gebhart/patrepeval huggingface dataset:
The Pharmacology of the Gastric Acid Pump: The H+,K+ ATPase (1995)

The gastric H+,K+ ATPase--the gastric acid pump--is the molecular target for the class of antisecretory drugs called the proton-pump inhibitors (PPIs). These compounds--omeprazole, lansoprazole, and pantoprazole--contain, as their core structure, 2-pyridyl methylsulfinyl benzimidazole. The H+,K+ ATPase is a heterodimer composed of a 1034-amino acid catalytic alpha peptide and a glycosylated 291-amino acid beta subunit. The alpha subunit probably contains 10 membrane-spanning sequences; the beta, a single transmembrane segment. The PPIs have a pKa of about 4.0; hence they accumulate only in the acidic secretory canaliculus of the stimulated parietal cell. Here they undergo conversion to a cationic sulfenamide, which then reacts with available cysteines on the extracytoplasmic face of the alpha subunit. Omeprazole reacts and forms disulfide bonds with cys813(822) and cys892; lansoprazole, with cys813(822), cys892, and cys321; and pantoprazole, with cys813 and -822. The antisecretory effect of the drugs reflects their short plasma half-life (approximately 60 min), the number of active pumps during that time, and the recovery of pumps following biosynthesis and reversal of inhibition. These drugs also show synergism with either amoxicillin or clari- thromycin in eradicating Helicobacter pylori, an organism shown to be important in duodenal and gastric ulcer disease. Their action is probably due to elevation of pH in the environment of the organism, rather than to any direct action.
A family of human lymphoid and myeloid Ig-like receptors, some of which bind to MHC class I molecules (1997)

Leukocyte Ig-like receptors (LIRs) are a newly discovered family of immunoreceptors expressed on monocytes and B cells and at lower levels on dendritic cells and NK cells. The amino acid sequences in the extracellular regions of eight of these receptors show between 63 and 84% identity to the prototypic LIR-1 sequence. LIRs contain either two or four Ig domains and fall into three classes: those with cytoplasmic domains containing two, three, or four immunoreceptor tyrosine-based inhibitory motif-like motifs; those with a short cytoplasmic domain and no immunoreceptor tyrosine-based inhibitory motif-like motifs; and those with no transmembrane domain represented by a single LIR molecule that is presumably secreted. The LIRs are structurally related to the human Fc(alpha)R and the killer inhibitory receptors and map to the same region of chromosome 19 as these genes. Like killer inhibitory receptors, at least two LIRs bind to MHC class I Ags, but their different cellular distribution suggests a distinct role in immune system modulation.
RNA editing by G-nucleotide insertion in mumps virus P-gene mRNA transcripts (1990)

A guanine nucleotide insertion event has been shown to occur at a specific site within mumps virus P-gene mRNA transcripts. The region of the mRNA containing the site expected to be used for RNA editing and the complementary portion of the genomic RNA were cloned, and their nucleotide sequences were obtained. The genomic RNA was found to possess six C residues at the insertion site, whereas 63% of the P-gene-specific mRNA transcripts were found to have from two to five G residues inserted at this position in the RNA. An unedited mRNA was shown to encode the mumps virus cysteine-rich protein V, and mRNA transcripts containing two and four inserted G residues were translated to yield the mumps virus P and I proteins, respectively.
Enhancement of radioimmunotherapy by drugs modifying tumour blood flow in a colonic xenograft model (1994)

Radioimmunotherapy (RIT) is hampered clinically by poor tumour localization of antibody. In order to enhance localization we have investigated the concomitant use of RIT with 2 drugs, flavone-8-acetic acid (FAA) and its analogue 5,6-dimethylxanthenone-4-acetic acid (XAA), which both reduce tumour blood flow and induce immunomodulation. A single i.v. dose of 0.5 mCi (18.5 MBq) intact 131I anti-CEA antibody significantly delayed growth and prolonged survival over that of untreated controls, in an established LS174T colon xenograft model in nude mice. The adjuvant use of a single i.p. dose of either FAA or XAA, given 24 or 48 hr after 131I-A5B7 to allow maximum tumour levels of antibody to be attained before drug-induced blood-flow inhibition, significantly enhanced the RIT. FAA caused entrapment of antibody within the tumour in relation to the time allowed for localization before drug administration. Repeated doses of FAA prolonged tumour growth inhibition but did not enhance the therapy achieved after a single dose. Although both drugs alone induced massive tumour necrosis of all but a thin peripheral rim of viable cells, tumour regrowth was inhibited for a few days only, with no effect on survival. Drug-induced tumour necrosis, immunomodulation and retention of higher doses of 131I-A5B7 within the tumour may contribute to the enhanced RIT produced by this combined therapy.
Automatic noise figure measurements with computer control and correction (1982)

