unique site by use of Escherichia coli DNA polymerase I (Klenow fragment) and Drosophila melanogaster polymerase .alpha.-primase complex (1990)

Synthesis of a 25-mer oligonucleotide template containing O4-methylthymine (m4T) at a unique site is reported. The sequence used is analogous to that studied previously to determine the mutation frequency of O6-methylguanine in vitro and in vivo. The templates containing m4T or unmodified T were used in a primer-extension gel assay to determine kinetic parameters for incorporation by DNA polymerases of dGTP and dATP opposite either m4T or T. Both Escherichia coli DNA polymerase I (Klenow fragment, Kf) and Drosophila melanogaster polymerase alpha-primase complex (pol alpha) were used. On the basis of the Vmax/Km ratios, the pairing of m4T.G was preferred over that of both m4T.A and T.G by more than 10-fold. The two polymerases gave almost identical values for the frequency of formation of all pairs investigated including m4T.G pairs, suggesting that the 3'----5' exonuclease activity of the Klenow fragment does not efficiently edit such pairs. Extension beyond m4T.G was demonstrated with both Klenow and pol alpha. In similar kinetic experiments, bacteriophage T4 DNA polymerase, which has a very high 3'----5' exonuclease activity, allows stable incorporation of G opposite m4T in contrast to G opposite T. This kinetic approach allows quantitation of the mutagenic potential in the absence of alkylation repair and additionally provides qualitative data on mutagenesis that are in accord with our previous in vivo studies showing that replication of m4T causes T----C transitions.
PCR-Based DNA Amplification and Presumptive Detection ofEscherichia coliO157:H7 with an Internal Fluorogenic Probe and the 5′ Nuclease (TaqMan) Assay (1998)

Presumptive identification of Escherichia coli O157:H7 is possible in an individual, nonmultiplexed PCR if the reaction targets the enterohemorrhagic E. coli (EHEC) eaeA gene. In this report, we describe the development and evaluation of the sensitivity and specificity of a PCR-based 5' nuclease assay for presumptively detecting E. coli O157:H7 DNA. The specificity of the eaeA-based 5' nuclease assay system was sufficient to correctly identify all E. coli O157:H7 strains evaluated, mirroring the previously described specificity of the PCR primers. The SZ-primed, eaeA-targeted 5' nuclease detection assay was capable of rapid, semiautomated, presumptive detection of E. coli O157:H7 when >/=10(3) CFU/ml was present in modified tryptic soy broth (mTSB) or modified E. coli broth and when >/=10(4) CFU/ml was present in ground beef-mTSB mixtures. Incorporating an immunomagnetic separation (IMS) step, followed by a secondary enrichment culturing step and DNA recovery with a QIAamp tissue kit (Qiagen), improved the detection threshold to >/=10(2) CFU/ml. Surprisingly, immediately after IMS, the sensitivity of culturing on sorbitol MacConkey agar containing cefeximine and tellurite (CT-SMAC) was such that identifiable colonies were demonstrated only when >/=10(4) CFU/ml was present in the sample. Several factors that might be involved in creating these false-negative CT-SMAC culture results are discussed. The SZ-primed, eaeA-targeted 5' nuclease detection system demonstrated that it can be integrated readily into standard culturing procedures and that the assay can be useful as a rapid, automatable process for the presumptive identification of E. coli O157:H7 in ground beef and potentially in other food and environmental samples.
Molecular Cloning, Sequence Analysis, and Chromosomal Localization of the Human Protease Inhibitor 4 (Kallistatin) Gene (PI4) (1994)

The gene encoding human protease inhibitor 4 (kallistatin; gene symbol PI4), a novel serine proteinase inhibitor (serpin), has been isolated and completely sequenced. The kallistatin gene is 9618 bp in length and contains five exons and four introns. The structure and organization of the kallistatin gene are similar to those of the genes encoding alpha 1-antichymotrypsin, protein C inhibitor, and alpha 1-antitrypsin. The kallistatin gene is also similar to the genes encoding rat and mouse kallikrein-binding proteins. The first exon of the kallistatin gene is a noncoding 89-bp fragment, as determined by primer extension. The fifth exon, which contains 308 bp of noncoding sequence, encodes the reactive center of kallistatin. In the 5'-flanking region of the kallistatin gene, 1125 bp have been sequenced and a consensus promoter segment with potential transcription regulatory sites, including CAAT and TATA boxes, an AP-2 binding site, a GC-rich region, a cAMP response element, and an AP-1 binding site, has been identified within this region. The kallistatin gene was localized by in situ hybridization to human chromosome 14q31-q32.1, close to the serpin genes encoding alpha 1-antichymotrypsin, protein C inhibitor, alpha 1-antitrypsin, and corticosteroid-binding globulin. In a genomic DNA Southern blot, kallistatin-related genes were identified in monkey, mouse, rat, bovine, dog, cat, and a ground mole. The patterns of hybridization revealed clues of human serpin evolution.
Functional expression of Escherichia coli enzymes synthesizing GDP-L-fucose from inherent GDP-D-mannose in Saccharomyces cerevisiae (2000)

