gebhart/patrepeval huggingface dataset:
Oxford Textbook of Rheumatology (1993)

Part 1 Clinical presentation of rheumatic disease: clinical presentation in different age groups, John S. Percy et al common clinical problems, Andrew Frank et al views from different perspectives, W.Watson Buchanan et al. Part 2 Pathophysiology of musculoskeletal disease: molecular genetics and its relevance in rheumatology, Patricia Woo molecular abnormalities of collagen, M. Pope articular cartilage, Giles Campion and Timothy Hardingham bone in health and disease, Roger Smith the physiology of the joint and its disturbance in inflammation, Paul I. Mapp et al skeletal muscle and the effects of inflammation, Diane J. Newham biomechanics of articulations and derangement in disease, Bahaa B. Seedham. Part 3 The process of inflammation: cells and mediators of inflammation, Mark Walport and Gordon Duff lymphocyte traffic in inflammation, Dorian O. Haskard specific immune responses, P. Wordsworth and John I. Bell modification of inflammation, Peter M. Brooks et al. Part 4 Investigation of the rheumatic diseases: acute phase response, Rosamonde E. Banks et al haematology, Lynne Turner-Stokes biochemistry, Rosamonde E. Banks et al microbiology and diagnostic serology, Geoffrey Scott autoantibody profile, Peter Maddison synovial fluid analysis, J.C. Edwards polymorphic genetic marker analysis, J. Lanchbury immune-complex detection, Bryan D. Williams imaging, Philipp Lang et al histopathological diagnosis, P.J. Gallagher and Janice R. Anderson electrophysiology, Adam Young growth and skeletal maturation, Christopher Lovell and Patricia Woo. Part 5 The scope of rheumatic diseases: epidemiology, Alan J. Silman et al nosology of the chronic inflammatory rheumatic diseases, Patricia Woo and David Glass infections, Marc L. Miller et al rheumatoid arthritis, R.N. Maini et al spondylarthropathies, Andrei Calin et al arthropathies primarily occuring in childhood, David W. Sherry et al systemic lupus erythematosus, David Isenberg et al systemic sclerosis (scleroderma), Carol M. Black et al poly- and dermatomyositis, Ira N. Targoff and Lauren M. Pachman Sjogren's syndrome, H.M. Moutsopoulos et al primary vasculitides, D. Scott et al overlap syndromes, Michael L. Snaith and Roger Allen miscellaneous inflammatory conditions, G. Husby et al soft tissue rheumatism, B. Hazelman osteoarthritis, M. Doherty et al gout and hyperuricaemia, G. Nuki diseases of bone and cartilage, A.K. Bhalla disorders of the spine, Malcolm I.V. Jayson and Allan Ivan Binder miscellaneous abnormalities of connective tissue structure and function, Thomas G. Benedek et al. Part 6 Rehabilitation: the surgery of rheumatic disease in adults, D.S. Barrett et al the role of surgery in the management of rheumatic diseases in children, Malcolm Swann non-surgical rehabilitation of adults with rheumatic diseases, A. Clarke non-surgical rehabilitation in the child, H. Emery.
Soybean nodulin genes: Analysis of cDNA clones reveals several major tissue-specific sequences in nitrogen-fixing root nodules (1983)

Plant gene products that could play a role in the process of symbiotic nitrogen fixation in leguminous plants were detected by screening a cDNA library prepared from soybean nodule poly(A)(+) RNA. About 13% of the 5,700 clones screened contained sequences detectable with a root cDNA probe while about 2,100 clones (37% of the library) contained sequences that were detectable only with nodule cDNA. Five unique sequence species, accounting for more than half of the 2,100 nodule-specific clones, were identified by cross-hybridization experiments. The most abundant species, represented by 860 clones, encodes the well-characterized protein, leghemoglobin (Lb). The other four species, designated NodA, NodB, NodC, and NodD, are represented by 350, 55, 61, and 6 clones, respectively. Each of these four species was found to be encoded by the plant nuclear genome at low copy number. The transcripts corresponding to the nodule-specific clones represented 12-15% (Lb), 6% (NodA), and 0.5-1.1% (NodB, NodC, and NodD) mole fraction of nodule polysomal mRNAs but could not be detected in root polysomal RNA. Hybrid-selection of nodule mRNAs by representative clones and in vitro translation indicated that polypeptides of M(r) 44,000, 27,000, 24,000, and 100,000-120,000 are encoded by NodA, NodB, NodC, and NodD sequences, respectively. These polypeptides reacted with antiserum prepared against total soluble nodule proteins suggesting that the cloned sequences encode nodule-specific proteins, nodulins.
Valacyclovir and Acyclovir for Suppression of Shedding of Herpes Simplex Virus in the Genital Tract (2004)

