gebhart/patrepeval huggingface dataset:
Progress in Ion Torrent semiconductor chip based sequencing (2012)

In order for next‐generation sequencing to become widely used as a diagnostic in the healthcare industry, sequencing instrumentation will need to be mass produced with a high degree of quality and economy. One way to achieve this is to recast DNA sequencing in a format that fully leverages the manufacturing base created for computer chips, complementary metal‐oxide semiconductor chip fabrication, which is the current pinnacle of large scale, high quality, low‐cost manufacturing of high technology. To achieve this, ideally the entire sensory apparatus of the sequencer would be embodied in a standard semiconductor chip, manufactured in the same fab facilities used for logic and memory chips. Recently, such a sequencing chip, and the associated sequencing platform, has been developed and commercialized by Ion Torrent, a division of Life Technologies, Inc. Here we provide an overview of this semiconductor chip based sequencing technology, and summarize the progress made since its commercial introduction. We described in detail the progress in chip scaling, sequencing throughput, read length, and accuracy. We also summarize the enhancements in the associated platform, including sample preparation, data processing, and engagement of the broader development community through open source and crowdsourcing initiatives.
Effect of Fish Oil Treatment on Gentamicin Nephrotoxicity in Rats (1994)

The effect of fish oil on gentamicin-induced nephrotoxicity was investigated in rats. Gentamicin (80 mg/kg/day intramuscularly for 6 days) produced the typical pattern of nephrotoxicity as shown by increases in serum creatinine and urea concentrations, and urinary N-acetyl-beta-D-glucosaminidase (NAG) activity and proximal renal tubular necrosis. Fish oil (5.0 ml/kg/kday per os for 10 days) partially protected against the nephrotoxicity induced by gentamicin administered during the last 6 days of treatment with fish oil by returning the creatinine and urea concentrations and NAG activity to normal and by ameliorating the histopathological damage. Olive oil (5 mg/kg/day per os for 10 days) was ineffective in protecting rats against gentamicin nephrotoxicity.
Catalytic Asymmetric Dihydroxylation (1994)

ADVERTISEMENT RETURN TO ISSUEPREVArticleCatalytic Asymmetric DihydroxylationHartmuth C. Kolb, Michael S. VanNieuwenhze, and K. Barry SharplessCite this: Chem. Rev. 1994, 94, 8, 2483–2547Publication Date (Print):December 1, 1994Publication History Published online1 May 2002Published inissue 1 December 1994https://pubs.acs.org/doi/10.1021/cr00032a009https://doi.org/10.1021/cr00032a009research-articleACS PublicationsRequest reuse permissionsArticle Views36251Altmetric-Citations3457LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Tunable infrared laser detection of pyrolysis products of explosives in soils (1996)

A research program involving two applications of tunable infrared laser differential absorption spectroscopy (TILDAS) with multipass, long-path absorption cells to the detection of explosives contamination in soils is reported. In the first application, sensitive, specific real-time species concentration measurements by TILDAS have led to new understanding of the processes involved in explosives detection by the heating of contaminated soils and the quantification of the resulting pyrolysis gases. In the second, we present results of our calculations of the properties of astigmatic off-axis resonator absorption cells, which show that useful TILDAS path lengths can be achieved inside a cone penetrometer probe.
Systemic Administration of Human Bone Marrow-Derived Mesenchymal Stromal Cell Extracellular Vesicles Ameliorates <i>Aspergillus</i> Hyphal Extract-Induced Allergic Airway Inflammation in Immunocompetent Mice (2015)

There is a growing experience demonstrating benefit of mesenchymal stromal cell (MSC)-based cell therapies in preclinical models of asthma. In the current study, conditioned media (CM) and, in particular, the extracellular vesicle fraction obtained from the CM were as potent as the MSCs themselves in mitigating Th2/Th17-mediated allergic airway inflammation in a mouse model of severe refractory clinical asthma. Moreover, human MSC CM and extracellular vesicles were effective in this immunocompetent mouse model. These data add to a growing scientific basis for initiating clinical trials of MSCs or extracellular vesicles derived from MSCs in severe refractory asthma and provide further insight into the mechanisms by which the MSCs may ameliorate the asthma.
A textbook of orthodontics (1975)

