gebhart/patrepeval huggingface dataset:
Frameshift Deletion by Sulfolobus solfataricus P2 DNA Polymerase Dpo4 T239W Is Selective for Purines and Involves Normal Conformational Change Followed by Slow Phosphodiester Bond Formation (2009)

The human DNA polymerase kappa homolog Sulfolobus solfataricus DNA polymerase IV (Dpo4) produces "-1" frameshift deletions while copying unmodified DNA and, more frequently, when bypassing DNA adducts. As judged by steady-state kinetics and mass spectrometry, bypass of purine template bases to produce these deletions occurred rarely but with 10-fold higher frequency than with pyrimidines. The DNA adduct 1,N(2)-etheno-2'-deoxyguanosine, with a larger stacking surface than canonical purines, showed the highest frequency of formation of -1 frameshift deletions. Dpo4 T239W, a mutant we had previously shown to produce fluorescence changes attributed to conformational change following dNTP binding opposite cognate bases (Beckman, J. W., Wang, Q., and Guengerich, F. P. (2008) J. Biol. Chem. 283, 36711-36723), reported similar conformational changes when the incoming dNTP complemented the base following a templating purine base or bulky adduct (i.e. the "+1" base). However, in all mispairing cases, phosphodiester bond formation was inefficient. The frequency of -1 frameshift events and the associated conformational changes were not dependent on the context of the remainder of the sequence. Collectively, our results support a mechanism for -1 frameshift deletions by Dpo4 that involves formation of active complexes via a favorable conformational change that skips the templating base, without causing slippage or flipping out of the base, to incorporate a complementary residue opposite the +1 base, in a mechanism previously termed "dNTP-stabilized incorporation." The driving force is attributed to be the stacking potential between the templating base and the incoming dNTP base.
Atmospheric‐Pressure Plasmas for Wide‐Area Thin‐Film Deposition and Etching (2007)

Abstract The present paper is focused on coating technologies compatible with industrial requirements, particularly on atmospheric pressure plasma technologies which are compatible with scaling to wide substrate widths (≥0.5 m). The AP‐PECVD reactors are designed for continuous air‐to‐air processing, and can be used for deposition of non‐oxide films. Two thermal methods for atmospheric pressure processing are considered: microwave CVD and DC ArcJet‐CVD. Typical thin film growth rates for PECVD are in the range of 5–100 nm · s −1 (static) and up to 2 nm · m · s −1 (dynamic). The rates for plasma chemical etching are typically 10 times higher. A complimentary lower energy plasma source based on dielectric barrier glow discharge plasma CVD has also been explored. Developments are underway to explore uses for the coating technology, for example scratch resistant coatings on metals, barrier layers, self‐clean functional surfaces and antireflective coatings. Coating materials range from silica, titania, aluminium oxide, metal composite layers, carbon and silicon nitride. Layer properties are close to data known from low pressure PECVD. Plasma chemical etching has been developed for crystalline silicon photovoltaics. The surface textures strongly change with the precursors and the plasma parameters used. magnified image
Transseptal Conduction as an Important Determinant for Cardiac Resynchronization Therapy, as Revealed by Extensive Electrical Mapping in the Dyssynchronous Canine Heart (2013)

Due to slow transseptal conduction, the LV electric activation sequence is similar in LV and BiV pacing, especially in failing hearts. Optimal hemodynamic cardiac resynchronization therapy response coincides with minimal epicardial asynchrony and QRS vector and LV preexcitation.
From cells to embryos: the application of femtosecond laser pulses for altering cellular material in complex biological systems (2008)