Although the suppression of viral replication is not complete, valacyclovir and acyclovir are highly effective in suppressing the frequency and quantity of genital HSV shedding.
Energy consumption modeling and optimization for SRAM's (1995)

The recent trends in portable computing technologies have established the need for energy efficient design strategies. To achieve minimum energy design goals, system designers need a technique to accurately model the energy consumption of their design alternatives without performing a full physical design and full-circuit simulation. This paper presents and compares five approaches for modeling the energy consumption of CMOS circuits. These five modeling approaches have been chosen to represent the various levels of model complexity and accuracy found in the current literature. These modeling approaches are applied to the energy consumption of SRAM's to provide examples of their use and to allow for the comparison of their modeling qualities. It was found that a mixed characterization model-using a CV/sup 2/ prediction for digital subsections and fitted simulation results for the analog subsections-is satisfactory (within /spl plusmn/1 process variation) for predicting the absolute energy consumed per cycle. This same model is also very good (within 2%) for predicting an optimum organization for the internal structures of the SRAM. Several common architectures and circuit designs for SRAM's are analyzed with these models. This analysis shows that global, rather than local improvements, produce the largest energy savings.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Lovastatin and sodium phenylacetate normalize the levels of very long chain fatty acids in skin fibroblasts of X‐ adrenoleukodystrophy (1998)

The present study underlines the importance of lovastatin, an inhibitor of 3-hydroxy-3-methyl-glutaryl-coenzyme A (HMG-CoA) reductase, and the sodium salt of phenylacetic acid (NaPA), an inhibitor of mevalonate pyrophosphate decarboxylase, in normalizing the pathognomonic accumulation of saturated very long chain fatty acids (VLCFA) in cultured skin fibroblasts of X-adrenoleukodystrophy (X-ALD) in which the ALD gene is either mutated or deleted. Lovastatin or NaPA alone or in combination stimulated the beta-oxidation of lignoceric acid (C24:0) and normalized the elevated levels of VLCFA in skin fibroblasts of X-ALD. Ability of lovastatin and NaPA to normalize the pathognomonic accumulation of VLCFA in skin fibroblasts of X-ALD may identify these drugs as possible therapeutics for X-ALD.
c-Abl Tyrosine Kinase Regulates Caspase-9 Autocleavage in the Apoptotic Response to DNA Damage (2005)

Activation of the initiator caspase-9 is essential for induction of apoptosis by developmental signals, oncogenic transformation, and genotoxic stress. The c-Abl tyrosine kinase is also involved in the apoptotic response to DNA damage. The present results demonstrate that c-Abl binds directly to caspase-9. We show that c-Abl phosphorylates caspase-9 on Tyr-153 in vitro and in cells treated with DNA damaging agents. Moreover, inhibition of c-Abl with STI571 blocked DNA damage-induced autoprocessing of caspase-9 to the p35 subunit and activation of caspase-3. Caspase-9(Y153F) also attenuated DNA damage-induced processing of caspase-9 to p35, activation of caspase-3, and apoptosis. These findings indicate that caspase-9 autoprocessing is regulated by c-Abl in the apoptotic response to genotoxic stress.
Dietary Polyamine Intake and Polyamines Measured in Urine (2014)

Dietary polyamines have recently been associated with increased risk of pre-malignant colorectal lesions. Because polyamines are synthesized in cells and taken up from dietary sources, development of a biomarker of exposure is challenging. Excess polyamines are primarily excreted in the urine. This pilot study seeks to identify dietary correlates of excreted urinary polyamines as putative biomarkers of exposure. Dietary polyamines/other nutrients were estimated from a food frequency questionnaire (FFQ) and correlated with urinary levels of acetylated polyamines in 36 men using 24-h urine samples. Polyamines, abundant in cheese and citrus, were highly positively correlated with urinary N(8)-acetylspermidine (correlation coefficient; r = 0.37, P = 0.03), but this correlation was attenuated after adjustment for total energy intake (r = 0.07, P = 0.68). Dietary energy intake itself was positively correlated with urinary total acetylated polyamine output (r = .40, P = 0.02). In energy-adjusted analyses, folic acid and folate from food were associated with urinary N(1),N(12)-diacetylspermine (r = 0.34, P = 0.05 and r = -0.39, P = 0.02, respectively). Red meat negatively correlated with total urinary acetylated polyamines (r = -0.42, P = 0.01). Our findings suggest that energy, folate, folic acid, saturated fat, and red meat intake, as opposed to FFQ-estimated dietary polyamines, are correlated with urinary polyamines.
Heck Reaction in Ionic Liquids and the in Situ Identification of N-Heterocyclic Carbene Complexes of Palladium (2000)