Fucosylation of glycans on glycoproteins and -lipids requires the enzymatic activity of relevant fucosyltransferases and GDP-L-fucose as the donor. Due to the biological importance of fucosylated glycans, a readily accessible source of GDP-L-fucose would be required. Here we describe the construction of a stable recombinant S.cerevisiae strain expressing the E.coli genes gmd and wcaG encoding the two enzymes, GDP-mannose-4,6-dehydratase (GMD) and GDP-4-keto-6-deoxy-D-mannose-3,5-epimerase/4-reductase (GMER(FX)) respectively, needed to convert GDP-mannose to GDP-fucose via the de novo pathway. Taking advantage of the rich inherent cytosolic GDP-mannose pool in S.cerevisiae cells we could easily produce 0.2 mg/l of GDP-L-fucose with this recombinant yeast strain without addition of any external GDP-mannose. The GDP-L-fucose product could be used as the fucose donor for alpha1,3fucosyltransferase to synthesize sialyl Lewis x (sLex), a glycan crucial for the selectin-dependent leukocyte traffic.
Randomized Trial of the Effect of the Low Molecular Weight Heparin Nadroparin on Survival in Patients With Cancer (2011)

This study did not show a survival benefit of nadroparin in patients with advanced prostate, lung, or pancreatic cancer. Given the ongoing studies in this area and the previous data, the role of low molecular weight heparins in cancer survival remains undefined.
Comparative Analysis of Different Vaccine Constructs Expressing Defined Antigens fromMycobacterium tuberculosis (2004)

These results clearly demonstrate the importance of assessing vaccine function by use of multiple parameters and indicate which parameters are most reliable for assessing vaccine efficacy.
In silico analysis of the relation between conventional and high‐power short‐duration RF ablation settings and resulting lesion metrics (2020)

The findings support the clinical use of contact forces within a 10 to 20 g range. AI is more sensitive to RF duration, whereas LSI is more sensitive to contact force. HPSD RF settings can successfully be derived from lesion metric indices.
Leukotrienes and Other Products of the 5-Lipoxygenase Pathway (1990)

THE slow-reacting substance of anaphylaxis was recognized as a discrete biologic entity 1 , 2 three to four decades before it was chemically defined as three specific cysteinyl leukotriene products of the 5-lipoxygenase pathway.3 4 5 6 7 In the interim, it was hypothesized that this moiety might function as a proinflammatory mediator of bronchoconstriction and vasopermeability in diseases of immediate hypersensitivity.8 9 10 11 Since the chemical characterization of the slow-reacting substance of anaphylaxis as several cysteinyl leukotrienes and the identification and biochemical assessment of the enzymes in the 5-lipoxygenase pathway (Fig. 1 and Glossary), the products of this pathway have been implicated in a much broader variety of functions . . .
Pharmacological characterization of mouse GPRC6A, an L‐α‐amino‐acid receptor modulated by divalent cations (2007)

This is the first reported assay for a wild-type GPRC6A successfully applied for quantitative pharmacological characterization of amino acid and divalent cation responses at mouse GPRC6A. The assay enables further search for GPRC6A ligands such as allosteric modulators, which may provide essential information about the physiological function of GPRC6A.
Organic synthesis in a modular robotic system driven by a chemical programming language (2018)

The synthesis of complex organic compounds is largely a manual process that is often incompletely documented. To address these shortcomings, we developed an abstraction that maps commonly reported methodological instructions into discrete steps amenable to automation. These unit operations were implemented in a modular robotic platform by using a chemical programming language that formalizes and controls the assembly of the molecules. We validated the concept by directing the automated system to synthesize three pharmaceutical compounds, diphenhydramine hydrochloride, rufinamide, and sildenafil, without any human intervention. Yields and purities of products and intermediates were comparable to or better than those achieved manually. The syntheses are captured as digital code that can be published, versioned, and transferred flexibly between platforms with no modification, thereby greatly enhancing reproducibility and reliable access to complex molecules.
Asthma Therapy with Aerosols: Clinical Relevance for the Next Decade (1996)

Inhaled therapy is the mainstay of modern asthma management, as this optimizes the therapeutic ratio. Short-acting beta 2-agonists are the most effective bronchodilators and when given by inhalation give rapid relief of symptoms, without adverse effects, although there are concerns about overuse of these drugs. Inhaled long-acting beta 2-agonists are useful in some patients. Inhaled anticholinergics are particularly useful in patients with COPD and in the future long-acting drugs, such as tiotropium bromide, will be available. Inhaled glucocorticoids are the most effective therapy in controlling chronic asthma symptoms, and systemic effects are not a problem in the vast majority of patients. Improved inhalation devices and steroids with reduced oral bioavailability have resulted in reduced systemic side effects, which now arise largely from absorption from the lungs. In the future it is likely that new classes of drug will be developed, but whether they will be used by inhalation or given by mouth will depend on the frequency of side effects and the mode of action of the drugs. There are likely to be several improvements in inhaler delivery systems, so that the inhaled route will remain predominant for many years to come.
Targeting Nrf2 with the triterpenoid CDDO- imidazolide attenuates cigarette smoke-induced emphysema and cardiac dysfunction in mice (2008)

