gebhart/patrepeval huggingface dataset:
Resolving combustible gas mixtures using gas sensitive resistors with arrays of electrodes (1996)

Gas sensitive resistors using semiconducting oxides operating at elevated temperatures and having an array of different electrode spacings on a single device are functionally equivalent to an array of different sensors with differing patterns of response to different gases. Here, a single device with two different electrode spacings is used successfully to distinguish between gases having different combustion rates, and to analyse binary mixtures of combustible gases at low concentrations in air. Furthermore it is shown that devices of this type provide considerable insight into the mechanisms of both the surface-catalysed combustion and the gas response. The kinetic law for the surface catalysed combustion of the target gas is derived by comparison with the results of numerical simulations using an iterative procedure based on the Newton–Raphson method. The accurate analysis of the gas mixtures forced a reformulation of the response model which, for a mixture of n gases is shown to be (R/R0)1/β– 1 =∑nj= 1AjPj where R denotes the resistance (R0 in air), Aj the response coefficient and Pj the partial pressure of gas j. The response order, β, is the same for all gases.
Chemistry and Biology of Macrolide Antiparasitic Agents (2011)

Macrolide antibacterial agents inhibit parasite proliferation by targeting the apicoplast ribosome. Motivated by the long-term goal of identifying antiparasitic macrolides that lack antibacterial activity, we have systematically analyzed the structure-activity relationships among erythromycin analogues and have also investigated the mechanism of action of selected compounds. Two lead compounds, N-benzylazithromycin (11) and N-phenylpropylazithromycin (30), were identified with significantly higher antiparasitic activity and lower antibacterial activity than erythromycin or azithromycin. Molecular modeling based on the cocrystal structure of azithromycin bound to the bacterial ribosome suggested that a substituent at the N-9 position of desmethylazithromycin could improve selectivity because of species-specific interactions with the ribosomal L22 protein. Like other macrolides, these lead compounds display a strong "delayed death phenotype"; however, their early effects on T. gondii replication are more pronounced.
Tumor-Specific, Replication-Competent Adenovirus Vectors Overexpressing the Adenovirus Death Protein (2000)

We have constructed two novel adenovirus (Ad) replication-competent vectors, named KD1 and KD3, that may have use in anticancer therapy. The vectors have two key features. First, they markedly overexpress the Ad death protein (ADP), an Ad nuclear membrane glycoprotein required at late stages of infection for efficient cell lysis and release of Ad from cells. Overexpression of ADP was achieved by deleting the E3 region and reinserting the adp gene. Because ADP is overexpressed, KD1 and KD3 are expected to spread more rapidly and effectively through tumors. Second, KD1 and KD3 have two E1A mutations (from the mutant dl1101/1107) that prevent efficient replication in nondividing cells but allow replication in dividing cancer cells. These E1A mutations preclude binding of E1A proteins to p300 and pRB. As a result, the virus should not be able to drive cells from G(0) to S phase and therefore should not be able to replicate in normal tissues. We show that KD1 and KD3 do not replicate well in quiescent HEL-299 cells or in primary human bronchial epithelial cells, small airway epithelial cells, or endothelial cells; however, they replicate well in proliferating HEL-299 cells and human A549 lung carcinoma cells. In cultured A549 cells, KD1 and KD3 lyse cells and spread from cell to cell more rapidly than their control virus, dl1101/1107, or wild-type Ad. They are also more efficient than dl1101/1107 or wild-type Ad in complementing the spread from cell to cell of an E1(-) E3(-) replication-defective vector expressing beta-galactosidase. A549 cells form rapidly growing solid tumors when injected into the hind flanks of immunodeficient nude mice; however, when A549 cells were infected with 10(-4) PFU of KD3/cell prior to injection into mice, tumor formation was nearly completely suppressed. When established A549 tumors in nude mice were examined, tumors injected with buffer grew 13.3-fold over 5 weeks, tumors injected with dl1101/1107 grew 8-fold, and tumors injected with KD1 or KD3 grew 2.6-fold. Hep 3B tumors injected with buffer grew 12-fold over 3.5 weeks, whereas tumors injected with KD1 or KD3 grew 4-fold. We conclude that KD1 and KD3 show promise as anticancer therapeutics.
Cutting Edge: Lipid Raft Integrity Affects the Efficiency of MHC Class I Tetramer Binding and Cell Surface TCR Arrangement on CD8+ T Cells (2001)

