gebhart/patrepeval huggingface dataset:
Nonsense but Not Missense Mutations Can Decrease the Abundance of Nuclear mRNA for the Mouse Major Urinary Protein, While Both Types of Mutations Can Facilitate Exon Skipping (1994)

In an effort to understand the mechanisms by which nonsense codons affect RNA metabolism in mammalian cells, nonsense mutations were generated within the gene for the secretory major urinary protein (MUP) of mice. The translation of MUP mRNA normally begins within exon 1 and terminates within exon 6, the penultimate exon. Through the use of Northern (RNA) blot hybridization and assays that couple reverse transcription and PCR, a nonsense mutation within codon 50 of exon 2 or codon 143 of exon 5 was found to reduce the abundance of fully spliced, nuclear MUP mRNA to 10 to 20% of normal without an additional reduction in the abundance of cytoplasmic mRNA. In contrast, a nonsense mutation within codon 172 of exon 5 was found to have no effects on the abundance of MUP mRNA. These findings suggest that a boundary between nonsense mutations that do and do not reduce the abundance of nuclear mRNA exists within the exon preceding the exon that harbors the normal site of translation termination. In this way, the boundary is analogous to the boundary that exists within the penultimate exon of the human gene for the cytosolic enzyme triosephosphate isomerase. Assays for exon skipping, i.e., the removal of an exon as a part of the flanking introns during the process of splicing, reveal that 0.1, 2.0, and 0.1% of MUP mRNA normally lack exon 5, exon 6, and exons 5 plus 6, respectively. Relative to normal, the two nonsense mutations within exon 5 increase the abundance of RNA lacking exon 5 on average 20-fold and increase the abundance of RNA lacking exons 5 plus 6 on average 5-fold. Since only one of these nonsense mutations also reduces the abundance of fully spliced nuclear mRNA to 10 to 20% of normal, the two mechanisms by which a nonsense mutation can alter nuclear RNA metabolism must be distinct. The analysis of missense mutations within codons 143 and 172, some of which retain the nonsense mutation, indicates that the reduction in the abundance of fully spliced nuclear mRNA is dependent upon the premature termination of MUP mRNA translation, whereas skipping is attributable to nonsense mutation-mediated changes in exon 5 structure rather than to the premature termination of translation. The increase in exon 5 skipping by either the nonsense or missense mutations within codon 172 correlates with a decrease in the complementarity of exon 5 to U1 snRNA. This suggests that a 5' splice site may extend as far as 12 nucleotides into the upstream exon, which is, to our knowledge, the largest extension.
IQ-METER - An evaluation tool for data-transformation systems (2014)

We call a data-transformation system any system that maps, translates and exchanges data across different representations. Nowadays, data architects are faced with a large variety of transformation tasks, and there is huge number of different approaches and systems that were conceived to solve them. As a consequence, it is very important to be able to evaluate such alternative solutions, in order to pick up the right ones for the problem at hand. To do this, we introduce IQ-Meter, the first comprehensive tool for the evaluation of data-transformation systems. IQ-Meter can be used to benchmark, test, and even learn the best usage of data-transformation tools. It builds on a number of novel algorithms to measure the quality of outputs and the human effort required by a given system, and ultimately measures “how much intelligence” the system brings to the solution of a data-translation task.
El proceso de globalización: análisis de las propuestas alternativas al consenso de Washington (2007)

El presente trabajo tiene como objetivo exponer y plantear alternativas a las principales corrientes teoricas y practicas implementadas a nivel mundial por el proceso de globalizacion desde el punto de vista mas ortodoxo segun las pautas recogidas en los anos noventa en el llamado Consenso de Washington. Las sucesivas crisis experimentadas, principalmente, por las economias latinoamericanas a lo largo de los ultimos quince anos dejan entrever que pueden plantearse alternativas a la ejecucion de las politicas economicas contenidas en dicho Consenso. Asi, tras la exposicion de las teorias economicas neoliberales se desarrolla una serie de propuestas y soluciones alternativas relativas al comercio internacional, la deuda externa, la ayuda al desarrollo, la imposicion internacional, las prestaciones publicas y la cercania al ciudadano han surgido a lo largo de los ultimos anos procedentes de los movimientosantiglobalizacion, los cuales no se oponen al hecho en si de la mundializacion, sino a la forma en que esta ha sido llevada a cabo por parte de las principales organizaciones economicas mundiales.
Carbon dioxide and HF laser-induced decomposition of methanol (1982)