We report the application of high-intensity femtosecond laser pulses as a novel tool for manipulating biological specimens. When femtosecond laser pulses were focused to a near diffraction-limited focal spot, cellular material within the laser focal volume was surgically ablated. Several dissection cuts were made in the membrane of live mammalian cells, and membrane surgery was accomplished without inducing cell collapse or disassociation. By altering how the laser pulses were applied, focal adhesions joining live epithelial cells were surgically removed, resulting in single cell isolation. To further examine the versatility of this reported tool, cells were transiently permeabilized for introducing foreign material into the cytoplasm of live mammalian cells. Localizing focused femtosecond laser pulses on the biological membrane resulted in the formation of transient pores, which were harnessed as a pathway for the delivery of exogenous material. Individual mammalian cells were permeabilized in the presence of a hyperosmotic cryoprotective disaccharide. Material delivery was confirmed by measuring the volumetric response of cells permeabilized in 0.2, 0.3, 0.4 and 0.5 M cryoprotective sugar. The survival of permeabilized cells in increasing osmolarity of sugar was assessed using a membrane integrity assay. Further demonstrating the novelty of this reported tool, laser surgery of an aquatic embryo, the zebrafish (Danio rerio), was also performed. Utilizing the transient pores that were formed in the embryonic cells of the zebrafish embryo, an exogenous fluorescent probe FITC, Streptavidin-conjugated quantum dots or plasmid DNA (sCMV) encoding EGFP was introduced into the developing embryonic cells. To determine if the laser induced any short- or long-term effects on development, laser-manipulated embryos were reared to 2 and 7 days post-fertilization and compared to control embryos at the same developmental stages. Light microscopy and scanning electron microscopy were used to compare whole body mosaics of the developed larvae. Key developmental features that were compared included the olfactory pit, dorsal, ventral and pectoral fins, notochord, otic capsule and otic vesicle. No differences in the morphology and placement of the fore-, mid- and hindbrains were observed.
A temporal change in coda wave attenuation observed during an eruption of Mount St. Helens (1988)

During the past few years there have been numerous reports of changes in coda wave attenuation occurring before major earthquakes. These observations are important because they may provide insight into stress‐related structural changes taking place in the focal region prior to the occurrence of large earthquakes. The results of these studies led us to suspect that temporal changes in coda wave attenuation might also accompany volcanic eruptions. By measuring power decay envelopes for earthquakes at Mount St. Helens recorded before, during, and after an eruption that took place during September 3–6, 1981, we found that coda Q −1 for frequencies between 6 and 30 Hz was 20–30% higher before the eruption than after. The change is attributed to an increase in the density of open microcracks in the rock associated with inflation of the volcano prior to the eruption. Q −1 was found to be only weakly dependent on frequency and displayed a slight peak near 10 Hz. The weak frequency dependence is attributed to the dominance of intrinsic attenuation over scattering attenuation, since it is generally accepted that intrinsic attenuation is constant with frequency, whereas scattering attenuation decreases strongly at higher frequencies. The weak frequency dependence of Q −1 at Mount St. Helens contrasts with results reported for studies in non volcanic regions. The peak in Q −1 near 10 Hz at Mount St. Helens is attributed to the scale length of heterogeneity responsible for generating backscattered waves. Results for non volcanic regions have shown this peak to occur near 0.5 Hz. Thus a smaller scale length of heterogeneity is required to explain the 10‐Hz peak at Mount St. Helens.
ChemInform Abstract: STUDIES ON ORGANOPHOSPHORUS COMPOUNDS PART 4, HMPA AS PRECURSOR FOR DIMETHYLAMINE IN NUCLEOPHILIC AROMATIC SUBSTITUTION REACTIONS (1974)

Abstract ′21: Die Gruppen Rder Nitrobenzole (I) bzw. Benzonitrile (III) werden beim Erhitzen der Verbindungen in HMPA durch die Dimethylaminogruppe unter Bildung der Amine (II) bzw. (IV) s.ubstituiert [p‐Nitroanilin und 1‐Nitro‐4‐methylmercapto‐benzol reagieren nicht entsprechend.
Understanding metabolic pathways for skin anti-aging. (2009)

Global gene expression profiling provides a useful means to identify key aspects of the skin aging process, and provides information to help develop new skin technologies. Important aspects of skin aging that can be addressed include skin hydration, barrier, matrix, pigmentation and antioxidant capacity. Human skin equivalent cultures allow topical application of test compounds, combinations and products to their stratum corneum surface and measurement of predictive biomarkers. Using this in vitro biomarker approach, it is possible to detect skin barrier enhancement in response to the compounds niacinamide and hexamidine, matrix effects to the peptides Pal-KT and Pal-KTTKS, and hydration and matrix responses to niacinamide and N-acetylglucosamine.
Hepatic glucagon metabolism. Correlation of hormone processing by isolated canine hepatocytes with glucagon metabolism in man and in the dog. (1987)

