gebhart/patrepeval huggingface dataset:
Tagging English text with a probabilistic model (1994)

In this paper we present some experiments on the use of a probabilistic model to tag English text, i.e. to assign to eachword the correct tag #part of speech# in the context of the sentence. The main novelty of these experiments is the use of untagged text in the training of the model. Wehave used a simple triclass Markov model and are looking for the best way to estimate the parameters of this model, depending on the kind and amount of training data provided. Two approaches in particular are compared and combined: to use text that has been tagged by hand and compute relative frequency counts, to use text without tags and train the model as a hidden Markov process, according to a Maximum Likelihood principle.
Potential etiologic and functional implications of genome-wide association loci for human diseases and traits (2009)

We have developed an online catalog of SNP-trait associations from published genome-wide association studies for use in investigating genomic characteristics of trait/disease-associated SNPs (TASs). Reported TASs were common [median risk allele frequency 36%, interquartile range (IQR) 21%-53%] and were associated with modest effect sizes [median odds ratio (OR) 1.33, IQR 1.20-1.61]. Among 20 genomic annotation sets, reported TASs were significantly overrepresented only in nonsynonymous sites [OR = 3.9 (2.2-7.0), p = 3.5 x 10(-7)] and 5kb-promoter regions [OR = 2.3 (1.5-3.6), p = 3 x 10(-4)] compared to SNPs randomly selected from genotyping arrays. Although 88% of TASs were intronic (45%) or intergenic (43%), TASs were not overrepresented in introns and were significantly depleted in intergenic regions [OR = 0.44 (0.34-0.58), p = 2.0 x 10(-9)]. Only slightly more TASs than expected by chance were predicted to be in regions under positive selection [OR = 1.3 (0.8-2.1), p = 0.2]. This new online resource, together with bioinformatic predictions of the underlying functionality at trait/disease-associated loci, is well-suited to guide future investigations of the role of common variants in complex disease etiology.
Identification and Epitope Enhancement of a PAX-FKHR Fusion Protein Breakpoint Epitope in Alveolar Rhabdomyosarcoma Cells Created by a Tumorigenic Chromosomal Translocation Inducing CTL Capable of Lysing Human Tumors (2006)

Fusion proteins created by chromosomal translocations in tumors can create neoantigenic determinants at the breakpoint, which are unique to the tumor cells but shared by the vast majority of tumors of that histologic type. If the fusion protein is responsible for the malignant transformation, its expression cannot be lost by the tumor to escape immune responses against this tumor antigen. Here, we identify such a fusion protein breakpoint epitope in the PAX-FKHR fusion protein created by the t(2;13) translocation present in 80% of cases of alveolar rhabdomyosarcoma, a highly aggressive pediatric soft-tissue sarcoma. We use autologous dendritic cells pulsed with the RS10 breakpoint fusion peptide to raise a human CTL line from a normal healthy HLA-B7+ blood donor specific for this peptide. These CTLs are CD8+ (CD4-CD56-) and restricted by HLA-B7. These human peptide-specific CTL lyse human HLA-B7+ rhabdomyosarcoma tumor cells. Therefore, the fusion protein is endogenously processed to produce this natural epitope presented by HLA-B7 and thus this peptide is a bone fide human tumor antigen. We also define a substitution that increases the affinity for HLA-B7 without loss of antigenicity. This epitope-enhanced peptide may serve as a candidate cancer vaccine for HLA-B7+ patients with alveolar rhabdomyosarcoma.
Case Study of Permeability, Vug Quantification, and Rock Typing in a Complex Carbonate (2006)