Methanol absorbs HF laser radiation in the O-H stretching mode and CO 2 laser radiation in its C-O stretching mode. Thus multiphoton absorption (MPA) and multiphoton decomposition (MPD) experiments determining the effect on product yields of irradiating different modes of the same small molecule are possible for methanol. Such a comparison has been reported previously. 1 However, another study of CO 2 laser-induced MPD 2 disagreed with the product ratios reported.
FORMATION OF PORPHYRINS FROM PYRROLE AND ALDEHYDES (1935)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTFORMATION OF PORPHYRINS FROM PYRROLE AND ALDEHYDESPaul RothemundCite this: J. Am. Chem. Soc. 1935, 57, 10, 2010–2011Publication Date (Print):October 1, 1935Publication History Published online1 May 2002Published inissue 1 October 1935https://pubs.acs.org/doi/10.1021/ja01313a510https://doi.org/10.1021/ja01313a510research-articleACS PublicationsRequest reuse permissionsArticle Views6221Altmetric-Citations208LEARN 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
Safe, rapid administration of cisplatin in the outpatient clinic. (1986)

The records of 147 cancer patients who received at least three courses of cisplatin-containing chemotherapy in the Arizona Cancer Center clinic between 1982 and 1985 were reviewed to determine the safety and tolerance of cisplatin administered in the outpatient setting. Cisplatin was administered at doses of 50-120 mg/m2 every 3-4 weeks. The drug was added to 400 ml of 10% mannitol, was brought up to 1-L volume with normal saline containing 3 g of magnesium sulfate, and was administered iv over 1 hour. An additional liter of normal saline was administered over approximately 1 hour in patients who received cisplatin doses of 70-120 mg/m2. Courses were interrupted if the serum creatinine was greater than 1.5 mg/dl just prior to the next scheduled dose. The median total doses of cisplatin per patient were 487, 595, and 683 mg/m2 and complete plus partial response rates were 64%, 71%, and 78% for those patients who received 50-60, 70-90, and 100-120 mg/m2/course, respectively. Cisplatin-containing therapy was tolerated without evidence of renal failure and with only moderate to severe emesis in 25% of the patients. Calculated creatinine clearances dropped only 4.9%, 13.9%, and 14.9% between Courses 1 and 6 in patients receiving cisplatin doses of 50-60, 70-90, and 100-120 mg/m2, respectively. We conclude that cisplatin doses of 50-120 mg/m2 can be administered safely and with acceptable tolerance in the outpatient setting.
Acoustic Interactions of a Pulse Detonation Engine Array with a Gas Turbine (2006)

*† ‡ Peak pressure attenuation data is presented for pulse detonation combustor (PDC) firing into a single stage axial flow turbine. Cases are presented for both single PDC tubes and for an annular array of six PDC tubes. Pressure attenuation is characterized for a wide array of PDC operating parameters, including fill fraction, equivalence ratio, nitrogen dilution percentage, and firing frequency. Effects of additional cold air flow mixed into the PDC exhaust prior to the turbine inlet are also quantified. It is shown that certain PDC operating conditions lead to a maximum peak pressure attenuation, which should correspond to the greatest energy extraction by the turbine from the PDC exhaust flow.
A computationally identified compound antagonizes excess FGF-23 signaling in renal tubules and a mouse model of hypophosphatemia (2016)

