gebhart/patrepeval huggingface dataset:
Handbook of Record Linkage: Methods for Health and Statistical Studies, Administration, and Business. (1989)

Introduction. Part 1 The basics and their application: including probabilistic linkage, betting odds and frequency ratios, using global and specific discriminating powers. Part 2 Exploiting more of the discriminating power: including what to do with missing identifiers, comparing names, years of birth, places of birth, geographical identifiers and marital status, linked and unlinkable pairs, some pitfalls. Part 3 Saving central processor time: including blocking the files, the preliminary rejections, the comparison sequence and its early cut-off, the application of value-specific discriminating powers. Part 4 Organizing the product: including calculating absolute versus relative odds, setting an optimum threshold, grouping the matched pairs. Part 5 Recapitulation and further thoughts. Appendices: A - definitions. B - derivations. C - typical identifier frequencies. D - linking special disease registers. E - errors, their sources and magnitudes. F - calculating the outcome frequencies for a non-existent file of unlinkable pairs. G - constructing a file of randomly matched unlinkable pairs. H - details of phonetic coding systems for names. I - design of a computer linkage system. Bibliography. Index.
CRISPR‐Cas Systems and Cas Protein Families (2013)

This chapter presents an overview of all proteins families related to the Clustered regularly interspaced short palindrome repeats (CRISPR)-CRISPR-associated (Cas) systems, with particular emphasis on their characteristic domains and domain architectures, and briefly discusses the functional and evolutionary implications. By far the most common domain in Cas proteins is the RNA recognition motif (RRM). The RRM domains show remarkable diversity within the CRISPR-Cas systems and in particular comprise the scaffold of the Cascade complex. The combination of experimental structural studies and comparative analysis provides for detailed models of the structures of the Cascade complexes from different CRISPR-Cas types, revealing remarkable architectural uniformity.
The Friedreich's ataxia mutation confers cellular sensitivity to oxidant stress which is rescued by chelators of iron and calcium and inhibitors of apoptosis (1999)

Expansions of an intronic GAA repeat reduce the expression of frataxin and cause Friedreich's ataxia (FRDA), an autosomal recessive neurodegenerative disease. Frataxin is a mitochondrial protein, and disruption of a frataxin homolog in yeast results in increased sensitivity to oxidant stress, increased mitochondrial iron and respiration deficiency. These previous data support the hypothesis that FRDA is a disease of mitochondrial oxidative stress, a hypothesis we have tested in cultured cells from FRDA patients. FRDA fibroblasts were hypersensitive to iron stress and significantly more sensitive to hydrogen peroxide than controls. The iron chelator deferoxamine rescued FRDA fibroblasts more than controls from oxidant-induced death, consistent with a role for iron in the differential kinetics of death; however, mean mitochondrial iron content in FRDA fibroblasts was increased by only 40%. Treatment of cells with the intracellular Ca2+chelator BAPTA-AM rescued both FRDA fibroblasts and controls from oxidant-induced death. Treatment with apoptosis inhibitors rescued FRDA but not control fibroblasts from oxidant stress, and staurosporine-induced caspase 3 activity was higher in FRDA fibroblasts, consistent with the possibility that an apoptotic step upstream of caspase 3 is activated in FRDA fibroblasts. These results demonstrate that FRDA fibroblasts are sensitive to oxidant stress, and may be a useful model in which to elucidate the FRDA mechanism and therapeutic strategies.
Wild perennial sunflower as a potential source of reduced palmitic and stearic fatty acids in sunflower oil (2002)