Postnatal growth of the skull and jaws the occlusion of the teeth the development of the occlusion of the teeth skeletal factors affecting occlusal development muscle factors affecting occlusal development dental factors affecting occlusal development.
Engineering plastics from lignin II. Characterization of hydroxyalkyl lignin derivatives (1984)

Abstract Several types of hydroxyalkyl lignin derivatives were synthesized from milled wood, organosolv, steam explosion, acid (H 2 SO 4 ) hydrolysis, and kraft lignin with ethylene oxide, propylene oxide, and butylene oxide by either batch reaction in toluene at 180°C using KOH as catalyst, or in aqueous alkali at room temperature. The isolated derivatives were characterized in terms of their chemical structures by H‐NMR and FT‐IR spectroscopy. Thermal properties were determined by differential scanning calorimetry. Molecular weights were measured by gel permeation chromatography on polystyrene/lignin model compound calibrated high pressure μ‐spherogel columns. Solubilities in various organic solvents spanning a solubility parameter (δ) range from 9.3 to 14.5 and a hydrogen bonding index (γ) range from 1.5 to 18.7 were tested using UV 280 absorption of solutions of up to with degrees of substitution of between 1 and 2.6 (except for ethylene oxide derivatives which were higher) and with lignin contents of around 60%. The drastic reduction of glass transition temperature of between 50° and 100° is explained with increased free volume of the copolymer and with disruption of hydrogen bonds involving especially phenolic hydroxy groups. The greatly enhanced solubility in organic solvents indicates absence of the gel structure typical of network polymers. No molecular breakdown was observed as a consequence of oxyalkylation. The derivatives had molecular weights ( M w ) of between 2000 and 50,000 at dispersity factors of between 2.5 and 25. The derivatives seem to constitute useful prepolymers for thermosetting engineering plastics.
Value Analysis of Battery Energy Storage Applications in Power Systems (2006)

Stressed and less secure power system operating conditions have encouraged both power utilities and large power consumers to look for bulk energy storage systems. Battery energy storage systems (BESS) have excellent records and are used for decades in power systems. This paper describes a methodology for a monetary value analysis of the BESS for load leveling, control power and peak shaving applications. The purpose of this value analysis is to highlight the application with the highest financial benefit for the owner of the BESS. To determine the overall economic viability, revenue of each application has been compared with capital and operating costs over the BESS lifetime. The results of the value analysis show that primary control power is the application that most likely will be asked for by utilities during next 3-5 years
Glial Fibrillary Acidic Protein is Highly Correlated With Brain Injury (2008)

GFAP is a serum marker of TBI, and persistent elevation on day 2 is predictive of increased mortality. Excellent specificity for CT-documented brain injury was found using a cutoff point of 1 pg/mL.
The future of onychomycosis therapy may involve a combination of approaches (2008)

Onychomycosis is a fungal infection of the nail unit, most commonly caused by the anthropophilic dermatophyte fungi. It is generally accepted that this disease is increasing in prevalence despite the introduction of new and efficacious antifungal drugs. Several studies have documented health-related quality-of-life issues associated with onychomycosis and it is clear that patient treatment is both necessary and desirable. The aetiology and pathogenesis of onychomycosis is coming under increasing scrutiny and work in this field has grown substantially in recent years. This is reflected by the increased assurance with which clinicians can now prescribe treatment and be confident of improvement in a majority of their patients. However, a significant proportion of patients, perhaps as many as 25-40% of those encountered in clinical practice, are classified as treatment failures. Clinical indicators for poor prognosis include the development of residual foci of subungual fungal growth, onycholysis and severe disease. These observations have led to a resurgence of interest in combination treatments for use in patients at risk of failure/relapse. Several types of combination can be considered, including the use of oral or topical drugs and the concomitant use of surgical techniques, all of which have a place in the treatment of onychomycosis.
Pretreatment of myoblast cultures with basic fibroblast growth factor increases the efficacy of their transplantation in mdx mice (1995)