We have found that canine and rat hepatocytes convert (125I)iodoTyr10-glucagon to a peptide metabolite lacking the NH2-terminal three residues of the hormone. The peptide is released into the cell incubation medium and its formation is unaffected by a variety of lysosomotropic or other agents. Use of specific radioimmunoassays and gel filtration demonstrated in both normal subjects and in chronic renal failure patients a plasma peptide having the properties of the hormone fragment identified by cell studies. Studies of the dog revealed a positive gradient of the fragment across the liver and no differential gradient of the fragment and glucagon across the kidney. We conclude that the glucagon fragment arises from the cell-mediated processing of the hormone on a superficial aspect of the hepatocyte, the glucagon fragment identified during experiments in vitro represents the cognate of a peptide formed during the hepatic metabolism of glucagon in vivo, and measurement of the fragment by COOH-terminal radioimmunoassays could lead to an understimulation of hepatic glucagon extraction.
Progress of combining trigram and Winnow in Thai OCR error correction (2002)

From specific characteristics of Thai, Thai OCR errors frequently depend on nearby characters. To capture this characteristic of Thai OCR errors more appropriately, we propose the idea of using the varied n-gram of the character confusion probability for scoring approximately matched words. The value of n depends on characteristics of each character. For languages which have no explicit word boundary, word boundary ambiguity has to be resolved before correcting errors. In this paper, a maximal matching algorithm is used instead of a more complicated word segmentation algorithm to reduce a time complexity problem. Finally, a hybrid method which combines a part-of-speech trigram model with Winnow algorithm is used to selected the most probable correction.
Organic Phase Change Nanoparticles for in-Product Labeling of Agrochemicals (2015)

There is an urgent need to develop in-product covert barcodes for anti-counterfeiting of agrochemicals. This paper reports a new organic nanoparticle-based in-product barcode system, in which a panel of organic phase change nanoparticles is added as a barcode into in a variety of chemicals (herein agrochemicals). The barcode is readout by detecting melting peaks of organic nanoparticles using differential scanning calorimetry. This method has high labeling capacity due to small sizes of nanoparticles, sharp melting peaks, and large scan range of thermal analysis. The in-product barcode can be effectively used to protect agrochemical products from being counterfeited due to its large coding capacity, technical readiness, covertness, and robustness.
Module-based biomarker discovery in breast cancer (2010)

The availability of genome-wide biological network data opens up new possibilities to discover novel biomarkers and elucidate cancer-related complex mechanisms at network level. In this paper, we propose a novel module-based feature selection framework, which integrates biological network information and gene expression data to identify biomarkers, not as individual genes but as functional modules. Also, a large-scale analysis of ensemble feature selection concept is presented. The method allows combining features selected from multiple runs with various data subsampling to increase the reliability and classification accuracy of the final set of selected features. The results from four breast cancer studies demonstrate that the identified module biomarkers achieve: i) higher classification accuracy in independent validation datasets; ii) better reproducibility than individual gene biomarkers; iii) improved biological interpretability; and iv) enhanced enrichment in cancer-related “disease drivers”.
The antigen-binding T cell factor PCl-F sensitizes mast cells for in vitro release of serotonin. Comparison with monoclonal IgE antibody. (1988)

Picryl chloride factor (PC1-F) is an antigen (TNP hapten)-binding T cell factor that initiates PC1 contact sensitivity (CS). PC1-F initiates PC1 CS by mediating an early 2-h skin swelling reaction that is due to local release of the vasoactive amine serotonin (5-HT) by mast cells, and perhaps other 5-HT-containing cells. Experiments were conducted to determine if PC1-F could sensitize normal mast cells in vitro for subsequent release of 3H-5-HT that had been taken up previously. It was found that PC1-F could sensitize mast cells, inasmuch as incubation with PC1-F, followed by washing, resulted in the ability to release 5-HT by challenge with Ag (TNP-bovine serum albumin), or by an anti-factor mAb called 14-30. As with release induced by anti-TNP IgE mAb PC1-F-induced release required phosphatidyl serine. Mast cell sensitization and activation for 5-HT release by PC1-F was not due to contamination of PC1-F with IgE antibody, because IgE (and not PC1-F) was sensitive to reduction and alkylation. Also, affinity columns linked with 14-30 or anti-IgE showed that the mast cell sensitizing and activating property of PC1-F was clearly separate from that of IgE. PC1-F-induced release was not IgE dependent, because mast cells that were acid-stripped and largely depleted of surface IgE, could then be sensitized by PC1-F. In vivo experiments demonstrated that local challenge with 14-30 antibody induced a 2-h ear swelling reaction in actively contact sensitized mice, or adoptive recipients of sensitized cells, and in normal mice that received PC1-F i.v. These findings suggest that in vitro sensitization of mast cells with PC1-F, and subsequent in vitro release of 5-HT induced by challenge with 14-30 antibodies, correlates with the initiation of PC1 CS in vivo. Therefore, in the initiation of CS by PC1-F, mast cells can be one source of 5-HT, to cause the early, vasoactive phase of CS.
Pneumatosis Intestinalis Presenting in Autoimmune Diseases (2009)

