gebhart/patrepeval huggingface dataset:
Mining Disease Susceptibility Genes through SNP Analyses and Expression Profiling Using MALDI-TOF Mass Spectrometry (2004)

To find genes that underlie disease susceptibilities, genome-wide single nucleotide polymorphisms (SNPs) have been analyzed using high-throughput matrix assisted laser desorption/ionization (MALDI) time-of-flight (TOF) mass spectrometry (MS). As a proof-of-concept for this approach, gene regions have been identified that were previously associated by others with certain diseases or traits. On the same technology platform, accurate and absolute transcriptional profiling can be performed and applied to allele expression analysis. Here, we provide a brief review of the technology and its applications to disease gene discovery.
Long-read sequence assembly of the gorilla genome (2016)

Accurate sequence and assembly of genomes is a critical first step for studies of genetic variation. We generated a high-quality assembly of the gorilla genome using single-molecule, real-time sequence technology and a string graph de novo assembly algorithm. The new assembly improves contiguity by two to three orders of magnitude with respect to previously released assemblies, recovering 87% of missing reference exons and incomplete gene models. Although regions of large, high-identity segmental duplications remain largely unresolved, this comprehensive assembly provides new biological insight into genetic diversity, structural variation, gene loss, and representation of repeat structures within the gorilla genome. The approach provides a path forward for the routine assembly of mammalian genomes at a level approaching that of the current quality of the human genome.
Effect of Adding Phosphorylation Sites for cAMP-Dependent Protein Kinase to Rat Testis 6-Phosphofructo-2-kinase/Fructose-2,6-bisphosphatase (1994)

In contrast to liver and heart 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatases, the testis isozyme lacks a phosphorylation site for cAMP-dependent protein kinase. In order to determine the effect of phosphorylation site location for the protein kinase on rat testis bifunctional enzyme, consensus amino acid sequences (RRXS) were added at different distances from the N-terminus by site-directed mutagenesis. The expressed wild-type enzyme (WT) and mutant enzymes containing a phosphorylation site at Ser7 (mutant enzyme RT2KS7, where RT2K = rat testis 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase), Ser15 (RT2KS15), or Ser30 (RT2KS30) were purified to apparent homogeneity. All the mutant enzymes served as substrates for the protein kinase, and the phosphate incorporation was over 90%. The Km values of protein kinase A for RT2KS7, RT2KS15, and RT2KS30 were 250 microM, 110 microM, and 50 microM, respectively, and the relative rates were 1, 8, and 23. Various kinetic parameters of dephospho and phospho forms of these enzymes were determined. The kinetic constants of the dephospho form of RT2KS30 were similar to those of WT, but those of RT2KS15 and RT2KS7 showed an 8-fold increase in KmFru6P, an approximately 30% decrease in the Fru-6-P,2-kinase activity, and a 3-fold increase in fructose-2,6-bisphosphatase activity. Phosphorylation of RT2KS30 resulted in a shift in the Fru-6-P saturation curve from Michaelis-Menten kinetics to sigmoidal, with increased KmFru6P and activation of fructose-2,6-bisphosphatase. The kinetic constants of RT2KS15 and RT2KS7 were not altered by phosphorylation. All the mutant enzymes were more sensitive to heat inactivation than was WT.(ABSTRACT TRUNCATED AT 250 WORDS)
Effects of Ibuprofen on the physiology and outcome of rabbit endotoxic shock (2002)

Ibuprofen appears to increase survival in endotoxic shock-induced animals. Therefore, it may be helpful for the prophylaxis and treatment of patients with, or who are likely to develop, septic shock.
F901318 represents a novel class of antifungal drug that inhibits dihydroorotate dehydrogenase (2016)

Significance New antifungal drugs that act via novel mechanisms are urgently needed to combat the high mortality of invasive fungal disease and the emergence of resistance to existing therapies. We describe the discovery, structure, activity, and mechanism of action of F901318, a new antifungal agent. A member of a novel class of antifungals, the orotomides, F901318 acts via inhibition of dihydroorotate dehydrogenase, an enzyme of de novo pyrimidine biosynthesis. F901318 is currently in clinical development for the treatment of invasive aspergillosis.
ATPG-based preimage computation: efficient search space pruning with ZBDD (2004)