The effect of pretreatment of cultures with basic fibroblast growth factor (bFGF) on myoblast allotransplantation to C57BL/10ScSn mdx/mdx mouse (mdx mouse) muscles not previously damaged and not irradiated was studied. Transgenic CD1 mice which have a beta-galactosidase gene under the control of the promoter of the quail fast skeletal muscle troponin I gene, were used as donors. The myoblasts were grown with 100 ng/mL bFGF during the last 2 days before injecting them in the left tibialis anterior (TA) muscles of mdx mice. Myoblasts from the same primary cultures were also grown without bFGF and injected in the right TA muscles as control. The recipient mice were immunosuppressed with FK 506. Twenty-eight days after myoblast transplantation, the percentage of beta-galactosidase-positive fibers was significantly higher (more than fourfold) following culture with bFGF than without bFGF. Almost all beta-galactosidase-positive fibers were also dystrophin positive. Direct intramuscular injections of bFGF or of Hank's balanced salt solution (HBSS) at the time of myoblast transplantation and at several intervals afterwards were also investigated. The percentage of beta-galactosidase-positive fibers did not differ significantly following intramuscular injection of bFGF from controls injected with HBSS. In vitro, this high concentration of bFGF significantly reduced the formation of myotubes, and the percentage of mononuclear cells which were myoblasts was significantly increased by 34%. These observations alone do not account for the fourfold increase in transplantation success. The presence of bFGF in the culture did not significantly increase the cell survival 3 days after their transplantation.(ABSTRACT TRUNCATED AT 250 WORDS)
Normalized maximum likelihood model of order-1 for the compression of DNA sequences (2007)

We present the NML model for classes of models with memory described by first order dependencies. The model is used for efficiently locating and encoding the best regressor present in a dictionary. By combining the order-1 NML with the order-0 NML model the resulting algorithm achieves a consistent improvement over the earlier order-0 NML algorithm, and it is demonstrated to have superior performance on the practical compression of the human genome
Acidimicrobium ferrooxidans gen. nov., sp. nov.: mixed-culture ferrous iron oxidation with Sulfobacillus species (1996)

A new species of ferrous-iron-oxidizing, moderately thermophilic, acidophilic bacteria, <i>Acidimicrobium ferrooxidans</i>, has been described. Two isolates of the species differed only in the tendency of one, previously known as strain TH3, to grow in filaments. The chromosomal DNA base composition is between 67 and 69 mol% G + C. The capacity of this species to fix CO<sub>2</sub> from air was greater than that of iron-oxidizing thermoacidophiles of the genus <i>Sulfobacillus</i>, which required an enhanced CO<sub>2</sub> concentration for optimum autotrophic growth. Under air, ferrous iron oxidation in mixed cultures of <i>A. ferrooxidans</i> with either <i>Sulfobacillus thermosulfidooxidans</i> or <i>Sulfobacillus acidophilus</i> was more extensive than in pure cultures of these three strains. The greater part of ferrous iron oxidation in mixed cultures probably resulted from activity of the <i>Sulfobacillus</i> species, which possess a greater tolerance of ferric iron, and which presumably grew mixotrophically utilizing organic compounds from <i>A. ferrooxidans</i>.
Vitamin K-dependent carboxylase. (1985)

Vitamin K-dependent carboxylase is found in the liver, where it is involved in the synthesis of four blood coagulation factors and protein C. The hepatic enzyme has partly been purified and several mechanisms have been postulated for the vitamin K-dependent carboxylation reaction. Recently the enzyme has also been detected in other tissues including the lung, kidney, spleen, testis, bone and arterial vessel wall. The proteins produced by these non-hepatic carboxylases are now being characterized, but in most cases their function is still unknown. This paper is meant to review our present knowledge in this field.
Fundamentals of Vibration Analysis (1956)