The Heck reaction was found to proceed markedly more efficiently in the ionic liquid 1-butyl-3-methylimidazolium bromide ([bmim][Br]) than in the analogous tetrafluoroborate salt ([bmim][BF4]). In relation to this observation, 1-butyl-3-methylimidazol-2-ylidene (bmiy) complexes of palladium [PdBr(μ-Br)(bmiy)]2 (1) and [PdBr2(bmiy)2] (2) have been isolated in [bmim][Br] but not in [bmim][BF4] under conditions similar to those employed for the Heck reaction. In both the ionic liquid [bmim][Br] and molecular solvents, complex 2 was formed via the intermediate 1. 2 has been shown to be active in the Heck reaction in [bmim][Br] but much less so in [bmim][BF4] due to transformation by the latter into less active species.
Emerging practices for mapping and linking life sciences data using RDF — A case series (2012)

Members of the W3C Health Care and Life Sciences Interest Group (HCLS IG) have published a variety of genomic and drug-related data sets as Resource Description Framework (RDF) triples. This experience has helped the interest group define a general data workflow for mapping health care and life science (HCLS) data to RDF and linking it with other Linked Data sources. This paper presents the workflow along with four case studies that demonstrate the workflow and addresses many of the challenges that may be faced when creating new Linked Data resources. The first case study describes the creation of linked RDF data from microarray data sets while the second discusses a linked RDF data set created from a knowledge base of drug therapies and drug targets. The third case study describes the creation of an RDF index of biomedical concepts present in unstructured clinical reports and how this index was linked to a drug side-effect knowledge base. The final case study describes the initial development of a linked data set from a knowledge base of small molecules. This paper also provides a detailed set of recommended practices for creating and publishing Linked Data sources in the HCLS domain in such a way that they are discoverable and usable by people, software agents, and applications. These practices are based on the cumulative experience of the Linked Open Drug Data (LODD) task force of the HCLS IG. While no single set of recommendations can address all of the heterogeneous information needs that exist within the HCLS domains, practitioners wishing to create Linked Data should find the recommendations useful for identifying the tools, techniques, and practices employed by earlier developers. In addition to clarifying available methods for producing Linked Data, the recommendations for metadata should also make the discovery and consumption of Linked Data easier.
Advances in Nanopore Sequencing Technology (2013)

Much tremendous break through have been obtained in recent years for nanopore sequencing to achieve the goal of $1000 genome. As a method of single molecule sequencing, nanopore sequencing can discriminate the individual molecules of the target DNA strand rapidly due to the current blockages by translocating the nucleotides through a nano-scale pore. Both the protein-pores and solid-state nanopore channels which called single nanopore sequencing have been studied widely for the application of nanopore sequencing technology. This review will give a detail representation to protein nanopore and solid-state nanopore sequencing. For protein nanopore sequencing technology, we will introduce different nanopore types, device assembly and some challenges still exist at present. We will focus on more research fields for solid-state nanopore sequencing in terms of materials, device assembly, fabricated methods, translocation process and some specific challenges. The review also covers some of the technical advances in the union nanopore sequencing, which include nanopore sequencing combine with exonuclease, hybridization, synthesis and design polymer.
Molecular Characterization of the Haptoglobin·Hemoglobin Receptor CD163 (2004)