By using computer control and correction, the noise parameters of an amplifying device can be obtained as an immediate display from system noise measurements without the need of having subsequently to make tedious calculations. The means of achieving this are described in the paper, together with results obtained by applying the facility to microwave amplifiers incorporating GaAs f.e.t.devices mounted in microstrip.
Synthesis of 3,4-Dihydroisocoumarins from α-Lithiated o-Toluates (1997)

Tellurides 2 prepared from α-bromo-o-toluesters 1 undergo lithium-tellurium exchange to give benzylic anions that can be condensed with aldehydes or ketones to afford 3,4-dihydroisocumarins 3.
Structured sampling and reconstruction of illumination for image synthesis (1994)

An important goal of image synthesis is to achieve accurate, efficient and consistent sampling and reconstruction of illumination varying over surfaces in an environment. A new approach is introduced for the treatment of diffuse polyhedral environments lit by area light sources, based on the identification of important properties of illumination structure. The properties of unimodality and curvature of illumination in unoccluded environments are used to develop a high quality sampling algorithm which includes error bounds. An efficient algorithm is presented to partition the scene polygons into a mesh of cells, in which the visible part of the source has the same topology. A fast incremental algorithm is presented to calculate the backprojection, which is an abstract representation of this topology. The behaviour of illumination in the penumbral regions is carefully studied, and is shown to be monotonic and well behaved within most of the mesh cells. An algorithm to reduce the mesh siz...
Codes in the damerau distance for DNA storage (2016)

We introduce the new problem of code design in the Damerau metric. The Damerau metric is a generalization of the Levenshtein distance which also allows for adjacent transposition edits. We first provide constructions for codes that may correct either a single deletion or a single adjacent transposition and then proceed to extend these results to codes that can simultaneously correct a single deletion and multiple adjacent transpositions. Bounds on the size of the codes and accompanying decoding algorithms are presented as well.
Lock-in amplifiers : principles and applications (1983)

Basic concepts in lock-in recovery phase-sensitive detectors lock-in amplifiers specifications two-phase lock-in amplifiers limitations of conventional lock-in amplifiers phase-locking to noisy signals heterodyne lock-in amplifiers P.W.M.systems computer-controlled lock-in amplifiers. Appendices: principal applications selected topics on signals and noise synchronous detection and noise signal conditioning filters amplifier selection and noise matching interference and ground loop suppression.
PIK3CA Mutation in Colorectal Cancer: Relationship with Genetic and Epigenetic Alterations (2008)

Somatic PIK3CA mutations are often present in colorectal cancer. Mutant PIK3CA activates AKT signaling, which up-regulates fatty acid synthase (FASN). Microsatellite instability (MSI) and CpG island methylator phenotype (CIMP) are important molecular classifiers in colorectal cancer. However, the relationship between PIK3CA mutation, MSI and CIMP remains uncertain. Using Pyrosequencing technology, we detected PIK3CA mutations in 91 (15%) of 590 population-based colorectal cancers. To determine CIMP status, we quantified DNA methylation in eight CIMP-specific promoters [CACNA1G, CDKN2A (p16), CRABP1, IGF2, MLH1, NEUROG1, RUNX3, and SOCS1] by real-time polymerase chain reaction (MethyLight). PIK3CA mutation was significantly associated with mucinous tumors [P = .0002; odds ratio (OR) = 2.44], KRAS mutation (P < .0001; OR = 2.68), CIMP-high (P = .03; OR = 2.08), phospho-ribosomal protein S6 expression (P = .002; OR = 2.19), and FASN expression (P = .02; OR = 1.85) and inversely with p53 expression (P = .01; OR = 0.54) and beta-catenin (CTNNB1) alteration (P = .004; OR = 0.43). In addition, PIK3CA G-to-A mutations were associated with MGMT loss (P = .001; OR = 3.24) but not with MGMT promoter methylation. In conclusion, PIK3CA mutation is significantly associated with other key molecular events in colorectal cancer, and MGMT loss likely contributes to the development of PIK3CA G>A mutation. In addition, Pyrosequencing is useful in detecting PIK3CA mutation in archival paraffin tumor tissue. PIK3CA mutational data further emphasize heterogeneity of colorectal cancer at the molecular level.
Image spam hunter (2008)