The trend in healthier human diets is to decrease the consumption of the saturated fatty acids. Sunflower oil, which is fourth in production among edible vegetable oils in the world, contains 65 g kg-1 palmitic and 45 g kg-1 stearic acids, both saturated fatty acids. These levels are high compared with rapeseed (Brassica napus L) oil with 40 g kg1 palmitic and 20 g kg-1 stearic acids. A reduction of saturated fats in traditional sunflower oil would lead to a healthier edible oil. The objective of this preliminary study was to search the vast genetic diversity available from wild ancestors of cultivated sunflower for potential sources of reduced palmitic and stearic fatty acids. Achene oil of one population of wild H. giganteus L. (GIG-102) from INRA, Montpellier, France, had 47 g kg-1 palmitic acid and 18 g kg-1 stearic acid. The combined 65 g kg-1 palmitic and stearic acids is 40% lower than the present level of these fats in sunflower oil. The level of saturated fatty acids observed in the population remained low when plants were grown in the greenhouse under uniform conditions. In the greenhouse, palmitic acid averaged 48 g kg-1, while stearic acid averaged 16 g kg-1. This would indicate that palmitic and stearic acid concentrations are under genetic control with potential for incorporation into cultivated sunflower. Crossing this population with an inbred cultivated line produced F1 plants with an achene oil that averaged 39 g kg-1 palmitic and 26 g kg-1 stearic acid. The inbred cultivated parent averaged 55 g kg-1 palmitic and 51 g kg-1 stearic acid. F2 plants produced an achene oil that averaged 47 g kg-1 palmitic and 29 g kg-1 stearic acid, for a total of 76 g kg-1. When F1 plants were back-crossed to the cultivated inbred, BC1F1 plants produced an achene oil that averaged 47 g kg-1 palmitic and 28 g kg1 stearic acid for a total of 75 g kg-1. The inbred cultivated parent averaged 54 g kg-1 palmitic and 56 g kg-1 stearic acid, for a total of 110 g kg-1. Preliminary information indicate that palmitic and stearic fatty acids in sunflower oil can be reduced by introducing genes from a wild perennial progenitor into cultivated sunflower. Further research will be needed to determine the inheritance of these fatty acids. Other agro-nomic traits will also have to be monitored during the introgression of genes for reduced saturated fatty acids into cultivated sunflower.
Methanococci Use the Diaminopimelate Aminotransferase (DapL) Pathway for Lysine Biosynthesis (2010)

The pathway of lysine biosynthesis in the methanococci has not been identified previously. A variant of the diaminopimelic acid (DAP) pathway uses diaminopimelate aminotransferase (DapL) to catalyze the direct conversion of tetrahydrodipicolinate (THDPA) to ll-DAP. Recently, the enzyme DapL (MTH52) was identified in Methanothermobacter thermautotrophicus and shown to belong to the DapL1 group. Although the Methanococcus maripaludis genome lacks a gene that can be unambiguously assigned a DapL function based on sequence similarity, the open reading frame MMP1527 product shares 30% amino acid sequence identity with MTH52. A Deltammp1527 deletion mutant was constructed and found to be a lysine auxotroph, suggesting that this DapL homolog in methanococci is required for lysine biosynthesis. In cell extracts of the M. maripaludis wild-type strain, the specific activity of DapL using ll-DAP and alpha-ketoglutarate as substrates was 24.3 + or - 2.0 nmol min(-1) mg of protein(-1). The gene encoding the DapL homolog in Methanocaldococcus jannaschii (MJ1391) was cloned and expressed in Escherichia coli, and the protein was purified. The maximum activity of MJ1391 was observed at 70 degrees C and pH 8.0 to 9.0. The apparent K(m)s of MJ1391 for ll-DAP and alpha-ketoglutarate were 82.8 + or - 10 microM and 0.42 + or - 0.02 mM, respectively. MJ1391 was not able to use succinyl-DAP or acetyl-DAP as a substrate. Phylogenetic analyses suggested that two lateral gene transfers occurred in the DapL genes, one from the archaea to the bacteria in the DapL2 group and one from the bacteria to the archaea in the DapL1 group. These results demonstrated that the DapL pathway is present in marine methanogens belonging to the Methanococcales.
Differential Effects of Estradiol and Estradiol-BSA Conjugates (1999)

The steroid 17beta-estradiol (E2) acts to modulate transcription through classical nuclear estrogen receptors (ER-alpha and ER-beta). However, E2 also induces a number of rapid responses (<10 min) within cells, including cells devoid of classical ERs, consistent with the presence of a membrane receptor for E2. Membrane impermeable steroids, typically bovine serum albumin (BSA) conjugates, are commonly used to characterize these non-genomic actions of E2 to exclude the involvement of nuclear ERs. Here we report that E2-BSA conjugate preparations, but not unconjugated E2, activate extracellular signal-regulated protein kinases (ERK1 and ERK2) in the SK-N-SH neuroblastoma cell line, raising concerns regarding the use of these reagents as E2 mimics. Freshly prepared solutions of E2-BSA were found to contain free immunoassayable E2 (iE2), which could be removed by filtration. E2-BSA solutions devoid of free iE2 failed to compete for binding of 125I16alpha-iodo-E2 to ER-alpha or ER-beta. Furthermore, in contrast to E2, E2-BSA conjugates did not bind to ER-alpha or ER-beta as assessed by electrophoretic mobility shift analyses. Protein analysis demonstrated that certain E2-BSA preparations were of very high molecular weight, suggesting extreme protein cross-linking. These findings suggest that E2-BSA does not mimic E2 and is not an appropriate ligand for investigating estrogen receptors. This underscores the need to design stable, cell impermeable analogs of estrogen for the characterization of membrane estrogen receptors.
Pioglitazone improves the cardiovascular profile in patients with uncomplicated systemic lupus erythematosus: a double-blind randomized clinical trial (2011)