Pneumatosis intestinalis (PI) is an uncommon condition characterized by the presence of gas within the wall of the gastrointestinal tract. PI is a physical or imaging finding that is the result of an underlying pathological process or a disease. This finding may present in diverse conditions, such as obstructive pulmonary disease and intestinal disease, including obstruction, inflammation, or ischemia. PI has also been reported in different autoimmune conditions, especially in systemic sclerosis and rarely with systemic lupus erythematosus. In this report we present PI occurring in three patients with different autoimmune conditions and review the literature.
Telomerase activity as an indicator of malignant potential in iodine-nonreactive lesions of the esophagus (2000)

Positive and negative telomerase activity was found to be correlated with the presence and absence, respectively, of immortalized tumor cells in iodine-nonreactive lesions. The measurement of telomerase activity in iodine-nonreactive lesions independently contributes to the selection of an appropriate therapeutic strategy.
Syntheses and electrochemical behaviour of novel dmit or dmio (dithiolato) cobalt(iii) complexes with a η<sup>5</sup>‐cyclopentadienyl or η<sup>5</sup>‐pentamethylcyclopentadienyl ring (1991)

Abstract Four novel cobalt(III) complexes with a cyclopentadienyl or pentamethylcyclopentadienyl ring and dmit or dmio ligands were synthesized, and their electrochemical behaviour was investigated. All these complexes exhibited three one‐electron transfer steps: one reduction and two oxidation steps. In addition, a novel organosulphur compound was afforded by electrochemical oxidation of dmit cobalt complex. Thus, these complexes may have considerable synthetic potential as precursors for electron reservoirs and organosulphur compounds.
A Uniform Format for IPv6 Extension Headers (2012)

In IPv6, optional internet-layer information is encoded in separate headers that may be placed between the IPv6 header and the transportlayer header. There are a small number of such extension headers currently defined. This document describes the issues that can arise when defining new extension headers and discusses the alternate extension mechanisms in IPv6. It also provides a common format for defining any new IPv6 extension headers, if they are needed.
The Impact of Intensive Insulin Protocols and Restrictive Blood Transfusion Strategies on Glucose Measurement in American Burn Association (ABA) Verified Burn Centers (2008)

The prevalence of intensive insulin and restrictive blood use protocols in burn centers is unknown, which may be problematic as the combined impact of these therapies is to concomitantly increase the prevalence of anemia and hypoglycemia in intensive care unit patients. Such a development is important because point-of-care (POC) glucometers report erroneously high values in the presence of low hematocrit (HCT), potentially masking the presence of hypoglycemia. We hypothesized that most American Burn Association (ABA) verified burn centers have adopted intensive insulin therapy while simultaneously restricting blood transfusions potentially increasing risk of hypoglycemia. All ABA verified burn centers (N = 44) were contacted. Clinical practices regarding intensive insulin therapy, restrictive transfusion practices, and the use of POC glucometers were evaluated. Intensive insulin protocols were implemented at 73% of ABA centers (defined as upper glucose target of < or = 120 mg/dl) and POC glucometers measurement was nearly universal; 95% of ABA centers use them routinely. Anemia is prevalent in intensive care units and may be increasing because of recent changes in practice. Defined hemoglobin and HCT levels trigger blood transfusion at 84% of centers, and of these, 51% restrict transfusion to hemoglobin < 7 g/dl or HCT < 22%. Most ABA centers now use intensive insulin protocols, many in combination with restrictive transfusion strategies. The combination of a higher prevalence of hypoglycemia in the presence of near universal anemia is concerning, particularly given the pervasiveness of glucometer use among burn centers.
Applying antimicrobial pharmacodynamics to resistant gram-negative pathogens (2006)