Spammers are constantly creating sophisticated new weapons in their arms race with anti-spam technology, the latest of which is image-based spam. The newest image-based spam uses simple image processing technologies to vary the content of individual messages, e.g. by changing foreground colors, backgrounds, font types, or even rotating and adding artifacts to the images. Thus, they pose great challenges to conventional spam filters. In this paper, we propose a system using a probabilistic boosting tree to determine whether an incoming image is a spam or not based on global image features, i.e. color and gradient orientation histograms. The system identifies spam without the need for OCR and is robust in the face of the kinds of variation found in current spam images. Evaluation results show the system correctly classifies 90% of spam images while mislabeling only 0.86% of non-spam images as spam.
Anti-CD20 Antibody Therapy for B-Cell Lymphomas (2012)

A 62-year-old man receives a diagnosis of diffuse large B-cell lymphoma; treatment with a regimen including the anti-CD20 antibody rituximab is recommended. Rituximab has been shown to improve progression-free survival when added to standard chemotherapy regimens for lymphoma.
MULTIVARIATE REGRESSION MODELING FOR THE PREDICTION OF INFLAMMATION, SYSTEMIC PRESSURE, AND END-ORGAN FUNCTION IN SEVERE SEPSIS (1997)

The purpose of this study was to evaluate the feasibility of developing multivariate equations that predicted blood pressure and measured levels of end-organ function indicators quantitatively up to 72 h in advance in critically ill patients with severe sepsis. Data collected prospectively from 59 patients entered into two sequential placebo-controlled clinical trials of recombinant interleukin-1 receptor antagonist in severe sepsis and septic shock was analyzed retrospectively. A series of multivariate equations were developed to predict systemic pressure, coagulation, and vital organ function indicators quantitatively at 24, 48, and 72 h after the onset of severe sepsis. These equations used physiologic and clinical laboratory measurements, plus circulating levels of eicosanoids and cytokines obtained when severe sepsis criteria first were met, and end-organ function indicators measured 24, 48, and 72 h later. Multivariate predictive equations were developed for temperature, white blood cell count, mean arterial pressure (MAP), Pao2/Fio2 ratio, the Murray acute lung injury score, alanine and aspartate aminotransferases, prothrombin time, partial thromboplastin time, platelet count, serum creatinine, and Glasgow Coma Scale. The percentage of data variation explained by the equations ranged from 11.4% (MAP at 48 h) to 85.1 % (platelet count at 24 h). Linear regression analysis of predicted values, obtained by entering baseline data from individual patients into the multivariate equations, versus observed results at 24, 48, and 72 h yielded regression coefficients ranging from .371 (MAP at 48 h) to .924 (platelet count at 24 h). Among patients without end-organ dysfunction at baseline, sensitivities for predicting values consistent with the onset of organ failure were ≥88% in 21/27 (78%) of the predictive equations. Resolution of organ failure indicators present at baseline was predicted successfully in individual patients, with 20/27 (74%) specificities ≥76%. In critically ill patients with severe sepsis, multivariate analysis of interactions among clinical observations, standard laboratory tests, and inflammatory response mediators produced equations that predicted systemic blood pressure and inflammatory and end-organ function indicators quantitatively up to 72 h in advance. Whether or not this methodology might be developed further to predict subclinically the onset and resolution of acute organ failure and shock in critically ill patients, and if it can be validated in a prospective trial will require further studies.
Super‐Efficient Exciton Funneling in Layer‐by‐Layer Semiconductor Nanocrystal Structures (2005)