Chronic obstructive pulmonary disease (COPD), which comprises emphysema and chronic bronchitis resulting from prolonged exposure to cigarette smoke (CS), is a major public health burden with no effective treatment. Emphysema is also associated with pulmonary hypertension, which can progress to right ventricular failure, an important cause of morbidity and mortality among patients with COPD. Nuclear erythroid 2 p45 related factor-2 (Nrf2) is a redox-sensitive transcription factor that up-regulates a battery of antioxidative genes and cytoprotective enzymes that constitute the defense against oxidative stress. Recently, it has been shown that patients with advanced COPD have a decline in expression of the Nrf2 pathway in lungs, suggesting that loss of this antioxidative protective response is a key factor in the pathophysiological progression of emphysema. Furthermore, genetic disruption of Nrf2 in mice causes early-onset and severe emphysema. The present study evaluated whether the strategy of activation of Nrf2 and its downstream network of cytoprotective genes with a small molecule would attenuate CS-induced oxidative stress and emphysema. Nrf2(+/+) and Nrf2(-/-) mice were fed a diet containing the potent Nrf2 activator, 1-[2-cyano-3-,12-dioxooleana-1,9(11)-dien-28-oyl]imidazole (CDDO-Im), while being exposed to CS for 6 months. CDDO-Im significantly reduced lung oxidative stress, alveolar cell apoptosis, alveolar destruction, and pulmonary hypertension in Nrf2(+/+) mice caused by chronic exposure to CS. This protection from CS-induced emphysema depended on Nrf2, as Nrf2(-/-) mice failed to show significant reduction in alveolar cell apoptosis and alveolar destruction after treatment with CDDO-Im. These results suggest that targeting the Nrf2 pathway during the etiopathogenesis of emphysema may represent an important approach for prophylaxis against COPD.
Detection of Porcine Circovirus from Lesions of a Pig with Wasting Disease in Japan. (1999)

A wasting disease characterized by progressive weight loss and dyspnea has been observed in weaning pigs on a farm in Yamagata Prefecture in 1998. Histopathologic findings in an affected pig were bronchointerstitial pneumonia and intracytoplasmic clusters of basophilic inclusions in macrophages of lymph nodes, which were similar to those in pigs with postweaning multisystemic wasting syndrome (PMWS) recently reported in North America and Europe. Porcine circovirus (PCV)-like particles were observed in bronchial lymph node of the pig by electron microscopy, and PCV antigens were detected in the lesions by immunohistochemical staining. PCV DNA was also detected in the lung and tonsil by PCR, and restriction fragment length polymorphism analysis of the PCR products with HinfI showed the same type of the PCV associated with PMWS (pmws PCV). Homology of nucleotide sequences between the PCR product and corresponding regions of published pmws PCV genomes was very high. These results indicated that virus detected in this study was pmws PCV. To our knowledge, this is the first report on the presence of pmws PCV in Japan.
Efficient CRISPR-mediated mutagenesis in primary immune cells using CrispRGold and a C57BL/6 Cas9 transgenic mouse line (2016)

Applying clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR associated protein 9 (Cas9)-mediated mutagenesis to primary mouse immune cells, we used high-fidelity single guide RNAs (sgRNAs) designed with an sgRNA design tool (CrispRGold) to target genes in primary B cells, T cells, and macrophages isolated from a Cas9 transgenic mouse line. Using this system, we achieved an average knockout efficiency of 80% in B cells. On this basis, we established a robust small-scale CRISPR-mediated screen in these cells and identified genes essential for B-cell activation and plasma cell differentiation. This screening system does not require deep sequencing and may serve as a precedent for the application of CRISPR/Cas9 to primary mouse cells.
Magnetically mediated hyperthermia: current status and future directions (2002)

The use of hyperthermia in the treatment of cancers is appealing because, as a physical therapy, hyperthermia would have far fewer restrictive side effects than chemotherapy and radiotherapy, and it could be used in combination with these therapies. However, the currently available modalities of hyperthermia are often limited by their inability to selectively target tumour tissue and, hence, they carry a high risk of collateral organ damage or they deposit heat in a very localized manner which can result in under-treatment of a tumour. Magnetically mediated hyperthermia (MMH) has the potential to address these shortcomings. MMH consists of the localization of magnetic particles or seeds within tumour tissue followed by exposure to an externally applied alternating magnetic field to cause them to heat. Since this concept was introduced (over 40 years ago), MMH has evolved into four general sub-classes: arterial embolization hyperthermia (AEH), direct injection hyperthermia (DIH), intracellular hyperthermia (IH) and interstitial implant hyperthermia (IIH). It is the purpose of this article to review these four sub-classes in terms of experimental or clinical results, advantages, limitations and current status.