gebhart/patrepeval huggingface dataset:
Autoantibody to th ribonucleoprotein (nucleolar 7–2 rna protein particle) in patients with systemic sclerosis (1990)

We studied sera of 371 consecutive new patients with systemic sclerosis (SSc; scleroderma) who were first evaluated during 1984-1988. All sera were tested for antinuclear antibodies by immunofluorescence staining using HEp-2 cells as substrate. We excluded 219 sera showing dark nucleoli and screened for antibodies to Th in the remaining 152 sera by immunoprecipitation of a 32P-labeled HeLa cell extract. Fifteen (4.0%) of 371 sera were anti-Th+. Anti-Th antibodies were present in 14 (8.4%) of 167 SSc patients with limited cutaneous involvement, in 1 of 167 with diffuse cutaneous involvement, and in 0 of 37 with SSc overlap syndrome. Among 244 controls with other connective tissue diseases, anti-Th was detected in only 3 patients, all having primary Raynaud's phenomenon of less than 2 years duration. In the subgroup with SSc with limited cutaneous involvement, the 14 anti-Th+ patients had a significantly greater frequency of puffy fingers, small bowel involvement, and hypothyroidism, and a significantly lower frequency of arthralgia and/or arthritis. Their cumulative survival rate from the time of onset of symptoms was lower than that for anti-Th- patients (78% versus 91% at 10 years), primarily due to 3 deaths from pulmonary arterial hypertension (2 from primary pulmonary hypertension and 1 from pulmonary hypertension secondary to pulmonary interstitial fibrosis). Serum anti-Th antibodies are present almost exclusively in patients with SSc with limited cutaneous involvement or in those with primary Raynaud's phenomenon whose disease may evolve to SSc with limited cutaneous involvement, and these antibodies may identify those patients who are at greater risk for reduced survival.
Sequence-Determined DNA Separations (1984)

The variation in electrophoretic mobility of DNA under conditions of marginal helix stability provides a useful means for investigation of the relation between the helix-random chain transition and base sequence in natural DNA and a powerful procedure for separation of DNA molecules according to sequence. The use of statistical mechanical theory for analysis of the transition equilibria together with new, simplified theoretical considerations on the effect of strand unravelling on mobility have shown that the gel behavior is predictable for known sequences. A number of the distinctive consequences of the theory and their correspondence with the properties of real molecules have been demonstrated. These include the extremely close cooperative linkage of large blocks of bases into domains, the existence of sharp boundaries between domains, the major role of nearest-neighbor interaction in determining stability, the dependence of domain structures on neighboring and more remote sequences, and the depression of domain melting temperature if the sequence lies at the end of a molecule. New and unusual applications derive from the possibility of separating DNA molecules by properties of their sequence. Exceedingly complex mixtures, such as the sum of all fragments produced by the action of a sixbase specific restriction endonuclease on a complete bacterial genome, can be resolved completely. Additional inserted sequences are easily discerned. The difference of a single base pair in a molecule permits detection and isolation of mutant sequences. The need for full sequential analysis of long molecules for characterization of mutants can be reduced by localizing a change within a small fragment.
Sobre cómo el paladio dominó al bencino (2005)

The aim of the present work was to verify that skilled volleyball players present specific adaptations in both neuromuscular control and movement biomechanics, showing an improved neuromuscular control around the knee joint than in non-jumper athletes. Seven male volleyball players and seven male non-jumper athletes were recruited for this study. The following tests were performed in a random order: single countermovement jump (CMJ), single squat jump. At the end of the series, subjects performed a repetitive CMJ test. Electromyographic signals were recorded from vastus lateralis and biceps femoris muscles on both sides. Ground reaction forces and moments were measured with a force plate. Volleyball athletes performed better in all tests and were more resistant to fatigue than non-jumper athletes. Furthermore, volleyball athletes showed a reduced co-activation of knee flexor/extensor muscles. The present results seem to stand for a neural adaptation of the motor control scheme to training.
Vascular effects of HMG CoA-reductase inhibitors (statins) unrelated to cholesterol lowering: new concepts for cardiovascular disease (2001)

Time for primary review 18 days. 