Abstract In semiconductor nanocrystals the electronic energy gap is determined not only by the material but also by the size of the nanocrystals. This allows the construction of an energy‐gap gradient normal to multiple layers of nanocrystals where the diameters of the nanocrystals are monotonically increasing or decreasing in subsequent layers. In such devices we observe a highly efficient funneling of excitation energy from layers comprising smaller nanocrystals towards the layer with the largest nanocrystals in the center of the funnel. Most importantly, not only are excitons in radiative states transferred, but also excitons from trapped states, usually lost for luminescence, can be effectively recycled, hence increasing the overall luminescence yield.
Unequal cleavage in leech embryos: zygotic transcription is required for correct spindle orientation in a subset of early blastomeres (1996)

Leech embryos undergo invariant sequences of equal and unequal cell divisions to give rise to identifiable progeny cells. While many of the early cleavages are under maternal control, the divisions of a subset of early blastomeres (the large cells of the D' lineage) are perturbed after the inhibition of zygotic transcription. Analysis of the different types of cells produced in embryos injected with the transcriptional inhibitor, alpha-amanitin, revealed that the symmetry of cell division is perturbed in these large D'-derived cells during this early period of development. These cells, which would normally undergo a series of equal and unequal cleavages, always undergo equal cleavages after the inhibition of zygotic transcription. It appears that zygotically transcribed gene product(s) are required in the large cells of the D' lineage to orient the mitotic spindles properly for these unequal cell cleavages.
Hypoxia-induced autophagy contributes to the chemoresistance of hepatocellular carcinoma cells (2009)

Hypoxia commonly exists in solid tumors. Under such adverse conditions, adaptive responses including autophagy are usually provoked to promote cell survival. In our study, autophagy, a lysosomal-mediated degradation pathway, is demonstrated as a protective way to make hepatocellular carcinoma cells resistant to chemotherapy under hypoxia. Compared with normoxia, chemotherapeutic agent-induced cell death under hypoxia was significantly decreased, as a result of the reduced apoptosis. However, when autophagy was inhibited by 3-MA or siRNA targeted Beclin 1, this reduction was reversed, i.e., chemoresistance was attenuated, which means autophagy mediates the chemoresistance under hypoxia. In conclusion, autophagy decreases hepatoma cells sensitization to chemotherapeutic agents by affecting their apoptotic potential.
Effects of ribosomal mutations on the read-through of a chain termination signal: studies on the synthesis of bacteriophage lambda O gene protein in vitro. (1977)

In a DNA-dependent protein-synthesizing system that contains streptomycin-sensitive ribosomes, lambda DNA directs the synthesis of two proteins that are products of the O gene. The larger is produced as a result of read-through of a UGA termination codon. In the system containing streptomycin-resistant ribosomes this read-through protein is not synthesized, indicating that the mutational alteration in the ribosomal protein S12 restricts the read-through. The mutant ribosomes also fail to synthesize the read-through coat protein of RNA phage Qbeta. In addition, the mutant ribosomes restrict suppression of amber mutations in vitro, similar to their effect in vivo.
On the Ontology Instance Matching Problem (2008)

Most of the existing work on ontology matching is focused at the schema level, while, at the time being, instance-level matching techniques are only marginally considered. In this paper, we address the problem of ontology instance matching by providing a reference definition and by discussing key requirements and possible application fields. The architectural design of the HMatch 2.0 ontology matching suite is also presented as a concrete example of an ontology instance matcher.
Bacteria detection with thin wetting film lensless imaging (2010)

Lensless on-chip imaging is a promising technique to count and monitor cells and micro-objects in liquid sample. In this paper we apply this technique to the observation of µL sample containing bacteria evaporated onto a microscope slide. Compared with previously reported techniques, a large improvement in signal to noise ratio is obtained due to the presence of a few μm thick wetting film creating a micro-lens on top of each bacteria. In these conditions, standard CMOS sensor are able to detect micro-objects as small as few μm, e.g. E.coli and Bacillus subtilis bacteria and 1 μm polymer beads with a large signal to noise ratio of 45 ± 10. An overall detection efficiency of 85 ± 7% and a co-localization error of σ(1D) = 1.1μm compared with reference fluorescence microscopy images are achieved. This novel technique will be used as a pre-positioning tool prior to other optical identification methods, e.g. Raman spectroscopy.
Analysis of Effective Composition of Hippophae Rhamnoides L. (2002)

