gebhart/patrepeval huggingface dataset:
The Hepatitis C Virus Non‐Structural Protein NS5A Alters the Trafficking Profile of the Epidermal Growth Factor Receptor (2008)

Hepatitis C virus (HCV) frequently establishes a persistent infection, leading to chronic liver disease. The NS5A protein has been implicated in this process as it modulates a variety of intracellular signalling pathways that control cell survival and proliferation. In particular, NS5A associates with several proteins involved in the endocytosis of the epidermal growth factor receptor (EGFR) and has been previously shown to inhibit epidermal growth factor (EGF)-stimulated activation of the Ras-Erk pathway by a mechanism that remains unclear. As EGFR signalling involves trafficking to late endosomes, we investigated whether NS5A perturbs EGFR signalling by altering receptor endocytosis. We demonstrate that NS5A partially localizes to early endosomes and, although it has no effect on EGF internalization, it colocalizes with the EGFR and alters its distribution. This redistribution correlates with a decrease in the amount of active EGF-EGFR ligand-receptor complexes present in the late endosomal signalling compartment and also results in a concomitant increase in the total levels of EGFR. These observations suggest that NS5A controls EGFR signalling by diverting the receptor away from late endosomes. This represents a novel mechanism by which a viral protein attenuates cell signalling and suggests that NS5A may perturb trafficking pathways to maintain an optimal environment for HCV persistence.
Comparison of the Nucleic Acid Sequence of Anglerfish and Mammalian Insulin mRNA's from Cloned cDNA's (1980)

Anglerfish (Lophius americanus) insulin complementary DNA was cloned in bacterial plasmids, and its sequence was determined. Fish insulin messenger RNA is larger (1.5 times) than the messenger RNA encoding mammalian (rat and human) insulin, in part because of a larger C peptide (an additional six amino acids or 18 nucleotides in length) but mainly because of increases in the 5' and 3' untranslated regions. Comparison of the fish, rat, and human insulin messenger RNA (from the complementary DNA) reveals that, in addition to the regions coding for the A and B peptides, sequence conservation is limited to a segment within the 5' untranslated region which may be involved in ribosomal binding, two small segments of the signal peptide, and two stretches of sequence in the 3' untranslated region.
Unsupervised strategies for information extraction by text segmentation (2010)

Information extraction by text segmentation (IETS) applies to cases in which data values of interest are organized in implicit semi-structured records available in textual sources (e.g. postal addresses, bibliographic information, ads). It is an important practical problem that has been frequently addressed in the recent literature. We report here partial results from a PhD thesis work in which we introduce ONDUX (On Demand Unsupervised Information Extraction), a new unsupervised probabilistic approach for IETS. As other unsupervised IETS approaches, ONDUX relies on information available on pre-existing data to associate segments in the input string with attributes of a given domain. Unlike other approaches, we rely on very effective matching strategies instead of explicit learning strategies. The effectiveness of this matching strategy is also exploited to disambiguate the extraction of certain attributes through a reinforcement step that explores sequencing and positioning of attribute values directly learned on-demand from test data, with no previous human-driven training, a feature unique to ONDUX. This assigns to ONDUX a high degree of flexibility and results in superior effectiveness, as demonstrated by experimental evaluation we have carried out with textual sources from different domains, in which ONDUX is compared with a state-of-art IETS approach.
The Physiology of Leukocyte Recruitment: An In Vivo Perspective (2008)

The mechanisms of leukocyte recruitment have been studied extensively in vitro and have shed light on the basic molecular structure-function relationship of adhesion and signaling molecules involved in this essential immune response. This review will summarize how these in vitro observations extend to leukocyte behavior in inflamed blood vessels in the microcirculation. We highlight physiological results that might not have been predicted from in vitro systems. Special attention is placed on the physiology of rolling, adhesion, and intralumenal crawling in blood vessels. The importance of the glycocalyx, secondary tethers, shear, and the microenvironment are discussed. Docking structures forming rings of adhesion molecules together with a novel endothelial dome-like structure in vivo during transmigration are highlighted. Transcellular and paracellular emigration out of inflamed blood vessels is also discussed. The last section highlights leukocyte recruitment in some organs that do not always follow the accepted paradigm of leukocyte recruitment.
Camera handoff: tracking in multiple uncalibrated stationary cameras (2002)