Computing image/preimage is a fundamental step in formal verification of hardware systems. Conventional OBDD-based methods for formal verification suffer from spatial explosion, since OBDDs can grow exponentially in large designs. On the other hand, SAT/ATPG based methods are less demanding on memory. But the run-time can be huge for these methods, since they must explore an exponential search space. In order to reduce this temporal explosion of SAT/ATPG based methods, efficient learning techniques are needed. In this paper, we present a new ZBDD based method to compactly store and efficiently search previously explored search-states for 'ATPG-based preimage computation'. We learn front these search-states and avoid searching their subsets or supersets. Both,solution and conflict subspaces are pruned based on simple set operations using ZBDDs. We integrate our techniques into an ATPG engine and demonstrate their efficiency on ISCAS '89 benchmark circuits. Experimental results show that significant search-space pruning for preimage computation is achieved, compared to previous methods.
Mutant<i>PIK3CA</i>-Bearing Colon Cancer Cells Display Increased Metastasis in an Orthotopic Model (2007)

Mutations in the PIK3CA gene are common in human cancers, including colon cancer. We compared two pairs of colon cancer cells (HCT116 and DLD1) bearing only the wild-type (WT) or mutant (MUT) PIK3CA allele for their survival capacity under stress conditions in vitro as well as their metastatic properties in an in vivo orthotopic model. When subjected to growth factor deprivation stress (GFDS), the MUT PIK3CA cells displayed resistance to GFDS-induced apoptosis relative to the WT cells. Phosphatidylinositol 3-kinase (PI3K) and its downstream effector AKT were constitutively activated during stress conditions in the MUT PIK3CA cells but not in the WT cells. The MUT cells showed hypersensitivity to PI3K inhibition. Moreover, the proapoptotic protein Bax was expressed at a very high level in the WT PIK3CA cells, whereas it was almost undetectable in the MUT cells. Inhibition of Bax expression by small interfering RNA protected the WT PIK3CA cells from GFDS-induced apoptosis, suggesting an important role of Bax in GFDS-induced apoptosis. These results indicated that the MUT PI3K confers resistance to GFDS-induced apoptosis and that the MUT cells are more dependent on the PI3K pathway for survival. In vivo studies showed that the MUT PIK3CA-bearing cells were more metastatic than the WT cells in an orthotopic model of colon cancer. Taken together, these results suggest that MUT PI3K imparts a more aggressive phenotype in colon cancer cells and could be a potential therapeutic target for treatment of colon cancer patients bearing PIK3CA mutations.
<title>Design and performance of a fiber Bragg grating distributed strain sensor system</title> (1995)

We describe the design and performance of a prototype fiber Bragg grating demodulation system based on the use of a scanning fiber Fabry-Perot filter. The computer driven system is capable of demodulating several arrays of wavelength division multiplexed gratings at various scanning rates for real-time strain display and data logging. The instrument represents a new measurement tool which should be useful in a variety of structural health monitoring applications. Results obtained by the system in several applications are presented and system performance limitations are discussed.
Enhancement of Australian VHF combat net radios (2002)

Conventional VHF combat net radios (CNR) employ noncoherent FSK to provide 16 kbps in a 25 kHz channel. The poor bit error rate (BER) performance, and relatively low data rate prevent high throughput for the digital networks and C3I systems built on them. A low cost enhancement has been proposed as a near to medium term measure. We report the initial efforts for this proposal, including design consideration, simulation and test results. A demonstration system has been constructed which retains the existing RF components of the radios while replacing the hardware FSK modem by a software modem based on an external PC. A number of forward error control (FEC) and modulation schemes have been proposed and a subset of them have been simulated and implemented in real time. Initial measurements show promising performance in terms of remarkably reduced BER, or increased data rate. Iterative decoding is used which can combat signal distortion and impulsive interference that is often encountered in tactical deployment. Coded QPSK at the current data rate yields 14.5 dB E/sub b//N/sub o/ improvement over the FSK modem. A data rate of 64 kbps is achieved with coded 64 QAM. The selected scheme(s) can be implemented with FPGA or ASIC technology on a replacement module for the current radio.
ControlWare: a middleware architecture for feedback control of software performance (2003)