The vitamin E, proteins, amino-acids, sugar, trace elements and fatty acids in the oil of Hippophae Rhamnoides L. seeds were quantitatively analyzed. Several methods for analyzing vitamin E were compared with each other and the content of gossypol in the oil was first determined.
Effects of different antigenic microenvironments on the course of CD8+ T cell responses in vivo (1996)

The influence of microenvironment on the course of CD8 + T cell responses in vivo was investigated by injecting H-2Kb-specific T cells from donor TCR transgenic (TCR-Tg) mice into H-2kb-Tg mice. H-2Kb expression in recipients was either ubiquitous (CBK mice) or restricted to myeloid and erythroid cells (K beta mice). Donor T cells proliferated as extensively and acquired similar surface phenotypes in spleen of both recipient types. Thus, neither the restricted pattern of H-2Kb expression nor the significantly reduced level of H-2Kb expression by myeloid cells in Kbeta recipients affects the ability of the splenic microenvironment to prime T cell proliferation in vivo. However, an unsustained burst of cytolytic activity was generated rapidly in spleen of CBK recipients, whereas relatively little cytolytic activity was generated in K beta spleen. This indicates that effector T cells were not generated efficiently in spleen of Kbeta recipients even though extensive T cell proliferation was taking place in this microenvironment. Furthermore, activated donor T cells dispersed rapidly throughout primary and secondary lymphoid organs of Kbeta recipients, whereas few T cells migrated from spleen in CBK recipients. Consequently, the course of CD8+ T cell responses and the anatomical distribution of activated T cells are profoundly influenced by the nature of the antigenic microenvironment encountered in vivo. We conclude that T cells rapidly proliferate and acquire new tissue-homing characteristics but do not differentiate into cytolytic effector cells at the site of priming when they encounter myeloid cells expressing low levels of antigen in vivo.
Circulating human leucocyte elastase in patients with inflammatory bowel disease. (1985)

The plasma concentration of human leucocyte elastase (HLE), measured by enzyme immunoassay as the complex with alpha 1-proteinase inhibitor, was determined in 94 patients with active and inactive inflammatory bowel disease. In Crohn's disease and in ulcerative colitis human leucocyte elastase levels were raised significantly above normal when the disease was active, and fell on remission. The mean human leucocyte elastase level in 31 cases of active Crohn's disease was significantly greater than the mean human leucocyte elastase level in 23 patients with active ulcerative colitis (p = 0.013). The values of human leucocyte elastase correlated significantly with Crohn's disease activity index scores (p = 0.05) and with the circulating concentration of C-reactive protein (p less than 0.05 and p less than 0.01 for ulcerative colitis and Crohn's disease respectively), but not with the erythrocyte sedimentation rate. These results indicate that the concentration of human leucocyte elastase in the plasma of patients with inflammatory bowel disease reflects the activity of their intestinal disease and suggest that serial measurements of human leucocyte elastase may be useful in the assessment and clinical management of these conditions.
Natural Image Denoising with Convolutional Networks (2008)

We present an approach to low-level vision that combines two main ideas: the use of convolutional networks as an image processing architecture and an unsupervised learning procedure that synthesizes training samples from specific noise models. We demonstrate this approach on the challenging problem of natural image denoising. Using a test set with a hundred natural images, we find that convolutional networks provide comparable and in some cases superior performance to state of the art wavelet and Markov random field (MRF) methods. Moreover, we find that a convolutional network offers similar performance in the blind denoising setting as compared to other techniques in the non-blind setting. We also show how convolutional networks are mathematically related to MRF approaches by presenting a mean field theory for an MRF specially designed for image denoising. Although these approaches are related, convolutional networks avoid computational difficulties in MRF approaches that arise from probabilistic learning and inference. This makes it possible to learn image processing architectures that have a high degree of representational power (we train models with over 15,000 parameters), but whose computational expense is significantly less than that associated with inference in MRF approaches with even hundreds of parameters. 1