Multiple cameras are needed to completely cover an environment for monitoring activity. To track people successfully in multiple perspective imagery, one needs to establish a correspondence between objects captured by multiple cameras. We present a system for tracking people using multiple uncalibrated cameras. The system is able to discover spatial relationships between the cameras' fields of view and to use this information to correspond between different perspective views of the same person. We employ the novel approach of finding the limits of the field of view of a camera that are visible by the other cameras. This helps us to disambiguate between possible candidates of correspondence. The proposed approach is very fast compared to camera calibration-based approaches.
Matched filters with interference suppression capabilities for DS-CDMA (1996)

This paper considers the design of near-far resistant matched filters (MFs) for direct-sequence code-division multiaccess (DS-CDMA) systems. We show how additional information on the individual powers and chip delays of locked users, that is available at the base station, can be exploited for the design of these MFs. The proposed receiver can specifically reduce the effects of the locked interferers at the expense of a partial increase in complexity over the conventional MF. Furthermore, this detection technique is a link between the linear minimum mean squared error (MMSE) centralized multiuser detector and the decentralized noise-whitening MF. Numerical results for the rectangular chip pulse illustrate the signal-to-noise ratio (SNR), near-far resistance, and bit-error rate (BER) improvement that the proposed MF yields over the conventional MF and noise-whitening MF.
Effect of time in lairage on caecal and carcass salmonella contamination of slaughter pigs (1987)

A longitudinal study of the effect of time spent in lairage on salmonellas in the caecum and on the skin surface of 450 slaughter pigs from a single producer was conducted. Pigs were tested in 6 groups at 2 abattoirs, with one-third of a group being slaughtered after 18 h, one-third after 42 h and one-third after 66 h spent in lairage. The salmonella isolation rate from caeca and carcass surfaces increased significantly with increasing time spent in lairage. Salmonellas were isolated from the caeca of 18.5% of pigs held less than 24 h in lairage, 24.1% of pigs held a further 24 h and 47.7% of pigs held for 66 h in lairage before slaughter. The salmonella isolation rates from carcasses were 9.3%, 12.8% and 27.3% for the same groups. Thirteen salmonella serotypes were isolated from the caecal contents and carcasses over the 6 weeks of the trial. One abattoir had a higher salmonella isolation rate from pigs than the other and this was probably related to lairage management. It appeared that lairage is an important factor in the manipulation of the salmonella contamination of pig carcasses.
An Engineering Interpretation of Seismic Data (1968)

ABSTRACT The reflection seismograph has long been the most important means for obtaining subsurface information prior to drilling. Interpretation of the seismic data is normally made by geophysicists to define subsurface structure. However, considerable information of great value to the drilling engineer is also contained in the seismic information. This paper discusses how the drilling engineer can use these data to estimate depth and magnitude of subsurface formation pressures, predict gross changes in lithology, and warn of possible drilling problems. Techniques are also presented for predicting relative drillability and fracture gradients in rank wildcat areas. The predictive techniques described have been used with good results over a wide area along the Texas Gulf Coast including Continental Shelf locations and might possibly be applicable to any sedimentary basin. INTRODUCTION The only means of obtaining subsurface information other than from drilling is by geophysical prospecting. Although the seismograph has been used by geophysicists and geologists for many years to help define subsurface structure, it is only recently that engineers have begun to discover useful applications. One of these applications is the use of routine seismic field data to predict both the depths to abnormal pressure formations and approximate pressure magnitudes.1 The predictive method results from the fact that velocities between subsurface reflecting layers can be obtained from seismic field data using well known geophysical techniques. Differences in interval velocities between these layers can be used to develop an average interval travel time (reciprocal of interval velocity) profile, which is in effect an acoustic log averaged over fairly long (500' - 1000') vertical intervals. Analysis of numerous well velocity surveys revealed a close correlation between interval velocity (interval travel time), and factors such as lithology and degree of rock compaction and that interval travel time varies exponentially and predictably with depth. Departure from this normal trend signifies abnormal pressure or gross lithologic changes.
In vitro and in vivo studies of ICE inhibitors (1997)