This trial is registered at ClinicalTrials.gov Protocol Registration System, with the number NCT01322308.
Pyrazole Derivatives as Partial Agonists for the Nicotinic Acid Receptor (2003)

Nicotinic acid as a hypolipidemic agent appears unique due to its potential to increase HDL cholesterol levels to a greater extent than other drugs. However, it has some side effects, among which severe skin flushing is the most frequent and often limits patients' compliance. In a search for novel agonists for the recently identified and cloned G protein-coupled nicotinic acid receptor, we synthesized a series of substituted pyrazole-3-carboxylic acids that proved to have substantial affinity for this receptor. The affinities were measured by inhibition of [(3)H]nicotinic acid binding to rat spleen membranes. Potencies and intrinsic activities relative to nicotinic acid were determined by their effects on [(35)S]GTPgammaS binding to rat adipocyte and spleen membranes. Interestingly, most compounds were partial agonists. In particular, 2-diazabicyclo[3,3,0(4,8)]octa-3,8-diene-3-carboxylic acid (4c) and 5-propylpyrazole-3-carboxylic acid (4f) proved active with K(i) values of approximately 0.15 microM and EC(50) values of approximately 6 microM, while their intrinsic activity was only approximately 50% when compared to nicotinic acid. Even slightly more active was 5-butylpyrazole-3-carboxylic acid (4g) with a K(i) value of 0.072 microM, an EC(50) value of 4.12 microM, and a relative intrinsic activity of 75%. Of the aralkyl derivatives, 4q (5-(3-chlorobenzyl)pyrazole-3-carboxylic acid) was the most active with a relatively low intrinsic activity of 39%. Partial agonism of the pyrazole derivatives was confirmed by inhibition of G protein activation in response to nicotinic acid by these compounds. The pyrazoles both inhibited the maximum effect elicited by 100 microM nicotinic acid and concentration dependently shifted nicotinic acid concentration-response curves to the right, pointing to a competitive mechanism of action.
Non-insulin-dependent (type II) diabetes mellitus. (1991)

Non-insulin-dependent (type II) diabetes mellitus is an inherited metabolic disorder characterized by hyperglycemia with resistance to ketosis. The onset is usually after age 40 years. Patients are variably symptomatic and frequently obese, hyperlipidemic and hypertensive. Clinical, pathological and biochemical evidence suggests that the disease is caused by a combined defect of insulin secretion and insulin resistance. Goals in the treatment of hyperglycemia, dyslipidemia and hypertension should be appropriate to the patient's age, the status of diabetic complications and the safety of the regimen. Nonpharmacologic management includes meal planning to achieve a suitable weight, such that carbohydrates supply 50% to 60% of the daily energy intake, with limitation of saturated fats, cholesterol and salt when indicated, and physical activity appropriate to the patient's age and cardiovascular status. Follow-up should include regular visits with the physician, access to diabetes education, self-monitoring of the blood or urine glucose level and laboratory-based measurement of the plasma levels of glucose and glycated hemoglobin. If unacceptably high plasma glucose levels (e.g., 8 mmol/L or more before meals) persist the use of orally given hypoglycemic agents (a sulfonylurea agent or metformin or both) is indicated. Temporary insulin therapy may be needed during intercurrent illness, surgery or pregnancy. Long-term insulin therapy is recommended in patients with continuing symptoms or hyperglycemia despite treatment with diet modification and orally given hypoglycemic agents. The risk of pancreatitis may be reduced by treating severe hypertriglyceridemia (fasting serum level greater than 10 mmol/L) and atherosclerotic disease through dietary and, if necessary, pharmacologic management of dyslipidemia. Antihypertensive agents are available that have fewer adverse metabolic effects than thiazides and beta-adrenergic receptor blockers. New drugs are being developed that will enhance effective insulin secretion and action and inhibit the progress of complications.
Demand response in radial distribution networks: Distributed algorithm (2012)