Geared toward advanced undergraduate and graduate students in engineering, this concise textbook discusses vibration problems, dealing with systems of one and more than one degree of freedom. Numerous examples and problems assist students in mastering the material and demonstrate the applicability of the methods of analysis used in the text. Starting with an overview of the fundamentals, the treatment examines undamped vibrations of single-degree-of-freedom systems, vibrations of single-degree-of-freedom systems with viscous damping, systems of one degree of freedom with nonviscous damping, and undamped vibrations of systems with more than one degree of freedom. Additional topics include application of generalized coordinates, damped vibrations of systems with more than one degree of freedom, and tabular methods for finding natural frequencies. Numerous figures illuminate the text, which concludes with a substantial section of answers to the problems.
Combined targeting of MAPK and AKT signalling pathways is a promising strategy for melanoma treatment (2007)

Combined targeting of MAPK and AKT signalling pathways is a promising strategy for melanoma treatment and should encourage further in-depth investigations.
Analysis of Methylated 6-Mercaptopurine Metabolites in Human Blood Cells (1997)

Blood samples from 34 recipients of kidney transplants who were on multidrug therapy including azathioprine were analyzed using two methods in parallel for red blood cell (RBC) concentrations of methylated 6-mercaptopurine (6-MP) metabolites. Chemical hydrolysis with high-performance liquid chromatography (HPLC) showed values ranging from 0 to 20,259 pmol/8 x 10(8) RBCs, compared with enzymatic hydrolysis with HPLC that resulted in values ranging from 16 to 22,252 pmol/100 microl packed RBC. Results of the two methods were highly correlated; the coefficient of correlation (r) was equal to 0.93 (95% confidence interval [CI] = 0.87-0.97 [y = 1.12x + 187]). Within series imprecision was 3.1% compared with 6.3%, and between-run imprecision was 10.3% compared with 20.7%, for the enzymatic and chemical methods, respectively. The enzymatic method was found to be more specific and to save time and labor, but with the chemical method methylated metabolites and 6-thioguanine nucleotides (6-TGN), the main active metabolites of azathioprine and 6-MP, can be measured in the same run. The results indicate that methylated 6-MP metabolites mainly exist as ribonucleotides in RBCs.
Purification and properties of glucose-6-phosphate dehydrogenase from Bacillus stearothermophilus. (1985)

Glucose-6-phosphate dehydrogenase (D-glucose-6-phosphate: NADP+ 1-oxidoreductase, EC 1.1.1.49) from the thermophilic bacteria, Bacillus stearothermophilus, was purified and its properties were examined. The enzyme was shown to consist of four identical subunits, each of about Mr 50,000. This enzyme utilized both NADP+ and NAD+ as cofactors, and the maximum velocity for both cofactors was similar. However, the Km values were quite different from each other, being 0.016 and 1.64 mM for NADP+ and NAD+, respectively. From the analysis of sulfhydryl groups it was shown that there is one sulfhydryl group and one disulfide bridge per subunit. This sulfhydryl group had no reactivity with 5,5'-dithiobis(2-nitrobenzoic acid) in the absence of guanidine hydrochloride. The enzyme showed a remarkable thermostability as well as storage stability.
Performance testing of combinatorial solvers with isomorph class instances (2007)

Combinatorial optimization problems expressed as Boolean constraint satisfaction problems (BCSPs) arise in several contexts, ranging from the classical unate set-packing problems to the binate minimum cover problems, including the Haplotype Inference by Pure Parsimony (HIPP) problem. These problems are being solved under different formulations and in different formats. Results of experiments that are reported can be seldom compared and replicated.
GABA uptake inhibitors containing mono- and diarylmethoxyalkyl N-substituents. (1989)