Various mechanisms account for resistance of bacteria to antibiotics. The appropriate use of pharmacokinetics and pharmacodynamics can guide antibiotic therapy and enhance the likelihood of success.
Modern main group chemistry (2016)

Guest editors Simon Aldridge and Cameron Jones introduce the Modern Main Group Chemistry issue of <italic>Chemical Society Reviews</italic>
Bacterial populations associated with the Arctic amphipod <i>Boeckosimus affinis</i> (1982)

Microbial populations associated with the amphipod Boeckosimus affinis were examined using scanning electron microscopy and by detailed characterization of viable isolates. Bacterial populations were observed on food particles in the midgut, on the anal plates, and on faecal matter, but no bacteria were observed on the outer surfaces or on the gut lining of the amphipod. The dominant bacterial populations associated with the amphipods were in the Vibrio–Beneckea group. Exposure to petroleum hydrocarbons resulted in a decreased dominance of the vibriolike bacterial populations associated with the amphipods. During captivity (without feeding) there were successional changes in the bacterial populations associated with the amphipods; the diversity of the bacterial community increased and the bacterial populations became less stringent in their physiological and nutritional requirements.
P34.05: Customized standards of estimated fetal weight as predictor of adverse perinatal outcome (2007)

To evaluate the predictive capacity of middle cerebral artery, umbilical artery and customized standards of estimated fetal weight for adverse perinatal outcome in a group of small-for-gestational age (SGA) fetuses. Data were collected from 105 singleton and non-malformed fetuses suspected of being SGA during the third trimester and with a confirmed birth weight below the 10th centile. At diagnosis, estimated fetal weight was customized according to maternal and fetal characteristics and middle cerebral artery pulsatility index and umbilical artery pulsatility index were recorded, and tranformed to Z-values. Adverse perinatal outcome was defined as umbilical artery pH at delivery ≤ 7.15, 5-minutes Apgar score ≤ 7, significant neonatal morbidity (seizures, respiratory distress syndrome, necrotising enterocolitis, grade II-III intraventricular hemorrhage, hypoxic-ischemic encephalopathy), need of intubation, neonatal intensive care unit admission or neonatal mortality. The prevalence of adverse perinatal outcome in our group of SGA fetuses was 50.5%. While the area under the curve (AUC) for Z-customized estimated fetal weight was 0.7 (95% CI, 0.59–0.81), for Z-umbilical artery Doppler was 0.5 (95% CI, 0.39–0.63) and for Z-middle cerebral artery was 0.55 (95% CI, 0.44–0.68). Paired analysis between parameters demonstrated that customized standards UAC was significantly larger than for both Doppler indices. Overall, the sensitivity and specificity for 10th centile cut-off of customized estimated fetal weight was 67.4% and 64%, respectively. In SGA fetuses, customized standards are a better predictor for adverse perinatal outcome than middle cerebral artery or umbilical artery Doppler indices.
A Designer's Guide for Dimensioning and Tolerancing SLS Parts (2012)

Because additive manufacturing (AM) is a relatively novel industry, with the first commercial machines introduced in the late 1980s, many designers are unaware of the capabilities of AM technologies. Many engineers also find it difficult to utilize AM because of a lack of “Design for AM” knowledge in the public domain. Reliable information on material properties, dimensions and tolerances, and other process-related specifications is often scattered throughout the literature, if it is publicly available at all. The objective of the research reported in this paper is to begin to create a designer's guide for dimensioning and tolerancing parts that are additively manufacturing using selective laser sintering (SLS) technology. The guide is based on a series of experiments designed to determine the limiting feature sizes for various types of features fabricated in commercially available SLS machines. The features include slits, holes, letters, mating gears, and shafts built in a preassembled state. The impact of part thickness, orientation, clearance, and dimensions on the resolvability of features is examined. Results are reported in a series of matrices that relate realizable feature sizes to other important variables such as part thickness.