In 1976, Endo et al. [1] reported on the discovery of a specific competitive inhibitor of the enzyme 3-hydroxy-3-methylglutaryl (HMG) CoA reductase. This compound, isolated from fungi, was called mevastatin. In 1988, Alberts [2] described a more potent HMG CoA reductase inhibitor, lovastatin, isolated from Aspergillus terreus . These two compounds started the development of a series of cholesterol lowering agents, now commonly called ‘statins’. Statins block the conversion of HMG CoA to mevalonic acid and thus dramatically attenuate the biosynthesis of cholesterol. These effects occur largely in the liver, where the statins primarily distribute [2]. The major effect of these pharmacologic agents is a marked reduction in LDL-cholesterol levels in the blood.

On the basis of these and other findings, the statins have been widely prescribed in humans with elevated serum cholesterol levels. These statins are well tolerated, are very safe, and effectively lower serum LDL-cholesterol levels and maintain this effect over periods of many years [3]. In one clinical trial, 4444 patients were carefully studied and not only was simvastatin shown to be safe and effective in lowering circulating cholesterol, it also significantly improved survival in patients with coronary heart disease (CHD) [4], and carried a 37% reduction in the risk of treated patients undergoing myocardial vascularization procedures [4]. These findings speak eloquently to the clinical usefulness of the statins. For many years, all the beneficial effects of the statins were attributed to their cholesterol lowering effect. Nevertheless, quite recently, the statins were found to exert direct cardiovascular effects which clearly are independent of their cholesterol lowering effects, and are not directly attributable to a reduction in serum cholesterol levels.

The purpose of this review is to describe, evaluate, and discuss the major mechanisms underlying these non-lipid-lowering effects … 

* Corresponding author. Tel.: +1-215-503-7760; fax: +1-215-503-2073 allan.m.lefer{at}mail.tju.edu
Targeted Killing of Cancer Cellsin Vivoandin Vitrowith EGF-Directed Carbon Nanotube-Based Drug Delivery (2009)

Carbon nanotube-based drug delivery holds great promise for cancer therapy. Herein we report the first targeted, in vivo killing of cancer cells using a drug-single wall carbon nanotube (SWNT) bioconjugate, and demonstrate efficacy superior to nontargeted bioconjugates. First line anticancer agent cisplatin and epidermal growth factor (EGF) were attached to SWNTs to specifically target squamous cancer, and the nontargeted control was SWNT-cisplatin without EGF. Initial in vitro imaging studies with head and neck squamous carcinoma cells (HNSCC) overexpressing EGF receptors (EGFR) using Qdot luminescence and confocal microscopy showed that SWNT-Qdot-EGF bioconjugates internalized rapidly into the cancer cells. Limited uptake occurred for control cells without EGF, and uptake was blocked by siRNA knockdown of EGFR in cancer cells, revealing the importance of EGF-EGFR binding. Three color, two-photon intravital video imaging in vivo showed that SWNT-Qdot-EGF injected into live mice was selectively taken up by HNSCC tumors, but SWNT-Qdot controls with no EGF were cleared from the tumor region in <20 min. HNSCC cells treated with SWNT-cisplatin-EGF were also killed selectively, while control systems that did not feature EGF-EGFR binding did not influence cell proliferation. Most significantly, regression of tumor growth was rapid in mice treated with targeted SWNT-cisplatin-EGF relative to nontargeted SWNT-cisplatin.
Human cytotoxic T cell clones directed against herpes simplex virus-infected cells. IV. Recognition and activation by cloned glycoproteins gB and gD. (1986)

Results of studies in mice and clinical observations in man indicate that T cell-mediated immunity is important in resistance to herpes simplex virus (HSV) infections. This study was undertaken to elucidate the viral antigen specificity of human HSV-immune T cells. Purified HSV-1 glycoproteins gB-1 and gD-1, cloned and expressed in mammalian cells, were found to stimulate proliferation of, and interleukin 2 (IL 2) production by, peripheral blood lymphocytes (PBL) of HSV seropositive individuals, indicating the presence of memory T cells to gB-1 and gD-1 in individuals with serologic evidence of immunity to HSV. Second, T cell clones, generated by stimulation of PBL with HSV-1, were found to recognize gB-1 or gD-1, as evidenced by the ability of the clones to proliferate in response to stimulation with gB-1 or gD-1 in the absence of exogenous IL 2. Third, HSV-specific T cell clones, lytic for HSV-1 or both HSV-1- and HSV-2-infected autologous target cells, were generated after stimulation of PBL with purified cloned gB-1 or gD-1. Our findings, that human HSV-specific T cells can recognize and be activated by HSV subunit antigens gB-1 or gD-1, imply that these glycoproteins play a role in human T cell-mediated immunity to HSV and support the contention that a gB-1 or gD-1 subunit vaccine may be protective in man.
E. coli,Antibiotics, and the Hemolytic–Uremic Syndrome (2000)