CD163 is the macrophage receptor for endocytosis of haptoglobin.hemoglobin complexes. The extracellular region consisting of nine scavenger receptor cysteine rich (SRCR) domains also circulates in plasma as a soluble protein. By ligand binding analysis of a broad spectrum of soluble CD163 truncation variants, the amino-terminal third of the SRCR region was shown to be crucial for the binding of haptoglobin.hemoglobin complexes. By Western blotting of the CD163 variants, a panel of ten monoclonal antibodies was mapped to SRCR domains 1, 3, 4, 6, 7, and 9, respectively. Only the two antibodies binding to SRCR domain 3 exhibited effective inhibition of ligand binding. Furthermore, analysis of purified native CD163 revealed that proteolytic cleavage in SRCR domain 3 inactivates ligand binding. Calcium protects against cleavage in this domain. Analysis of the calcium sensitivity of ligand binding to CD163 demonstrated that optimal ligand binding requires physiological plasma calcium concentrations, and an immediate ligand release occurs at the low calcium concentrations measured in acidifying endosomes. In conclusion, SRCR domain 3 of CD163 is an exposed domain and a critical determinant for the calcium-sensitive coupling of haptoglobin.hemoglobin complexes.
Perfect blackbody radiation from a graphene nanostructure with application to high-temperature spectral emissivity measurements (2013)

We report the successful fabrication of a novel type of blackbody material based on a graphene nanostructure. We demonstrate that the graphene nanostructure not only shows a low reflectance comparable to that of a carbon nanotube array but also shows an extremely high heat resistance at temperatures greater than 2500 K. The graphene nanostructure, which has an emissivity higher than 0.99 over a wide range of wavelengths, behaves as a standard blackbody material; therefore, the radiation spectrum and the temperature can be precisely measured in a simple manner. Here, the spectral emissivities of tungsten and tantalum are experimentally obtained using this ideal blackbody material and are compared to previously reported spectra. We clearly demonstrate the existence of a temperature-independent fixed point of emissivity at a certain wavelength. Both the spectral emissivity as a function of temperature and the cross-over point in the emissivity spectrum are well described by the complex dielectric function based on the Lorentz-Drude model with the phonon-scattering effect.
Adverse effects of G-CSF in sickle cell syndromes (2001)

Though likely past kindergarten, it was nevertheless early on when I learned that sickle cell anemia is a disease of the red cell. In view of this simple principle, it was a nasty surprise to find that administering G-CSF to patients with sickle cell disease, a maneuver designed to affect white
Use of knowledge-based restraints in phenix.refine to improve macromolecular refinement at low resolution (2012)

Traditional methods for macromolecular refinement often have limited success at low resolution (3.0-3.5 Å or worse), producing models that score poorly on crystallographic and geometric validation criteria. To improve low-resolution refinement, knowledge from macromolecular chemistry and homology was used to add three new coordinate-restraint functions to the refinement program phenix.refine. Firstly, a `reference-model' method uses an identical or homologous higher resolution model to add restraints on torsion angles to the geometric target function. Secondly, automatic restraints for common secondary-structure elements in proteins and nucleic acids were implemented that can help to preserve the secondary-structure geometry, which is often distorted at low resolution. Lastly, we have implemented Ramachandran-based restraints on the backbone torsion angles. In this method, a ϕ,ψ term is added to the geometric target function to minimize a modified Ramachandran landscape that smoothly combines favorable peaks identified from nonredundant high-quality data with unfavorable peaks calculated using a clash-based pseudo-energy function. All three methods show improved MolProbity validation statistics, typically complemented by a lowered R(free) and a decreased gap between R(work) and R(free).
B1 mapping by Bloch‐Siegert shift (2010)

A novel method for amplitude of radiofrequency field (B1+) mapping based on the Bloch-Siegert shift is presented. Unlike conventionally applied double-angle or other signal magnitude-based methods, it encodes the B(1) information into signal phase, resulting in important advantages in terms of acquisition speed, accuracy, and robustness. The Bloch-Siegert frequency shift is caused by irradiating with an off-resonance radiofrequency pulse following conventional spin excitation. When applying the off-resonance radiofrequency in the kilohertz range, spin nutation can be neglected and the primarily observed effect is a spin precession frequency shift. This shift is proportional to the square of the magnitude of B1(2). Adding gradient image encoding following the off-resonance pulse allows one to acquire spatially resolved B(1) maps. The frequency shift from the Bloch-Siegert effect gives a phase shift in the image that is proportional to B(1)(2). The phase difference of two acquisitions, with the radiofrequency pulse applied at two frequencies symmetrically around the water resonance, is used to eliminate undesired off-resonance effects due to amplitude of static field inhomogeneity and chemical shift. In vivo Bloch-Siegert B(1) mapping with 25 sec/slice is demonstrated to be quantitatively comparable to a 21-min double-angle map. As such, this method enables robust, high-resolution B(1)(+) mapping in a clinically acceptable time frame.
Quercetin and Its In Vivo Metabolites Inhibit Neutrophil-Mediated Low-Density Lipoprotein Oxidation (2008)