Physically distinct cholesterol/sphingolipid-rich plasma membrane microdomains, so-called lipid rafts, have been recognized to play an important regulatory role in various cellular processes, from membrane trafficking to signal transduction, in a number of cell types. We report here that the ability of TCR on activated, functional CD8+ T lymphocytes to efficiently bind MHC class I tetramer complexes is dependent on the integrity of lipid rafts on the T lymphocyte membrane. We further provide evidence that TCR interact (associate) with lipid raft elements on the T cell surface before receptor engagement and that the topological arrangement of TCR on the cell surface is likewise influenced by lipid raft integrity.
Oil shale of Pennsylvanian age in Indiana (1985)

Black organic-rich shales of Pennsylvanian age are present in southwestern Indiana and throughout the Illinois Basin. Many of these can be considered oil shales and most are associated with commercial coalbeds. The shales are generally thin, from a few feet to 15 feet thick, but they have the economic advantage of being unearthed in huge amounts during coal-mining operations. Oil yields from 126 samples of Pennsylvanian black shales were determined by the Western Research Institute using a modified Fischer Assay method. Oil yields ranged from trace amounts to 21 gallons per ton of shale (gal/ton). Oil yields correlated fairly well with carbon content; the correlation coefficient was 0.81 for all samples. Individual shales showed better carbon to oil correlations except for shales above the Springfield Coal Member. Hydrogen and nitrogen in the shales correlated well with carbon. The good correlations were surprising because the Pennsylvanian black shales were deposited in different types of environments from marine to fresh water.
A Rewritable, Random-Access DNA-Based Storage System (2015)

We describe the first DNA-based storage architecture that enables random access to data blocks and rewriting of information stored at arbitrary locations within the blocks. The newly developed architecture overcomes drawbacks of existing read-only methods that require decoding the whole file in order to read one data fragment. Our system is based on new constrained coding techniques and accompanying DNA editing methods that ensure data reliability, specificity and sensitivity of access, and at the same time provide exceptionally high data storage capacity. As a proof of concept, we encoded parts of the Wikipedia pages of six universities in the USA, and selected and edited parts of the text written in DNA corresponding to three of these schools. The results suggest that DNA is a versatile media suitable for both ultrahigh density archival and rewritable storage applications.
Thermal stability of spiro[adamantane‐[1,2]dioxetanes] (1983)

Abstract The thermal stability of several spiroadamantane‐substituted 1,2‐dioxetanes was determined by means of chemiluminescence (Table 1). The evident stabilization of dioxetanes by such substitution cannot be interpreted in terms of “inertial mass” or “torsional” arguments in the case of concerted decomposition nor by “compressional” arguments in the case of diradical decomposition. It is suggested that a transoid diradical 19t , in which the engaged orbitals are antiperiplanar arranged, promotes CC cleavage. The bulky adamantane substituent encumbers such conformational isomerization of the initially formed cisoid diradical 19c into the preferred 19t .
Immunogenicity screening in protein drug development (2007)

Most therapeutic proteins in clinical trials or on the market are, to a variable extent, immunogenic. Formation of antidrug antibodies poses a risk that should be assessed during drug development, as it possibly compromises drug safety and alters pharmacokinetics. The generation of these antibodies is critically dependent on the presence of T helper cell epitopes, which have classically been identified by in vitro methods using blood cells from human donors. As a novel development, in silico methods that identify T cell epitopes have been coming on line. These methods are relatively inexpensive and allow the mapping of epitopes from virtually all human leukocyte antigen molecules derived from a wide genetic background. In vitro assays remain important, but guided by in silico data they can focus on selected peptides and human leukocyte antigen haplotypes, thereby significantly reducing time and cost.
Automated determination of sublanguage syntactic usage (1984)