Attainment of software performance assurances in open, largely unpredictable environments has recently become an important focus for real-time research. Unlike closed embedded systems, many contemporary distributed real-time applications operate in environments where offered load and available resources suffer considerable random fluctuations, thereby complicating the performance assurance problem. Feedback control theory has recently been identified as a promising analytic foundation for controlling performance of such unpredictable, poorly modeled software systems, the same way other engineering disciplines have used this theory for physical process control. In this paper we describe the design and implementation of ControlWare, a middleware QoS-control architecture based on control theory, motivated by the needs of performance-assured Internet services. It offers a new type of guarantees we call convergence guarantees that lie between hard and probabilistic guarantees. The efficacy of the architecture in achieving its QoS goals under realistic load conditions is demonstrated in the context of web server and proxy QoS management.
Molten Salt Synthesis of Ceramic Powders (2011)

Molten salt synthesis, one of the methods of preparing ceramic powders, involves the use of a molten salt as the medium for preparing complex oxides from their constituent materials (oxides and carbonates). Ceramic powders are prepared from solid, liquid, and gas phases by various methods (Rahaman, 2003). For large-scale commercial production, ceramic powders are fabricated mainly from the solid phase by a conventional powder metallurgical method. Molten salt synthesis is a modification of the powder metallurgical method. Salt with a low melting point is added to the reactants and heated above the melting point of the salt. The molten salt acts as the solvent. Molten salts have been used as additives to enhance the rates of solid state reactions for a long time. The amount of salt is small, typically a few percent of the total weight. In contrast, in molten salt synthesis, a large amount of salt is used as the solvent to control powder characteristics (size, shape, etc.). In this sense, molten salt synthesis is different from the flux method, which uses the salt as an additive to enhance the reaction rate. Typical examples of salts used in molten salt synthesis are chlorides and sulfates. In many cases, eutectic mixtures of salts are used to lower the liquid formation temperature. The melting points of NaCl and KCl are 801°C and 770°C, respectively, and that of 0.5NaCl– 0.5KCl (eutectic composition) is 650°C. For example, 0.635Li2SO4–0.365Na2SO4 is the most commonly used salt among sulfates because of its low melting temperature, which is 594°C, whereas that of Na2SO4–K2SO4 is 823°C. The solubilities of oxides in molten salts vary greatly from less than 1 x 10–10 mole fraction to more than 0.5 mole fraction, typically 1×10–3 1×10–7 mole fraction (Arendt et al., 1979). In many cases, the formation reaction occurs in the presence of solid reactant particles. In this sense, molten salt is somewhat different from ordinary solvents, which dissolve all reactant particles and the product particles precipitate from a homogeneous liquid phase. Generally, a complex oxide powder is prepared from reactants by the following procedure. A mixture of the reactants and salt is heated above the melting temperature of the salt. At the heating temperature, the salt melts and the product particles form. The characteristics of the product powder are controlled by selecting the temperature and duration of the heating. Then, the reacted mass is cooled to room temperature and washed with an appropriate solvent (typically, water) to remove the salt. The complex oxide powder is obtained after drying. The procedure is the same as that of a conventional powder metallurgical method and is easily scaled up for the fabrication of large quantities of materials. The use of molten salt is a common method to grow single crystals from solution (Elwell & Scheel, 1975). In this method, the reactant materials are completely dissolved in molten salt
Insulin-like growth factors and their binding proteins before and after weight loss and their associations with hormonal and metabolic parameters in obese adolescent girls. (1996)