Demand response has recently become a topic of active research. Most of work however considers only the balance between aggregate load and supply, and abstracts away the underlying power network. In this paper, we study demand response in a radial distribution network, by formulating it as an optimal power flow problem that maximizes the aggregate user utilities and minimizes the supply cost and the power line losses, subject to the power flow constraints and operating constraints. We propose a fully distributed algorithm for the users to coordinate their demand response decisions through local communication with their neighbors so as to achieve the optimum. Numerical examples with the real-world distribution circuits are provided to complement our theoretical analysis.
A localisation signal in the 3′ untranslated region of c-myc mRNA targets c-myc mRNA and β-globin reporter sequences to the perinuclear cytoplasm and cytoskeletal-bound polysomes (1996)

There is increasing evidence that in mammalian cells some mRNAs are localised to specific parts of the cytoplasm and a proportion of mRNAs and polyribosomes are associated with the cytoskeleton. It has been shown previously that c-myc mRNA is present in the perinuclear cytoplasm and associated with the cytoskeleton, and that this localisation is dependent upon the 3' untranslated region of the mRNA. The present studies show that in transfected fibroblasts the c-myc 3' untranslated region is able to localise beta-globin reporter sequences to the perinuclear cytoplasm. Studies with constructs containing deletions within the 3' untranslated region identify the region between bases 194 and 280 as critical for localisation. Transfection of cells with constructs in which this region is linked to beta-globin sequences showed that it was sufficient to localise the chimaeric transcripts to the perinuclear cytoplasm and to cytoskeletal-bound polyribosomes. Transfection with constructs containing a mutated AUUUA sequence within the 194-280 base region showed that this conserved AUUUA is required for targeting of both c-myc mRNA and a chimaeric transcript of beta-globin transcripts linked to the c-myc 3' untranslated region. The region between bases 194 and 280 did not induce instability of beta-globin transcripts and the AUUUA mutation had little effect upon mRNA stability. We propose that this 86 nt region of the 3' untranslated region contains a localisation signal to target c-myc mRNA so that it is retained on cytoskeletal-bound polysomes in the perinuclear cytoplasm; a conserved AUUUA sequence appears to be a critical part of this signal.
Palladium(0) Catalyzed Cross Coupling Reactions of Hindered, Double Activated Aryl Halides with Organozinc Reagents - The Effect of Copper(I) Cocatalysis (1996)

Various organozinc reagents undergo palladium(0) catalyzed Negishi-Kumada-type cross coupling reactions, cocatalyzed by copper(I) iodide, with electronically activated aryl halides 1-d in the presence of an electron withdrawing ortho or meta substituent and an ester group.
THE LONG-TERM SUCCESS OF FRESH, SMALL FRAGMENT OSTEOCHONDRAL ALLOGRAFTS USED FOR INTRAARTICULAR POST-TRAUMATIC DEFECTS IN THE KNEE JOINT (1992)

Ninety-two fresh osteochondral allografts were implanted in 91 patients with posttraumatic osteoarticular defects of the knee joint. These patients have been prospectively followed since 1972. An analysis of long-term survival of these grafts has been performed to determine their success rates: 75% at 5 years, 64% at 10 years, and 63% at 14 years. An evaluation was made between unipolar grafts, which involve only one surface of the compartment, and bipolar grafts, which involve both surfaces. The unipolar grafts had a lower failure rate at all time periods compared to bipolar grafts, with 76% survival at 5 years, 69% at 10 years, and 67% at 14 years. While investigating other factors that might affect the survival of the fresh osteochondral allografts, we calculated the influence of the anatomical location of the graft, patient sex, and patient age. There was no meaningful impact on allograft survival by either the location of the allograft or the sex of the patient. However, there was a significant effect on allograft longevity in terms of patient age, with patients under age 60 doing better. The best indication for the use of unipolar fresh osteochondral allografts is for posttraumatic defects in relatively young, active patients. Joint malalignment should be corrected to achieve best results.
Nephropathy in Patients with Type 2 Diabetes (2002)

A 60-year-old man with recently diagnosed type 2 diabetes mellitus has a serum creatinine level of 1.5 mg per deciliter (133 μmol per liter), and a dipstick test shows proteinuria (++). His blood pressure is 150/90 mm Hg. He smokes half a pack of cigarettes daily. What can be done to reduce the risk of progressive renal disease?
4-Amino-2,3,4,5-tetrahydro-1-benzoxepin-5-ols, 4-amino-2,3,4,5-tetrahydro-1-benzothiepin-5-ols, and related compounds (1971)