Fibroblast growth factor-23 (FGF-23) interacts with a binary receptor complex composed of α-Klotho (α-KL) and FGF receptors (FGFRs) to regulate phosphate and vitamin D metabolism in the kidney. Excess FGF-23 production, which causes hypophosphatemia, is genetically inherited or occurs with chronic kidney disease. Among other symptoms, hypophosphatemia causes vitamin D deficiency and the bone-softening disorder rickets. Current therapeutics that target the receptor complex have limited utility clinically. Using a computationally driven, structure-based, ensemble docking and virtual high-throughput screening approach, we identified four novel compounds predicted to selectively inhibit FGF-23-induced activation of the FGFR/α-KL complex. Additional modeling and functional analysis found that Zinc13407541 bound to FGF-23 and disrupted its interaction with the FGFR1/α-KL complex; experiments in a heterologous cell expression system showed that Zinc13407541 selectivity inhibited α-KL-dependent FGF-23 signaling. Zinc13407541 also inhibited FGF-23 signaling in isolated renal tubules ex vivo and partially reversed the hypophosphatemic effects of excess FGF-23 in a mouse model. These chemical probes provide a platform to develop lead compounds to treat disorders caused by excess FGF-23.
The Modular Modeling System (MMS): User's Manual (1996)

The Modular Modeling System (MMS) is an integrated system of computer software that has been developed to provide the research and operational framework needed to support development, testing, and evaluation of physical-process algorithms and to facilitate integration of user-selected sets of algorithms into operational physical-process models. MMS uses a module library that contains modules for simulating a variety of water, energy, and biogeochemical processes. A model is created by selectively coupling the most appropriate modules from the library to create a 'suitable' model for the desired application. Where existing modules do not provide appropriate process algorithms, new modules can be developed. The MMS user's manual provides installation instructions and a detailed discussion of system concepts, module development, and model development and application using the MMS graphical user interface.
Blood Cell Palmitoleate-Palmitate Ratio Is an Independent Prognostic Factor for Amyotrophic Lateral Sclerosis (2015)

Growing evidence supports a link between fatty acid metabolism and amyotrophic lateral sclerosis (ALS). Here we determined the fatty acid composition of blood lipids to identify markers of disease progression and survival. We enrolled 117 patients from two clinical centers and 48 of these were age and gender matched with healthy volunteers. We extracted total lipids from serum and blood cells, and separated fatty acid methyl esters by gas chromatography. We measured circulating biochemical parameters indicative of the metabolic status. Association between fatty acid composition and clinical readouts was studied, including ALS functional rating scale-revised (ALSFRS-R), survival, disease duration, site of onset and body mass index. Palmitoleate (16:1) and oleate (18:1) levels, and stearoyl-CoA desaturase indices (16:1/16:0 and 18:1/18:0) significantly increased in blood cells from ALS patients compared to healthy controls. Palmitoleate levels and 16:1/16:0 ratio in blood cells, but not body mass index or leptin concentrations, negatively correlated with ALSFRS-R decline over a six-month period (p<0.05). Multivariate Cox analysis, with age, body mass index, site of onset and ALSFRS-R as covariables, showed that blood cell 16:1/16:0 ratio was an independent prognostic factor for survival (hazard ratio=0.1 per unit of ratio, 95% confidence interval=0.01-0.57, p=0.009). In patients with high 16:1/16:0 ratio, survival at blood collection was extended by 10 months, as compared to patients with low ratio. The 16:1/16:0 index is an easy-to-handle parameter that predicts survival of ALS
Automatic synthesis, analysis and implementation of a fuzzy controller (2002)

A method based on the cell-to-cell approach is proposed for extracting the control rules for a fuzzy controller. This procedure was implemented to control the position of a DC motor. To obtain high performance in terms of fuzzy inferences per second (FIPS) that complex control requires, the rules and the membership functions have been implemented via a hardware solution, WARP. WARP is a dedicated VLSI machine with an architecture designed to efficiently exploit data provided by the cell-to-cell approach. The global architecture along with some generalities on the particular approach are presented.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
The effect of wood‐derived inhibitors on 2, 3‐butanediol production by <i>Klebsiella pneumoniae</i> (1988)