The hemolytic–uremic syndrome is characterized by hemolytic anemia, thrombocytopenia, and acute renal insufficiency. There are at least four major causes of the syndrome: bacterial and viral infections, which are responsible for the epidemic form; hereditary factors, which are responsible for familial forms, in particular recurrent, or atypical, hemolytic–uremic syndrome; systemic conditions, such as systemic lupus erythematosus, cancer, transplant rejection, glomerulonephritis, and pregnancy; and exposure to toxins or potential toxins, such as cyclosporine, tacrolimus, mitomycin, and radiation.1 Among children the chief cause of the hemolytic–uremic syndrome is infection with enterohemorrhagic strains of Escherichia coli. Originally, a variety of serotypes were described . . .
Prognostic value of altered oral glutamine challenge in patients with minimal hepatic encephalopathy (2004)

Oral glutamine challenge (OGC) has been found to be safe, and an altered response predicts elevated risk of overt hepatic encephalopathy (HE) in patients with minimal hepatic encephalopathy (MHE). We assessed the survival prognosis of patients with cirrhosis, but without current overt HE, who have an altered OGC and MHE. MHE was inferred using 3 neuropsychological tests. Venous ammonia concentrations were measured pre- and post-60 minutes of a 10 g oral glutamine load. The median follow-up was 25.2 months, by which time 22 patients had had bouts of overt HE and 18 had died from liver-related causes. The results in 126 patients with cirrhosis, indicated 25 with MHE and abnormal OGC response. Survival among patients who developed overt HE was 59% at 1 year and 38% at 3 years. In patients without HE, survival was 96% and 86% at 1 and 3 years, respectively (log-rank 50.9, P <.0001). The presence of MHE was not related to survival (log-rank 2.21, P =.23). Patients with MHE and abnormal OGC test had elevated mortality risk (log-rank 13.1, P =.0003). Multivariate analyses indicated Child-Pugh score (hazard ratio [HR] 1.46; 95% CI, 1.46-2.08), and MHE plus altered OGC response (HR 5.5; 95% CI, 1.81-16.6) were predictors of mortality, whether from liver-related or non-liver-related causes. In conclusion, a pathological OGC response in patients with MHE appears to be associated with lower survival rate and may prove useful in the selection of candidates for liver transplantation.
Case study: e-commerce clickstream visualization (2005)

We have developed an interactive, scalable visualization tool for analyzing the behavior of users of a web site. Our system not only shows site topology and traffic flow, but by segmenting site traffic data based on user attributes, including demographic data and purchase history, we can present a more complete picture of web site usage. This can lead to a more focussed analysis that allows direct comparison between user segments, and ultimately a deeper understanding of how users interact with a site. The tool is designed for real world use, and we present a usage study of the tool by analyzing the data of a failed dot-com.
Influence of Surface Area on Charge Transport and Recombination in Dye-Sensitized TiO2 Solar Cells (2006)

The dependence of the electron transport and recombination dynamics on the internal surface area of mesoporous nanocrystalline TiO2 films in dye-sensitized solar cells was investigated. The internal surface area was varied by altering the average particle size in the films. The scaling of the photoelectron density and the electron diffusion coefficient at short circuit with internal surface area confirms the results of a recent study (Kopidakis, N.; Neale, N. R.; Zhu, K.; van de Lagemaat, J.; Frank, A. J. Appl. Phys. Lett. 2005, 87, 202106) that transport-limiting traps are located predominately on the surfaces of the particles. The recombination current density was found to increase superlinearly (with an exponent of 1.40 +/- 0.12) with the internal surface area. This result is at odds with the expected linear dependence of the recombination current density on the surface area when only the film thickness is increased. The observed scaling of the recombination current density with surface area is consistent with recombination being transport-limited. Evidence is also presented confirming that photoinjected electrons recombine with redox species in the electrolyte via surface states rather than from the TiO2 conduction band.
NMR solution structure of the 32-kDa platelet factor 4 ELR-motif N-terminal chimera: a symmetric tetramer (1995)