Abstract This case study demonstrates a new method to compute continuous permeability and estimate reservoir rock type from logs in a complex, heterogeneous, Middle Eastern carbonate reservoir. The 795 ft conventionally cored interval consists of interbedded limestones and dolomites with anhydrite cement and features a wide variety of textures. In some intervals the depositional textures are preserved, in others they are highly altered by diagenesis. Vugs are developed in several intervals. Computation of permeability from porosity alone yields scatter of a factor of 700. Rock typing using only conventional logs was unsatisfactory due to the poor permeability estimation. The effect of geological complexity on the log based prediction is overcome by including pore size distribution data from a combination of NMR and borehole electrical image logs. This data is sufficient to partition the porosity according the pore size, compute permeability and assess the rock types, independently of mineralogy, facies, and other variables. The results are validated by comparison to core derived properties and formation tester mobilities. Incorporation of the pore size information into the log based interpretation reduces the scatter in computed permeability to a factor of less than 10. The assumptions and principles of the log analysis method were validated in the lab through extensive characterization of the pore system over a range of scales. Data from a variety of methods including MICP, lab NMR, BET surface area, thin section analysis, continuous vuggy porosity analysis from the core slab, minpermeametry and other advanced research methods are included. A key result of this study is that a relatively simple method for log derived permeability and rock type analysis in carbonates, first developed in high porosity limestones, can be successfully applied in this lower porosity (10 – 20 p.u.) carbonate. This gives us confidence to project that the method could be applicable to many other carbonates worldwide.
Novel Proteinaceous Infectious Particles Cause Scrapie (1982)

After infection and a prolonged incubation period, the scrapie agent causes a degenerative disease of the central nervous system in sheep and goats. Six lines of evidence including sensitivity to proteases demonstrate that this agent contains a protein that is required for infectivity. Although the scrapie agent is irreversibly inactivated by alkali, five procedures with more specificity for modifying nucleic acids failed to cause inactivation. The agent shows heterogeneity with respect to size, apparently a result of its hydrophobicity; the smallest form may have a molecular weight of 50,000 or less. Because the novel properties of the scrapie agent distinguish it from viruses, plasmids, and viroids, a new term "prion" is proposed to denote a small proteinaceous infectious particle which is resistant to inactivation by most procedures that modify nucleic acids. Knowledge of the scrapie agent structure may have significance for understanding the causes of several degenerative diseases.
Sequence-Function Relationships of Prokaryotic and Eukaryotic Galactosyltransferases (1998)

Galactosyltransferases are enzymes which transfer galactose from UDP-Gal to various acceptors with either retention of the anomeric configuration to form alpha1,2-, alpha1,3-, alpha1,4-, and alpha1, 6-linkages, or inversion of the anomeric configuration to form beta1, 3-, beta1,4-, and beta1-ceramide linkages. During the last few years, several (c)DNA sequences coding for galactosyltransferases became available. We have retrieved these sequences and conducted sequence similarity studies. On the basis of both the nature of the reaction catalyzed and the protein sequence identity, these enzymes can be classified into twelve groups. Using a sensitive graphics method for protein comparison, conserved structural features were found in some of the galactosyltransferase groups, and other classes of glycosyltransferases, resulting in the definition of five families. The lengths and locations of the conserved regions as well as the invariant residues are described for each family. In addition, the DxD motif that may be important for substrate recognition and/or catalysis is demonstrated to occur in all families but one.
AdaNet: Adaptive Structural Learning of Artificial Neural Networks (2016)

We present new algorithms for adaptively learning artificial neural networks. Our algorithms (AdaNet) adaptively learn both the structure of the network and its weights. They are based on a solid theoretical analysis, including data-dependent generalization guarantees that we prove and discuss in detail. We report the results of large-scale experiments with one of our algorithms on several binary classification tasks extracted from the CIFAR-10 dataset. The results demonstrate that our algorithm can automatically learn network structures with very competitive performance accuracies when compared with those achieved for neural networks found by standard approaches.
Prognosis and prognostic factors in inflammatory bowel disease. (1995)