Four potential inhibitors, hydroxymethylfurfural, furfural, syringaldehyde and vanillin, were assayed over a range of concentrations and times to simulate the amounts that might be expected to accumulate when the hydrolyzed water-soluble fraction from steam-treated aspenwood was added in a fed-batch mode to K. pneumoniae. Combinations of the individual materials resulted in a cumulative inhibitory effect. Prolonged incubation could alleviate some of the inhibition.
The use of UDP-Glc:glycoprotein glucosyltransferase for radiolabeling protein-linked high mannose-type oligosaccharides. (1996)

A simple method for specifically radiolabeling high mannose-type oligosaccharides linked to protein backbones has been developed. The method is based on the fact that incubation of rat liver UDP-Glc:glycoprotein glucosyltransferase, glucose-labelled UDP-Glc and a denatured high mannose-type glycoprotein target leads to the glucosylation of the oligosaccharide. In the case described here it allowed to follow easily the purification, by HPLC and affinity chromatography, of labelled glycopeptides obtained by controlled proteolysis of cruzipain, a cysteine proteinase isolated from the human pathogen Trypanosoma cruzi. It was thus determined that the N-glycosylation site in Asn33 of cruzipain is occupied by high mannose-type oligosaccharides.
Photolabeling of Calmodulin with Basic, Amphiphilic α-Helical Peptides Containing p-Benzoylphenylalanine (1989)

A novel photoreactive amino acid has been incorporated synthetically into two model peptides and the calmodulin-binding domain from myosin light chain kinase. Cross-linked photoadducts of each peptide with calmodulin have been prepared and digested by chemical and/or enzymatic methods to determine the site of label attachment. Depending on the position of the photoprobe in the peptide sequence, either Met-144 or Met-71 is photolabeled. These results are discussed in relation to the three-dimensional structure of calmodulin obtained crystallographically and the known solution properties of calmodulin.
<title>Color 3D electronic imaging of the surface of the human body</title> (1994)

The NRC laboratories have developed a laser scanning technique to digitize shapes and colors in registration. The technique, known as synchronized scanning, is capable of digitizing topography as small as the relief of a bare finger tip, showing a clear picture of the skin structure (essentially a clean fingerprint without distortion), as well as the shape and size of body components such as hands, face, and feet, and the full body of one or more subjects simultaneously. The laser scanner uses a RGB laser, coupled to an optical fiber, which is projected in the field of view. The 3D color measurements are made by optical triangulation to a resolution of 10 micrometers for finger tip scans and a resolution of 1 mm for whole body scans. Experimental results are presented and discussed. Potential applications of this technology in the field of identification and inspection of humans include face recognition, finger, foot and teeth print identification, and 3D mugshots that can be rapidly broadcast through satellite communication. One of the unique properties of this technology is that absolute measurements, not only appearance and relative position of features, can be used for identification purposes.
Giardia intestinalis and Fructose Malabsorption: A Frequent Association (2019)

Nowadays, scientific studies are emerging on the possible etiological role of intestinal parasites in functional digestive disorders. Our study was carried out with healthy individuals (control group; <i>n</i> = 82) and symptomatic patients with lactose or fructose malabsorption, including positive (malabsorbers; <i>n</i> = 213) and negative (absorbers; <i>n</i> = 56) breath test, being analyzed for the presence of intestinal parasites. A high parasitic prevalence was observed in malabsorbers (41.8%), exclusively due to single-cell eukaryotes but not helminths. <i>Giardia intestinalis</i> was the predominant parasite in cases of abnormal absorption (26.5%), significantly associated with fructose malabsorption and doubling the probability of developing this pathology. Within controls, <i>Blastocystis</i> sp. (13.4%) was almost the only parasite, being the second among patients (12.6%), and <i>Cryptosporidium parvum</i>, the last species of clinical relevance, was detected exclusively in two malabsorbers (0.9%). The consumption of ecological food and professions with direct contact with humans arose as risk factors of parasitism. A diagnosis of carbohydrate malabsorption in adulthood is the starting point, making the search for the primary cause necessary. Accurate parasitological diagnosis should be considered another tool in the clinical routine for patients with recurrent symptoms, since their condition may be reversible with adequate therapeutic intervention.
Histopathological findings after treatment of prostate cancer using high‐intensity focused ultrasound (HIFU) (2010)