This study examined the effects of metabolic transformation of the common dietary flavonoid, quercetin, on its ability to protect low-density lipoprotein (LDL) from neutrophil-mediated modification. Quercetin was shown to be effective in protecting LDL against neutrophil-mediated modification at physiological concentrations (1 microM) and appears to act by inhibiting myeloperoxidase (MPO)-catalyzed oxidation (IC(50) = 1.0 microM). Quercetin was also shown to protect against radical-induced [2,2'-azobis(2-methylpropionamidine)dihydrochloride] oxidation (IC(50) = 1.5 microM). Studies of structure-activity relationships showed that methylation at the 3'-position or glucuronidation at the 3-position did not significantly affect inhibition by quercetin of the MPO activity, but conjugations at both positions significantly reduce its activity. Our results suggest that the common dietary flavonoid, quercetin, and some of its major in vivo metabolites are potential inhibitors of MPO at physiological concentrations. Dietary flavonoids that could modify MPO activity could protect lipoproteins from damage in chronic inflammatory states such as cardiovascular disease.
Management of anorexia and bulimia nervosa: An evidence-based review (2010)

Anorexia nervosa and bulimia nervosa are primarily psychiatric disorders characterized by severe disturbances of eating behavior. Eating disorders are most prevalent in the Western culture where food is in abundance and female attractiveness is equated with thinness. Eating disorders are rare in countries like India. Despite a plethora of management options available to the mental health professionals, no major breakthrough has been achieved in recent years. Nutritional rehabilitation along with some form of re educative psychotherapy remains the mainstay of management of anorexia nervosa. In bulimia nervosa, both fluoxetine and cognitive behavior therapy have been found to be effective. Although the above-mentioned management options have been in use for decades, the active ingredient is still to be ascertained.
A phase I trial of interferon-alpha-2a plus cyclophosphamide, vincristine, prednisone, and doxorubicin. (1989)

We conducted a Phase I trial of interferon-alpha-2a (IFN-alpha-2a) plus combination chemotherapy consisting of cyclophosphamide, vincristine, prednisone, and doxorubicin (COPA) in order to determine the maximum dose of IFN-alpha-2a that could be administered without compromising the dose intensity of COPA. Twenty-one patients received IFN-alpha-2a intramuscularly on days 1-5, followed by 600 mg/m2 cyclophosphamide intravenously (i.v.) on day 8; 50 mg/m2 doxorubicin i.v. on day 8; 1.2 mg/m2 vincristine i.v. on day 8; and 100 mg/m2 prednisone orally on days 8-12. IFN doses were escalated between patient groups; 7 patients received 12 x 10(6) U/m2, 11 patients received 6 X 10(6) U/M2, and 3 patients received 12 X 10(6)/m2. Because 79% of the cycles of COPA administered at the third dose level required a delay for hematologic recovery, further patient accrual at this dose level ceased. Grade III or IV granulocytopenia occurred on day 1 in 6, 9, and 0 of the patients treated at the three dose levels. Granulocyte counts rapidly recovered, however, and did not result in a delay in chemotherapy administration on day 8 in 94% of the cycles at the first two dose levels. The mean hematocrit following five cycles of therapy dropped from 40 to 31%. Only two patients required dose reductions due to constitutional symptoms related to the IFN-alpha-2a. Eight responses were observed, including five of five patients with nonHodgkin's lymphomas, one of five with melanoma, one of six with renal cell carcinoma, and one of one with adenoid cystic carcinoma. One patient with metastatic melanoma remains in a complete response on maintenance IFN-alpha-2a for three years. We conclude that 6 X 10(6) U/m2 of IFN-alpha-2a can be administered to cancer patients without significantly compromising the dose intensity of COPA. This observation, and the demonstrated activity of IFN-alpha-2a plus COPA (I-COPA) in low and intermediate grade histology nonHodgkin's lymphomas, provides the basis for the randomized Phase III trial comparing COPA to I-COPA in these neoplasms, which is currently being conducted in the Eastern Cooperative Oncology Group.