Sublanguages differ from each other, and from the "standard language", in their syntactic, semantic, and discourse properties. Understanding these differnces is important if we are to improve our ability to process these sublanguages. We have developed a semiautomatic procedure for identifying sublanguage syntactic usage from a sample of text in the sublanguage. We describe the results of applying this procedure to three text samples: two sets of medical documents and a set of equipment failure messages.
Preparation of a mRNA‐Dependent Cell‐Free Translation System from Whole Cells of Saccharomyces cerevisiae (1982)

A cell-free protein-synthesizing system has been prepared from Saccharomyces cerevisiae by mechanical breakage of cells, isolation of a 30000 x g supernatant fraction and removal of endogenous mRNA by treatment with micrococcal nuclease. The system thus isolated is dependent on added mRNA and translates yeast mRNA to discrete products, many of then identical with yeast proteins synthesized in vivo. Activity and properties of this system are comparable to those of other eukaryotic cell-free translation systems. It offers the following advantages, compared to yeast translation systems described previously. (a) Its isolation is simple and fast. (b) Since it is not isolated from spheroplasts there is no danger of its inactivation by contaminants in enzymes used for spheroplast preparation. (c) Isolation appears to be less strain-dependent and can be carried out starting from cells in various physiological states.
SHIP1 Inhibition Increases Immunoregulatory Capacity and Triggers Apoptosis of Hematopoietic Cancer Cells (2010)

Genetic studies revealed that SHIP1 limits blood cell production and immune regulatory cell numbers in vivo. We postulated that molecular targeting of SHIP1 might enhance blood cell production and increase immunoregulatory capacity. In this study, we report the identification of a chemical inhibitor of SHIP1, 3 alpha-aminocholestane (3AC). Treatment with 3AC significantly expands the myeloid immunoregulatory cell compartment and impairs the ability of peripheral lymphoid tissues to prime allogeneic T cell responses. In addition, 3AC treatment profoundly increases granulocyte production without triggering the myeloid-associated lung consolidation observed in SHIP1(-/-) mice. Moreover, 3AC also enhances RBC, neutrophil, and platelet recovery in myelosuppressed hosts. Intriguingly, we also find that chemical inhibition of SHIP1 triggers apoptosis of blood cancer cells. Thus, SHIP1 inhibitors represent a novel class of small molecules that have the potential to enhance allogeneic transplantation, boost blood cell production, and improve the treatment of hematologic malignancies.
Transcription factor activation in response to cutaneous injury: Role of AP‐1 in reepithelialization (2002)

Reepithelialization is the process responsible for restoring an intact epidermis following cutaneous injury. A change in the activity of keratinocytes is required for reepithelialization to occur, and this is likely to be regulated by the altered expression of effector genes, mediated by transcription factors. The injury itself provides a stimulus for transcription factor activation either directly due to mechanical stress, or via paracrine mechanisms such as the release of growth factors from damaged cells. Members of the activator protein-1 family, in particular c-fos and c-jun, have been the most widely studied wound-induced transcription factors. The signal transduction pathways linking cellular injury to activator protein-1 stimulation appear to involve an increase in intracellular Ca2+ and activation of mitogen-activated protein kinases. Given that a number of genes involved in the reepithelialization of wounds are regulated by activator protein-1, a distinct role for this transcription factor in reepithelialization is beginning to emerge. This article reviews the evidence for activator protein-1 involvement in reepithelialization, with particular focus on the activation of this transcription factor in response to wounding, the second messenger/kinase pathways involved, and the modulation of downstream genes that have the capacity to regulate keratinocyte function.
Using specifications to check source code (1994)