These studies of a homogeneous group of patients give further insight into possible physiological regulations and roles of IGFs and IGFBPs. The main conclusion is that obesity has to be considered for interpretation of serum concentrations of IGF-I, IGFBP-1, IGFBP-2, and IGFBP-3. Furthermore, out results suggest that (i) the decrease in IGF-I/IGFBP-3 after weight loss could be partly responsible for the impaired growth velocity seen in obese children during hypocaloric feeding and (ii) low IGFBP-2 and high IGFBP-1 levels are associated with an unfavorable atherogenic risk factor profile.
Effects of heparin versus saline solution on intermittent infusion device irrigation. (1990)

The purpose of this study was to compare the effectiveness of 1 ml of 0.9% sodium chloride with 10 units of heparin in 1 ml sodium chloride solution, both containing benzyl alcohol, in maintaining patency and reducing the incidence of phlebitis in patients with intermittent infusion devices. The subjects (N = 32) were randomly assigned in a double-blind experimental design. Repeated-measures analysis of variance revealed no significant difference between the groups in phlebitis or patency variables. The results from this controlled study would suggest that 0.9% sodium chloride is as effective as 10 units of heparin in sodium chloride solution in maintaining intermittent infusion device patency and preventing phlebitis.
Targeted single‐cell induction of gene products in <i>Caenorhabditis elegans:</i> A new tool for developmental studies (1993)

Heat shock promoters have been employed to achieve tightly regulated expression of transformed genes in a wide variety of model systems including tissue culture cells, bacteria, yeast, Drosophila, and more recently Caenorhabditis elegans. Here we investigate the feasibility of using a laser microbeam to induce a sub-lethal heat shock response in individual cells of C. elegans. We demonstrate that in transgenic strains carrying heat shock promoter-lacZ fusions, single cell expression of beta-galactosidase in a variety of cell types of endodermal, mesodermal, or ectodermal origin can be achieved after pulsing with a laser. A tissue-general, inducible promoter can therefore be converted into one of single cell specificity which can be induced rapidly at any point in development, offering unique opportunities to study cell-cell interactions in C. elegans. This technique defines a new approach to generate mosaic animals and may be adaptable to other organisms or tissues.
An SOA-Based Software Development Management System (2006)

The object of the research was to develop a deployment management framework that supported dynamic reconfiguration for home gateway services. This system uses a Service Oriented Architecture (SOA) that contains four subsystems. These include: a management agent, a deployment management server, a process management module, and an operation portal. The architecture of this system not only improves the efficiency of application delivery, but also provides a platform that can effectively support process changes when needed.
Hypoxia-inducible factor-1α regulates β cell function in mouse and human islets (2010)

Hypoxia-inducible factor-1alpha (HIF-1alpha) is a transcription factor that regulates cellular stress responses. While the levels of HIF-1alpha protein are tightly regulated, recent studies suggest that it can be active under normoxic conditions. We hypothesized that HIF-1alpha is required for normal beta cell function and reserve and that dysregulation may contribute to the pathogenesis of type 2 diabetes (T2D). Here we show that HIF-1alpha protein is present at low levels in mouse and human normoxic beta cells and islets. Decreased levels of HIF-1alpha impaired glucose-stimulated ATP generation and beta cell function. C57BL/6 mice with beta cell-specific Hif1a disruption (referred to herein as beta-Hif1a-null mice) exhibited glucose intolerance, beta cell dysfunction, and developed severe glucose intolerance on a high-fat diet. Increasing HIF-1alpha levels by inhibiting its degradation through iron chelation markedly improved insulin secretion and glucose tolerance in control mice fed a high-fat diet but not in beta-Hif1a-null mice. Increasing HIF-1alpha levels markedly increased expression of ARNT and other genes in human T2D islets and improved their function. Further analysis indicated that HIF-1alpha was bound to the Arnt promoter in a mouse beta cell line, suggesting direct regulation. Taken together, these findings suggest an important role for HIF-1alpha in beta cell reserve and regulation of ARNT expression and demonstrate that HIF-1alpha is a potential therapeutic target for the beta cell dysfunction of T2D.
Touch & Share (2008)