Analogues of GABA and the GABA uptake inhibitors, nipecotic acid and guvacine, carrying N-(mono)- or N-(diarylmethoxy)alkyl substituents were synthesized and tested in vitro as inhibitors of synaptosomal GABA uptake and GABAA receptor binding. Whereas the N-(diphenylmethoxy)ethyl derivative GABA (compound 23) (see Figures 1 and Scheme 1 for structures) was only a moderately potent inhibitor of GABA uptake, corresponding derivatives of nipecotic acid and guvacine compounds 7e and 16, respectively) were potent inhibitors having IC50 values in the low micromolar range. In the case of 7e, (a) the (R)-isomer (10) was three times more potent than the (S)-isomer (13), (b) the bis-4-chlorophenyl analogue (compound 7g) was more potent than 7e, (c) the introduction of an additional methylene group into the linkage between the nipecotic acid and benzhydryl ether moiety (to give 7f) did not significantly affect in vitro biological activity, and (d) removal of one of the phenyl groups, or replacement of the benzhydryl ether group by the conformationally restrained fluorenyloxy group (to give 7i), resulted in substantial loss of activity. None of the compounds synthesized showed detectable affinity for GABAA receptor sites.
Effect of Triamcinolone Acetonide Injections on Hemiplegic Shoulder Pain (2000)

-In the 37 participants included in this study, triamcinolone injections seemed to decrease hemiplegic shoulder pain and to accelerate recovery, but this effect was not statistically significant. Therefore, on the basis of the results of this study, these injections cannot be recommended for the treatment of patients with hemiplegic shoulder pain.
Expression of a connexin 43/beta-galactosidase fusion protein inhibits gap junctional communication in NIH3T3 cells. (1995)

Gap junctions contain membrane channels that mediate the cell-to-cell movement of ions, metabolites and cell signaling molecules. As gap junctions are comprised of a hexameric array of connexin polypeptides, the expression of a mutant connexin polypeptide may exert a dominant negative effect on gap junctional communication. To examine this possibility, we constructed a connexin 43 (Cx43)/beta-galactosidase (beta-gal) expression vector in which the bacterial beta-gal protein is fused in frame to the carboxy terminus of Cx43. This vector was transfected into NIH3T3 cells, a cell line which is well coupled via gap junctions and expresses high levels of Cx43. Transfectant clones were shown to express the fusion protein by northern and western analysis. X-Gal staining further revealed that all of the fusion protein containing cells also expressed beta-gal enzymatic activity. Double immunostaining with a beta-gal and Cx43 antibody demonstrated that the fusion protein is immunolocalized to the perinuclear region of the cytoplasm and also as punctate spots at regions of cell-cell contact. This pattern is similar to that of Cx43 in the parental 3T3 cells, except that in the fusion protein expressing cells, Cx43 expression was reduced at regions of cell-cell contact. Examination of gap junctional communication (GJC) with dye injection studies further showed that dye coupling was inhibited in the fusion protein expressing cells, with the largest reduction in coupling found in a clone exhibiting little Cx43 localization at regions of cell-cell contact. When the fusion protein expression vector was transfected into the communication poor C6 cell line, abundant fusion protein expression was observed, but unlike the transfected NIH3T3 cells, no fusion protein was detected at the cell surface. Nevertheless, dye coupling was inhibited in these C6 cells. Based on these observations, we propose that the fusion protein may inhibit GJC by sequestering the Cx43 protein intracellularly. Overall, these results demonstrate that the Cx43/beta-gal fusion protein can exert a dominant negative effect on GJC in two different cell types, and suggests that it may serve as a useful approach for probing the biological function of gap junctions.
KEYWORD EXTRACTION FROM A SINGLE DOCUMENT USING WORD CO-OCCURRENCE STATISTICAL INFORMATION (2004)

We present a new keyword extraction algorithm that applies to a single document without using a corpus. Frequent terms are extracted first, then a set of co-occurrences between each term and the frequent terms, i.e., occurrences in the same sentences, is generated. Co-occurrence distribution shows importance of a term in the document as follows. If the probability distribution of co-occurrence between term a and the frequent terms is biased to a particular subset of frequent terms, then term a is likely to be a keyword. The degree of bias of a distribution is measured by the χ 2 -measure. Our algorithm shows comparable performance to tfidf without using a corpus.