Native human platelet factor 4 (PF4) is a homotetrameric protein (70 residues/subunit) known for its anticoagulant heparin binding activity. 2D 15N--1H HSQC NMR experiments of native PF4 in solution show the presence of conformational heterogeneity consistent with the formation of asymmetric homo-tetramers as observed in the X-ray crystal structure of both human and bovine PF4. A chimeric mutant of PF4 (called PF4-M2) which substitutes the first 11 N-terminal residues for the first eight residues from homologous interleukin-8 forms symmetric homo-tetramers with essentially the same heparin binding activity as native PF4. The solution structure of PF4-M2 has been investigated by using two- and three-dimensional 1H- and 15N-NMR spectroscopy and NOE-restrained simulated annealing molecular dynamics. As with other members of the CXC chemokine family whose structures are known, the PF4-M2 subunit monomer consists of a mostly hydrophobic, triple-stranded antiparallel beta-sheet onto which is folded an amphipathic C-terminal helix and a less periodic N-terminal domain. Although N-terminal substitution with the less acidic interleukin-8 sequence most affects the quarternary structure relative to native PF4 at the AC and AD dimer interfaces, AB dimer stability is weakened as reflected in reduced equilibrium association binding constants.
DNA bifunctional intercalators. 1. Synthesis and conformational properties of an ethidium homodimer and of an acridine ethidium heterodimer (1978)

An ethidium homodimer and an acridine ethidium heterodimer have been synthesized. The ethidium and the acridine chromophore were introduced in such bifunctional intercalators in order to allow the fluorometric study of the interaction of such molecules with DNA, which is reported in the companion paper (Gaugain, B., Barbet, J., Capelle, N., Roques, B.P., & Le Pecq, J.B.(1978) Biochemistry 17 (following paper in this issue)). In the preparation of the acridine-ethidium dimer, we report the use of acetyl groups as new protecting agents in the phenanthridine series. Conformational studies of these molecules by visible absorption and NMR spectroscopy indicate that these dimers exist in equilibrium between folded and unfolded conformations and that this equilibrium is pH and temperature dependent. Models for the geometry of the folded forms are proposed.
DNA Containing Side Chains with Terminal Triple Bonds: Base‐Pair Stability and Functionalization of Alkynylated Pyrimidines and 7‐Deazapurines (2006)

The synthesis of a series of oligonucleotides containing 5-substituted pyrimidines as well as 7-substituted 7-deazapurines bearing diyne groups with terminal triple bonds is reported. The modified nucleosides were prepared from the corresponding iodo nucleosides and diynes by the Sonogashira cross-coupling reaction. They were converted into phosphoramidites and employed in solid-phase synthesis of oligonucleotides. The effect of the diyne modifications on the duplex stability was investigated. The modified nucleosides were used for further functionalization using the protocol of Huisgen-Sharpless [2+3] cycloaddition ('click chemistry').
New Iyotropic phases (thermally-reversible organogels) of simple tertiary amines and related tertiary and quaternary ammonium halide salts (1996)

Small concentractions of some structurally simple tertiary amines and related tertiary and quaternary ammonium halide salts form viscoelastic, thermally reversible gels with a wide variety of organic liquids.
Multiple View Geometry in Computer Vision (2004)

A basic problem in computer vision is to understand the structure of a real world scene given several images of it. Techniques for solving this problem are taken from projective geometry and photogrammetry. Here, the authors cover the geometric principles and their algebraic representation in terms of camera projection matrices, the fundamental matrix and the trifocal tensor. The theory and methods of computation of these entities are discussed with real examples, as is their use in the reconstruction of scenes from multiple images. The new edition features an extended introduction covering the key ideas in the book (which itself has been updated with additional examples and appendices) and significant new results which have appeared since the first edition. Comprehensive background material is provided, so readers familiar with linear algebra and basic numerical methods can understand the projective geometry and estimation algorithms presented, and implement the algorithms directly from the book.
Local beam angle optimization with linear programming and gradient search (2007)