Traditional static checkers are limited to detecting simple anomalies since they have no information regarding the intent of the code. Program verifiers are too expensive for nearly all applications. This thesis investigates the possibilities of using specifications to do lightweight static checks to detect inconsistencies between specifications and implementations. A tool, LCLint, was developed to do static checks on C source code using LCL specifications. It is similar to traditional lint, except it uses information in specifications to do more powerful checks. Some typical problems detected by LCLint include violations of abstraction barriers and modifications of caller-visible state that are inconsistent with the specification. Experience using LCLint to check a specified program and to understand and maintain a program with no specifications illustrate some applications of LCLint and suggest future directions for using specifications to check source code.
Gene Therapy for Diabetes Mellitus (1997)

1. This review describes experimental approaches to test the feasibility of using gene therapy to administer insulin to type 1 and type 2 diabetic patients. Two approaches, i.e. ex vivo and in vivo transfer of the insulin gene, are described. 2. Substantial progress has been made in recent years in engineering glucose-responsive beta-cell lines that have been genetically engineered to proliferate or differentiate in response to appropriate extracellular signals. 3. Non-beta-cell lines have been engineered to constitutively secrete insulin at a constant rate. These cells may improve glycaemic control in patients over longer periods when used in combination with insulin injections. Engineering glucose-stimulated insulin secretion in such cells has proved extremely difficult and several genes may he required. 4. In vivo transfer of the insulin gene to animals results in improved control of diabetes. However, for safety reasons this approach may have limited use in the treatment of diabetes in humans.
BLSTM-based handwritten text recognition using Web resources (2015)

Handwriting recognition systems usually rely on static dictionaries and language models. Full coverage of these dictionaries is generally not achieved when dealing with unrestricted document corpora due to the presence of Out-Of-Vocabulary words. In a previous work, dynamic dictionaries were built from Web resources and successfully applied to isolated word recognition. In the present work we extend this approach to text-line recognition. Line segmentation into words is needed to exploit dynamic dictionaries and it is performed using BLSTM classifiers to align filler models and word sequence outputs. Words are then classified based on the confidence score into anchor and non-anchor words (AWs and NAWs). AWs are equated to the BLSTM outputs and used as such. Dynamic dictionaries are built for NAWs by exploiting Web resources for their character sequence and for neighboring AWs. Text-lines are decoded again using dynamic dictionaries and re-estimated language model. We conduct experiments on the publicly available RIMES database and show that the introduction of the dynamic dictionary is beneficial. Equally important, we show that the gain increases as the proportion of OOVs increases.
Fate of viruses during wastewater sludge treatment processes (1989)

Infectious viruses are shed from humans by many routes. These include coughing and sneezing, contact with and aerosolization from external body lesions, urinary and intestinal excretions. Viruses shed by the latter two routes, urinary and intestinal excretions, are likely to be present as contaminants in domestic wastewater. The purpose of this review is to summarize recent information on the pathways which viruses follow during wastewater sludge‐generation processes and to examine information pertinent to the fate of viruses during wastewater sludge disposal. Information is included on viruses capable of causing human illness, as well as on bacterial viruses also present in wastewater, which, in some ways, may serve as indicators when assessing the likely fate of human viruses.
Polyoma Virus Pseudocapsids as Efficient Carriers of Heterologous DNA into Mammalian Cells (1995)