A number of 4-amino-2,3,4,5-tetrahydro-1-benzoxepin-5-ols and related compounds in the 1-benzothiepin series have been prepared, and methods of separation of the cis- and trans-isomers have been studied. Pharmacological studies have revealed that some of the compounds show activity on the central nervous system in mice. The synthesis of a number of multicyclic molecules containing the 2,3,4,5-tetrahydro-1-benzothiepin system is described.
Properties of thrombin- and elastase-modified human antithrombin III (1988)

Proteolytically modified forms of human antithrombin III have been prepared by reaction of native antithrombin with thrombin, human neutrophil elastase, or porcine pancreatic elastase. These forms have two chains disulfide linked and are of the same molecular weight as native antithrombin III. 1H NMR spectroscopy has been used to characterize these proteins and to compare them to one another and to native antithrombin III. The three modified proteins have very similar NMR spectra and histidine residues with identical pH titration parameters, and they undergo the same spectral changes upon binding heparin. They differ from native antithrombin III in all of these respects. In addition, the proteins are much more stable than native antithrombin III. The three modified proteins behave identically as a function of temperature; at 372 K, 44 K above the unfolding temperature for native antithrombin III, the proteins are still folded and possess approximately 70 unexchanged amide protons even after several hours. The unfolding of the heparin binding domain at low concentrations of deuteriated guanidine hydrochloride seen in native thrombin III is absent in the modified forms. It is concluded that the thrombin- and elastase-modified forms of antithrombin have identical structures when allowance is made for the slightly different sites of cleavage by the two types of elastase and by thrombin. This structure is very different from that of native antithrombin III.(ABSTRACT TRUNCATED AT 250 WORDS)
Extracting semantic relations from query logs (2007)

In this paper we study a large query log of more than twenty million queries with the goal of extracting the semantic relations that are implicitly captured in the actions of users submitting queries and clicking answers. Previous query log analyses were mostly done with just the queries and not the actions that followed after them. We first propose a novel way to represent queries in a vector space based on a graph derived from the query-click bipartite graph. We then analyze the graph produced by our query log, showing that it is less sparse than previous results suggested, and that almost all the measures of these graphs follow power laws, shedding some light on the searching user behavior as well as on the distribution of topics that people want in the Web. The representation we introduce allows to infer interesting semantic relationships between queries. Second, we provide an experimental analysis on the quality of these relations, showing that most of them are relevant. Finally we sketch an application that detects multitopical URLs.
Chemistry with [18F]Fluoride Ion (Eur. J. Org. Chem. 17/2008) (2008)

Abstract The cover picture shows the “Chemistry with [ 18 F]Fluoride Ion?”in PET radiotracer production. The procedure includes: (i) production of aqueous [ 18 F]fluoride ion from the cyclotron‐promoted 18 O(p,n) 18 F nuclear reaction on 18 O‐enriched water, (ii) conversion of the aqueous [ 18 F]fluoride ion into a more nucleophilic species by complexation with kryptand‐K + , (iii) incorporation of fluorine‐18 into a radiotracer, namely [ 18 F]SP203, for brain mGluR5 receptors, (iv) positron emission tomography (PET) of the radiotracer in a human subject, and (v) generation of the corresponding PET image of the brain mGluR5 receptor distribution. These steps are presented over a clock background to stress the necessity to work quickly and efficiently with short‐lived fluorine‐18 ( t 1/2 = 109.7 min) and according to a tight time schedule from radionuclide production through to PET imaging. Details are presented in the Microreview by L. S. Cai, S. Y. Lu and V. W. Pike on p. 2853 ff. The authors thank Dr. A. K. Brown and other staff of the Molecular Imaging Branch at the National Institute of Mental Health (Bethesda, Maryland, USA) for the generation of the PET image.
Adenovirus Internalization and Infection Require Dynamin (1998)

The cell receptors that facilitate adenovirus internalization into cells have been identified; however, the infectious pathway of virus entry has not been established. Adenovirus entry and infection were examined in HeLa cells lacking or overexpressing mutant dynamin, a protein that specifically regulates clathrin-mediated endocytosis. Expression of mutant dynamin significantly reduced adenovirus internalization and gene delivery, indicating a functional requirement for this molecule. These findings are consistent with virus entry via the clathrin-coated pit pathway.