The chance of normal survival for patients with inflammatory bowel disease is generally good. There may be a small excess mortality for those with Crohn's disease; however recent studies do not confirm this trend. For those with ulcerative colitis, there may be an excess mortality in the first two years after diagnosis, especially in those who undergo surgery. The necessity for an operation varies, but at least 50% of patients with Crohn's disease will be an operation in the first 10 years; whereas only about 20% of patients with ulcerative colitis will require a colectomy. Most patients with inflammatory bowel disease are able to lead a normal life and are not disabled by their disease. The prognosis in the elderly is usually good; however there is an increased mortality over younger patients, which is probably due to the presence of coexistent disease. Children also have a slightly higher mortality; this may be due to the relative frequency of a particularly extensive disease and the development of colorectal cancer. Growth retardation occurs in up to one-third of children with Crohn's disease, but it may be resolved if remission can be obtained. Pregnancy has not been shown to have an impact on inflammatory bowel disease, but its onset during pregnancy confers a significant risk for both mother and child. Extensive involvement is a poor prognosis factor in both diseases; conversely, isolated small bowel Crohn's disease and ulcerative proctitis carry particularly good prognoses. A short clinical history, fistulae or abscesses at presentation probably represent an aggressive form of Crohn's disease. Hypoalbuminemia, anemia and raised inflammatory markers are laboratory markers which suggest a worse prognosis in the short and possibly long-term.
Direct Electron TransferA Favorite Electron Route for Cellobiose Dehydrogenase (CDH) from Trametes villosa. Comparison with CDH from Phanerochaete chrysosporium (2006)

This paper presents some functional differences as well as similarities observed when comparing the newly discovered cellobiose dehydrogenase (CDH) from Trametes villosa (T.v.) with the well-characterized one from Phanerochaete chrysosporium (P.c.). The enzymes were physically adsorbed on spectrographic graphite electrodes placed in an amperometric flow through cell connected to a flow system. In the case of T.v.-CDH-modified graphite electrodes, a high direct electron transfer (DET) current was registered at the polarized electrode in the presence of the enzyme substrate reflecting a very efficient internal electron transfer (IET) process between the reduced FAD-cofactor and the oxidized heme-cofactor. In the case of P.c.-CDH-modified graphite electrodes, the DET process is not as efficient, and the current will greatly increase in the presence of a mediator (mediated electron transfer, MET). As a consequence, when comparing the two types of enzyme-modified electrodes an inverted DET/MET ratio for T.v.-CDH is shown, in comparison with P.c.-CDH. The rates of the catalytic reaction were estimated to be comparable for both enzymes, by measuring the combined DET + MET currents. The inverted DET/MET ratio for T.v.-CDH-modified electrodes might suggest that probably there is a better docking between the two domains of this enzyme and that the linker region of P.c.-CDH might have an active role in modulating the rate of the IET (by changing the interdomain distance), with respect to pH. Based on the new properties of T.v.-CDH emphasized in the present study, an analytical application of a third-generation biosensor for lactose was recently published.
The Notch ligand, Delta-1, inhibits the differentiation of monocytes into macrophages but permits their differentiation into dendritic cells (2001)

Notch-mediated cellular interactions are known to regulate cell fate decisions in various developmental systems. A previous report indicated that monocytes express relatively high amounts of Notch-1 and Notch-2 and that the immobilized extracellular domain of the Notch ligand, Delta-1 (Delta(ext-myc)), induces apoptosis in peripheral blood monocytes cultured with macrophage colony-stimulating factor (M-CSF), but not granulocyte-macrophage CSF (GM-CSF). The present study determined the effect of Notch signaling on monocyte differentiation into macrophages and dendritic cells. Results showed that immobilized Delta(ext-myc) inhibited differentiation of monocytes into mature macrophages (CD1a+/-CD14+/- CD64+) with GM-CSF. However, Delta(ext-myc) permitted differentiation into immature dendritic cells (CD1a+CD14-CD64-) with GM-CSF and interleukin 4 (IL-4), and further differentiation into mature dendritic cells (CD1a+CD83+) with GM-CSF, IL-4, and tumor necrosis factor-alpha (TNF-alpha). Notch signaling affected the differentiation of CD1a-CD14+ macrophage/dendritic cell precursors derived in vitro from CD34+ cells. With GM-CSF and TNF-alpha, exposure to Delta(ext-myc) increased the proportion of precursors that differentiated into CD1a+CD14- dendritic cells (51% in the presence of Delta(ext-myc) versus 10% in control cultures), whereas a decreased proportion differentiated into CD1a-CD14+ macrophages (6% versus 65%). These data indicate a role for Notch signaling in regulating cell fate decisions by bipotent macrophage/dendritic precursors.
Conditions for underflow and overflow of an arithmetic stack (1977)