Here, we present Touch & Share, an application for sharing multimedia content in our everyday environment. Our main design criterion is ease of use. Visual icons placed in the environment act as data storage (file containers). Users can drop multimedia files into the containers and pick files from them by touching the icons with their mobile terminals. The icons are placed on, or near, the physical objects the files are related to. RFID tags are placed behind the icons and they store metadata information about the files available in the corresponding containers. When users bring their terminals near the icons, the terminals' RFID readers communicate with the tags, read the contents of a container from the tag and possibly write information about new files. The actual files are stored in a server, but the user experiences the files to be in the containers. The main contributions of this work are a general application for storing multimedia content in nearly any place or everyday object and a fully functional prototype built using only commercial off-the-self technology.
Some extended results on the search for good convolutional codes (1997)

We provide useful results on two classes of convolutional codes: binary codes and nonbinary codes. The best codes or the best known codes for these two classes of convolutional codes are found, by computer search. Some of them are better than those found in the past. We specify these codes by their transfer function matrices, distance spectra, and information-weight spectra. Furthermore, we derive an upper bound on the free distances of binary-to-M-ary codes and q-ary-to-M-ary codes. Numerical values of this bound closely fit the computer-searched values.
The Therapeutic Potential and Limitations of Ketones in Traumatic Brain Injury (2021)

Traumatic brain injury (TBI) represents a significant health crisis. To date, no FDA approved pharmacotherapies are available to prevent the neurological deficits caused by TBI. As an alternative to pharmacotherapy treatment of TBI, ketones could be used as a metabolically based therapeutic strategy. Ketones can help combat post-traumatic cerebral energy deficits while also reducing inflammation, oxidative stress, and neurodegeneration. Experimental models of TBI suggest that administering ketones to TBI patients may provide significant benefits to improve recovery. However, studies evaluating the effectiveness of ketones in human TBI are limited. Unanswered questions remain about age- and sex-dependent factors, the optimal timing and duration of ketone supplementation, and the optimal levels of circulating and cerebral ketones. Further research and improvements in metabolic monitoring technology are also needed to determine if ketone supplementation can improve TBI recovery outcomes in humans.
Glucuronide and sulfate conjugation in the fungal metabolism of aromatic hydrocarbons (1982)

Cunninghamella elegans oxidized naphthalene to ethyl acetate-soluble and water-soluble metabolites. Experiments with [14C]-naphthalene indicated that 21% of the substrate was converted into metabolites. The ratio of organic-soluble metabolites to water-soluble metabolites was 76:24. The major ethyl acetate-soluble naphthalene metabolites were trans-1,2-dihydroxy-1,2-dihydro-naphthalene, 4-hydroxy-1-tetralone, and 1-naphthol. Enzymatic treatment of the aqueous phase with either arylsulfatase or beta-glucuronidase released metabolites of naphthalene that were extractable with ethyl acetate. In both cases, the major metabolite was 1-naphthol. The ratio of water-soluble sulfate conjugates to water-soluble glucuronide conjugates was 1:1. Direct analysis of the aqueous phase by high-pressure liquid and thin-layer chromatographic and mass spectrometric techniques indicated that 1-naphthyl sulfate and 1-naphthyl glucuronic acid were major water-soluble metabolites formed from the fungal metabolism of naphthalene. C. elegans oxidized biphenyl primarily to 4-hydroxy biphenyl. Deconjugation experiments with biphenyl water-soluble metabolites indicated that the glucuronide and sulfate ester of 4-hydroxy biphenyl were metabolites. The data demonstrate that sulfation and glucuronidation are major pathways in the metabolism of aromatic hydrocarbons by fungi.
Amperometric Titrations (1966)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTAmperometric TitrationsJohn T. StockCite this: Anal. Chem. 1966, 38, 5, 452–460Publication Date (Print):April 1, 1966Publication History Published online1 May 2002Published inissue 1 April 1966https://pubs.acs.org/doi/10.1021/ac60237a032https://doi.org/10.1021/ac60237a032research-articleACS PublicationsRequest reuse permissionsArticle Views236Altmetric-Citations4LEARN 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