The optimization of beam angles in IMRT planning is still an open problem, with literature focusing on heuristic strategies and exhaustive searches on discrete angle grids. We show how a beam angle set can be locally refined in a continuous manner using gradient-based optimization in the beam angle space. The gradient is derived using linear programming duality theory. Applying this local search to 100 random initial angle sets of a phantom pancreatic case demonstrates the method, and highlights the many-local-minima aspect of the BAO problem. Due to this function structure, we recommend a search strategy of a thorough global search followed by local refinement at promising beam angle sets. Extensions to nonlinear IMRT formulations are discussed.
Oxidizing and reducing agents (1999)

Partial table of contents: Aluminum Amalgam. Aluminum Hydride. Borane-Tetrahydrofuran. Bromine. Chromium(II) Chloride. Chromium(VI) Oxide. Hydrogen Sulfide. Iodosylbenzene. Lithium-Ethylamine. Lithium Naphthalenide. Manganese Dioxide. Mercury(II) Oxide. Palladium on Carbon. Palladium(II) Hydroxide on Carbon. Peracetic Acid. Rhodium on Alumina. Ruthenium Catalysts. Ruthenium(VIII) Oxide. Sodium-Alcohol. Sodium Amalgam. Sodium-Ammonia. Sulfur. Thallium(III) Nitrate Trihydrate. Thallium(III) Trifluoroacetate. Thexylborane. Zinc. Zinc Borohydride. Zinc/Copper Couple. List of Contributors. Indexes.
Effects of Soil Osmotic Potential on Nitrification, Ammonification, N-assimilation, and Nitrous Oxide Production (1997)

Previous studies have examined the effects of soil osmotic potential (Ψs) on net rates of mineralization and nitrification. Because net rates represent the difference between gross production and consumption processes, it is unclear which process is being affected. We used an 15N isotopic dilution method to evaluate the effects of Ψs on gross rates of nitrification, ammonification, NH+4 assimilation, and NO-3 assimilation, and net rates of nitrous oxide production in a Penoyer sandy loam at field capacity. To avoid creating specific ion toxicities that normally do not occur in this soil, we used a chemical equilibrium model to predict how solute concentrations in the soil solution change during evapo-concentration; then we used solutions containing these mixtures of solutes to create individual Ψs treatments. A nitrification potential assay was also performed to determine the effect of Ψs on nitrification rates at high substrate concentrations. In soil slurries with elevated NH+4 concentration (1110 μM), nitrification rates declined exponentially with reduced Ψs (increased salt concentration); however, in soil samples incubated at field capacity without added NH+4 (9.7 μM, or 2 mg N kg -1), the gross nitrification rate was independent of Ψs. The differential response between slurries and soil at field capacity was attributed to differences in NH+4 concentrations, and indicated that the effects of Ψs were secondary to NH+4 concentrations in controlling nitrification rates. Nitrification rates in slurries declined more when a single salt (K2SO4) was used than when the mixture of salts that more closely approximated the solute composition predicted to occur in the field was used to lower Ψs. This suggests that nitrifying bacteria are capable of adapting to specific ion toxicities. Gross rates of ammonification declined exponentially with decreased Ψs between 0 and -500 kPa but were independent of Ψs at potentials of -500 to -1750 kPa. Rates of microbial assimilation of NO-3 exceeded NH+4 assimilation by a factor of 4, indicating that under NH+4 limited conditions substantial NO-3 assimilation can occur. Microbial assimilation of both NH+4 and NO-3 declined exponentially with decreased Ψs, and were insignificant at <-1500 kPa Ψs. Because NO-3 assimilation declined more rapidly than gross nitrification, net nitrification rates actually increased with declining Ψs. Rates of nitrous oxide (N2O) production were also inversely correlated with Ψs. Our results indicate that in previous studies, measurement of net rates, use of inappropriate salts, and addition of substrate may have resulted in over-estimation of the adverse effects of low Ψs on rates of N-transformations.
LIGATURE AND SUTURE MATERIAL (1913)

For a number of years I have had it in mind to call attention to the particular method of employing silk ligatures and sutures which has been practiced in the surgical clinic of the Johns Hopkins University since the opening of the Johns Hopkins Hospital in 1889, but have hesitated and also been eager to do so for the same reason, namely, that our school seems to be almost alone in its advocacy of the use of this material. Theodor Kocher, however, has for many years employed silk quite to the exclusion of catgut and our position is greatly strengthened by the support of such eminent authority. Surgeons, old and young, those who have been active and masterful in the marvelous period of development of antiseptic surgery, and the medical student who takes for granted the healing of wounds per primam and the achievements of modern surgery as he does