The behaviour of an arithmetic stack is formally described as the loading of an arbitrary string of a context free language symbol by symbol on to a stack. Instances of a special symbol in the string being loaded invoke an operation which removes the top cell of the stack in some undefined way. Necessary and sufficient conditions for stack length boundedness are stated and proved. One application of the results concerns the choice between compile time and run time checks for underflow and overflow. Another concerns the testing for applicability of a certain algorithm for inverting Metcalfe-Reeves translators.
Bio‐Inspired Hierarchical Macromolecule–Nanoclay Hydrogels for Robust Underwater Superoleophobicity (2010)

Robust underwater superoleophobicity – oil repellence that is stable under loading – is achieved by constructing hierarchical macromolecule-nanoclay hydrogels (see images), inspired by the oil-repellent nature of the composite surface of fish. The synergetic effect of micro-/nanostructures and the mechanical strength of hybrid hydrogels in general supports the stability of trapped water on the hydrogel surface, endowing hybid hydrogels with robust superoleophobicity (upper right inset) even under loading forces. Detailed facts of importance to specialist readers are published as ”Supporting Information”. Such documents are peer-reviewed, but not copy-edited or typeset. They are made available as submitted by the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Light-induced radiative recombination centers in hydrogenated amorphous silicon (1980)

Laser irradiation of hydrogenated amorphous silicon produces recombination centers which shorten the lifetime of carriers. Some of the light-induced centers are radiative. The generation of the new radiative recombination centers increases with increasing temperature. All the light-induced centers disappear upon thermal anneal at about 210 °C.
Properties and Synthetic Applications of Enzymes in Organic Solvents (2000)

Biotransformations already represent an effective and sometimes preferable alternative to chemical synthesis for the production of fine chemicals and optically active compounds. To further widen the versatility of the biological approach, the so-called "nonaqueous enzymology", which now represents an important area of research and biotechnological development, has emerged in the last ten years or so. This new methodology is especially suitable for the modification of precursors of pharmaceutical compounds and fine chemicals, which, in most cases, are insoluble or poorly soluble in water. Even though the idea of carrying out an enzymatic process in organic solvent was initially considered with scepticism, biocatalysis in such media is now investigated and exploited in numerous academic and industrial laboratories. One of the reasons that makes enzymatic catalysis in nonaqueous media so appealing, is the important new properties that enzymes exhibit in organic solvents. For example, they are often more stable and can catalyze reactions that are impossible or difficult in water. Furthermore, enzyme selectivity can also differ from that in water and can change, or even reverse, from one solvent to another. This phenomenon, which can be called "medium engineering", can be exploited as a valid alternative to protein engineering. The first part of this review examines the thermodynamic, kinetic, spectroscopic, and physical approaches that have been adopted to investigate the factors that affect activity, stability, structure, and selectivity of enzymes in organic solvents. These combined studies have brought the understanding of enzyme catalysis in organic solvents to a level almost comparable to that reached for biocatalysis in aqueous media. The second part surveys a number of the synthetic applications of enzymes in organic media, which span from the preparation of milligrams of specifically labeled compounds to the modification of fats on multiton scale and from the preparation of complex key intermediates for the pharmaceutical industry to the synthesis of polymers.
Pediatric risk of mortality (PRISM) score (1988)

The Pediatric Risk of Mortality (PRISM) score was developed from the Physiologic Stability Index (PSI) to reduce the number of physiologic variables required for pediatric ICU (PICU) mortality risk assessment and to obtain an objective weighting of the remaining variables. Univariate and multivariate statistical techniques were applied to admission day PSI data (1,415 patients, 116 deaths) from four PICUs. The resulting PRISM score consists of 14 routinely measured, physiologic variables, and 23 variable ranges. The performance of a logistic function estimating PICU mortality risk from the PRISM score, age, and operative status was tested in a different sample from six PICUs (1,227 patients, 105 deaths), each PICU separately, and in diagnostic groups using chi-square goodness-of-fit tests and receiver operating characteristic (ROC) analysis. In all groups, the number and distribution of survivors and nonsurvivors in adjacent mortality risk intervals were accurately predicted: total validation group (chi 2(5) = 0.80; p greater than .95), each PICU separately (chi 2(5) range 0.83 to 7.38; all p greater than .10), operative patients (chi 2(5) = 2.03; p greater than .75), nonoperative patients (chi 2(5) = 2.80, p greater than .50), cardiovascular disease patients (chi 2(5) = 4.72; p greater than .25), respiratory disease patients (chi 2(5) = 5.82; p greater than .25), and neurologic disease patients (chi 2(5) = 7.15; p greater than .10). ROC analysis also demonstrated excellent predictor performance (area index = 0.92 +/- 0.02).
Tumor Antigens Recognized by T Cells and Antibodies (2003)