The pathologist should be aware of common histologic findings in prostatic biopsies after HIFU treatment. We recommend routine reporting of Gleason scores in post-HIFU needle biopsies.
Acceleration of the sliding movement of actin filaments with the use of a non-motile mutant myosin in in vitro motility assays driven by skeletal muscle heavy meromyosin (2017)

We examined the movement of an actin filament sliding on a mixture of normal and genetically modified myosin molecules that were attached to a glass surface. For this purpose, we used a Dictyostelium G680V mutant myosin II whose release rates of Pi and ADP were highly suppressed relative to normal myosin, leading to a significantly extended life-time of the strongly bound state with actin and virtually no motility. When the mixing ratio of G680V mutant myosin II to skeletal muscle HMM (heavy myosin) was 0.01%, the actin filaments moved intermittently. When they moved, their sliding velocities were about two-fold faster than the velocity of skeletal HMM alone. Furthermore, sliding movements were also faster when the actin filaments were allowed to slide on skeletal muscle HMM-coated glass surfaces in the motility buffer solution containing G680V HMM. In this case no intermittent movement was observed. When the actin filaments used were copolymerized with a fusion protein consisting of Dictyostelium actin and Dictyostelium G680V myosin II motor domain, similar faster sliding movements were observed on skeletal muscle HMM-coated surfaces. The filament sliding velocities were about two-fold greater than the velocities of normal actin filaments. We found that the velocity of actin filaments sliding on skeletal muscle myosin molecules increased in the presence of a non-motile G680V mutant myosin motor.
Hyperammonemia and Coma without Hepatic Dysfunction Induced by Valproate Therapy (2001)

The authors report a case of a 41-year-old mentally disabled man with bipolar disorder who presented to the emergency department with altered mental status. He was found to have a significantly elevated ammonia level (377 microM/L) with no signs of hepatic insufficiency. His coma and hyperammonemia were attributed to his chronic valproate therapy. This patient had the highest serum ammonia level ever reported with a therapeutic valproate level in the absence of any other anticonvulsant therapy, metabolic abnormality, or hepatic dysfunction. The authors discuss this case and review the current literature on hyperammonemia in valproic acid therapy and the use of L-carnitine in these patients.
Irradiation effects test series, test IE-5. Test results report. [PWR] (1978)

Test IE-5, conducted in the Power Burst Facility at the Idaho National Engineering Laboratory, employed three 0.97-m long pressurized water reactor type fuel rods, fabricated from previously irradiated zircaloy-4 cladding and one similar rod fabricated from unirradiated cladding. The objectives of the test were to evaluate the influence of simulated fission products, cladding irradiation damage, and fuel rod internal pressure on pellet-cladding interaction during a power ramp and on fuel rod behavior during film boiling operation. The four rods were subjected to a preconditioning period, a power ramp to an average fuel rod peak power of 65 kW/m, and steady state operation for one hour at a coolant mass flux of 4880 kg/s-m/sup 2/ for each rod. After a flow reduction to 1800 kg/s-m/sup 2/, film boiling occurred on one rod. Additional flow reductions to 970 kg/s-m/sup 2/ produced film boiling on the three remaining fuel rods. Maximum time in film boiling was 80s. The rod having the highest initial internal pressure (8.3 MPa) failed 10s after the onset of film boiling. A second rod failed about 90s after reactor shutdown. The report contains a description of the experiment, the test conduct, test results, and results from the preliminary postirradiation examination. Calculations using a transient fuel rod behavior code are compared with the test results.