Polyoma virus VP1 pseudocapsids, generated from a recombinant baculovirus, have been successfully used to transfer exogenous DNA stably into rodent (rat-2) cells. To evaluate the efficiency and biological usefulness of this route for introducing heterologous DNA into cells, the gene for a transforming deletion mutant of the middle T antigen of polyoma virus, dl8 MT, was used initially. Whereas the amount of DNA packaged together with pseudocapsids was found to be variable (2-30%), even at low efficiency its transfer as biologically functional information was high. The dl8 MT gene was stably transferred and integrated in low copy numbers into the host chromosome. Transformed cell lines (derived from single foci) were shown to produce high levels of the corresponding mutant protein, which was active in an in vitro protein kinase assay. In comparisons with the calcium phosphate DNA coprecipitation procedure (or lipofectin route), the VP1 pseudocapsid approach was shown to have many advantages in terms of maintenance of DNA fidelity and increased efficiency of gene expression. This system was also assessed for its ability to transfer into and express the chloramphenicol acetyl transferase (CAT) gene in a human liver cell line. Here again, the assay for functional CAT expression showed the pseudocapsid transfer procedure to compare favorably with lipofectin transfer. In another transient assay, a low-level endogenously expressed gene, p43, was complexed with pseudocapsids and transferred into human embryo lung fibroblasts, thereby increasing the expression levels. The ease of production of VP1 pseudocapsids, coupled with their efficient transfer of biologically useful information, should make this route of gene delivery an attractive proposition for further exploration with regard to gene therapy.
Enhancement of voltage contrast inspection signal using scan direction (2007)

In-line voltage contrast inspection has taken off in popularity in the last decade. While the impact of this technique has already been dramatic, the best known practices are still rapidly evolving. This paper shows that scan direction can have a very large influence on signal intensity for defects of interest and that flexibility to be able to scan in both the X and Y directions can prove very advantageous. Two examples are presented illustrating this point. The underlying physics behind this phenomenon are explained. A new best practice for voltage contrast inspection is then proposed.
Troponin T and creatinine kinase isoenzyme MB mass in the diagnosis of myocardial infarction (1998)

The aim of this study was to compare troponin T (TnT) and creatine kinase isoenzyme MB mass (CK-MBm) with conventional enzymes, ie CK, CK-MB activity and lactate dehydrogenase isoenzyme 1, in the diagnosis of myocardial infarction (MI). 624 patients (351 men and 273 women, median age 69 years) were admitted to hospital with suspicion of an acute coronary heart disease event. TnT was elevated (> 0.10 microg/L) in 100%, CK-MBm (> 5.0 microg/L) in 99%, and both markers in 99% of the 89 patients with the diagnosis of a definite MI according to modified FINMONICA criteria. In the 60 patients with the diagnosis of a probable MI, TnT was elevated in 65%, CK-MBm in 67% and both markers in 60%. In the patients with unstable coronary artery disease (unstable angina or prolonged chest pain attack) and conventional enzymes within normal limits, TnT was elevated in 14%, CK-MBm in 17% and both markers in 9%. The use of TnT and CK-MBm did not lead to a major change in the diagnostics of definite MI. However, TnT and CK-MBm did not confirm the diagnosis of probable MI in one-third of the events. These new markers revealed a myocardial injury in about 15% of those patients who had unstable coronary artery disease and conventional enzymes within normal limits.
Density Functional Theory Study of Carboxylic Acids Adsorption and Enolization on Monoclinic Zirconia Surfaces (2011)

Computational modeling is a valuable tool for understanding atomic-level catalytic processes on metal oxides. Carboxylic acid adsorption and enolization with varied degrees of α branching on monoclinic zirconia's most important surfaces, (1̅11), (111), and (1̅01), have been studied by the density functional theory (DFT). Carboxylates on zirconia (1̅11) and (111) surfaces are preferentially stabilized in the bidentate bridging mode, with O–H bond dissociation and hydrogen bonding to a 2-fold coordinated (2-fc) lattice oxygen. Carboxylic α hydrogen abstraction by another 2-fc lattice oxygen results in enolization of adsorbed carboxylates most readily on the (1̅11) surface of monoclinic zirconia with activation energy ∼25 kcal/mol, which is not sensitive to acid branching. Enolization on the (111) surface requires higher activation energy, 29–33 kcal/mol depending on acid branching. This study demonstrates the origin of an important intermediate in the carboxylic acid ketonization mechanism—often named “surface ketene”.