Tumor Antigens Recognized by Antibodies. Human Tumor Antigens Recognized by Antibodies (SEREX). Antibodies to Tumor Oncoproteins in Cancer Patients. Antibody and CTL Responses to the NY-ESO Antigen. Tumor Antigens Recognized by CD4+ T Cells (predominantly TH1). Melanoma Antigens Recognized by CD4+ T Cells. Mouse Models in the Recognition of Tumor Antigens. Antigens of the MAGE Family Recognized by CD4+ T Cells. Tumor antigens Recognized by CD8 T Cells. Melanoma Antigens Recognized by CD8 T Cells. Squamous Cells and Adeno Cancer Antigens Recognized by T Cells. Heat/Shock Proteins and Tumor Antigens. The Wilms Tumor Antigens as CTL Target. Ex vivo and in situ Tetramer Analysis of CTL Responses to Tumors. Altered Peptide Ligands of Tumor T Cell Epitopes: Implications for More Effective Vaccine Therapy in Human Neoplasia.
Ultrahigh-speed logic gate family with Nb/Al-AlOx/Nb Josephson junctions (1986)

The modified variable threshold logic (MVTL) OR gate has a wide operating margin and occupies a small area, so that a gate family using this OR gate is suitable for LSI logic circuits. This paper describes the design, fabrication process, and evaluation of the MVTL gate family. The gate family is composed of OR, AND, and 2/3 MAJORITY gates. The gates were made with all refractory material including Nb/ Al-AlO <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">x</inf> /Nb junctions and Mo resistors, and they were patterned by using a reactive ion etching (RIE) technique. The logic delay of the gate was measured with a Josephson sampler. The minimum delays for OR, AND, and 2/3 MAJORITY gates were 5.6, 16, and 21 ps/gate, respectively.
Improvement of product attributes of mayonnaise by enzymic hydrolysis of egg yolk with phospholipase A2 (1981)

Abstract Egg yolk fermented with pancreatic phospholipase A 2 has been shown to be a more potent emulsifier for mayonnaise than untreated egg yolk. The mayonnaise withstood heating at 100°C for 30 min without the emulsion breaking. The treatment also effected a considerable thickening of the product. Animal feeding trials with lysolecithin and fermented egg yolk suggested that the enzymic hydrolysis does not pose any toxicological hazards.
Immunochemical localization of heparanase in mouse and human melanomas (1990)

Heparanase, an endo-beta-D-glucuronidase, has been associated with melanoma metastasis. Polyclonal antibodies directed against the murine N-terminal heparanase peptide detected a Mr approximately 97,000 protein on SDS-PAGE of mouse melanoma and human melanoma cell lysates. In an indirect immunocytochemical study, human A375-SM and mouse B 16-BL6 melanoma cells were stained with the anti-heparanase antibodies. Heparanase antigen was localized in the cytoplasm of permeabilized melanoma cells as well as at the cell surface of unpermeabilized cells. Immunohistochemical staining of frozen sections from syngeneic mouse lungs containing micrometastases of B16-BL6 melanoma demonstrated heparanase localized in metastatic melanoma cells. Similar studies using frozen sections of malignant melanomas resected from patients indicated that heparanase is localized in invading melanoma cells. Our studies suggest that (a) the N-terminus of the heparanase molecule in mouse and human is antigenically related; (b) heparanase antigens are localized at the cell surface and in the cytoplasm of metastatic human and mouse melanoma cells; and (c) heparanase antigens are enriched in invasive and metastatic murine and human melanomas in vivo.