Interleukin-1 beta-converting enzyme (ICE) is a cysteine protease responsible for proteolytic activation of the biologically inactive interleukin-1 beta precursor to the proinflammatory cytokine. ICE and homologous proteases also appear to mediate intracellular protein degradation during programmed cell death. Inhibition of ICE is a new antiinflammatory strategy being explored by the design of both reversible inhibitors and irreversible inactivators of the enzyme. Such compounds are capable of blocking release of interleukin-1 beta from human monocytes. ICE inhibitors that cross react against multiple ICE homologs can also block apoptosis in diverse cell types. ICE inhibitors impart protection in vivo from endotoxin-induced sepsis and collagen-induced polyarthritis in rodent models. Further optimization of the current generation of peptidyl ICE inhibitors will be required to produce agents suitable for administration in chronic inflammatory and neurodegenerative diseases.
Repercusión psicológica de la comorbilidad médica en pacientes con trastornos temporomandibulares. (2010)

Introduccion: la comorbilidad medica es frecuente en pacientes con trastornos temporomandibulares (TTM). Los autores examinan la relacion entre la comorbilidad medica de pacientes con TTM y su estado psicologico. Metodos: la muestra de pacientes se compuso de 1.060 adultos con TTM, de los cuales el 85% (n = 901) eran mujeres. Los pacientes, atendidos en un centro universitario de tratamiento del dolor entre 1997 y 2007, cumplimentaron cuestionarios sobre antecedentes medicos y psicologicos. Basandose en revisiones retrospectivas de las historias medicas, los autores valoraron la relacion entre la comorbilidad medica y el estado psicologico, utilizando un analisis multivariante de la covarianza y tambien introduciendo factores de correccion segun la gravedad del dolor. Resultados: la media del numero total de trastornos comorbidos fue 3, 49 (desviacion estandar [DE] = 2, 87; rango, 0-16). Los autores encontraron una relacion lineal entre el numero de trastornos comorbidos y el grado de angustia psicologica general (t[1, 959] = 16, 79, P< 0, 001) y la discapacidad producida por el dolor (t[1, 1.028] = 18, 03, P< 0, 001). Conclusiones: la probabilidad de que el estado psicologico se encuentre afectado aumenta cuando los pacientes con TTM presentan trastornos medicos comorbidos. Es necesario realizar mas estudios para investigar si la relacion observada cambia a lo largo del tiempo. Implicaciones clinicas: la salud fisica y psicologica de los pacientes con TTM puede influir en la evolucion de su proceso doloroso. El dentista debe valorar sistematicamente no solo los sintomas propios del TTM sino tambien el estado de salud general del paciente. Palabras clave: dolor orofacial; trastornos temporomandibulares; antecedentes personales; estado de salud; trastornos medicos comorbidos; disfuncion psicologica.
Active Learning with Real Annotation Costs (2008)

The goal of active learning is to minimize the cost of training an accurate model by allowing the learner to choose which instances are labeled for training. However, most research in active learning to date has assumed that the cost of acquiring labels is the same for all instances. In domains where labeling costs may vary, a reduction in the number of labeled instances does not guarantee a reduction in cost. To better understand the nature of actual labeling costs in such domains, we present a detailed empirical study of active learning with annotation costs in four real-world domains involving human annotators. 1
Computational Topology in Reconstruction, Mesh Generation, and Data Analysis. (2014)

Many applications involving shapes and data not only require analyzing and processing their geometries, but also associated topologies. In the past two decades, computational topology, an area rekindled by computational geometry has emphasized processing and exploiting topological structures of shapes and data. The understanding of topological structures in the context of computations has resulted into theoretically sound practical algorithms and has also put a thrust in developing further synergy between mathematics and computations in general. This talk aims to delineate this perspective by considering three applications, namely, (i) surface/manifold reconstructions, (ii) mesh generation, and (iii) topological data analysis for which computational topology has played a crucial role. For each of the three topics, we will give the necessary backgrounds in topology, state some of the key results, and indicate open questions/problems. The hope is that the talk will further stimulate the interest in tying topology and computation together.
Functional renormalization-group theory of universal<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"><mml:mfrac><mml:mrow><mml:mn>1</mml:mn></mml:mrow><mml:mrow><mml:mi>f</mml:mi></mml:mrow></mml:mfrac></mml:math>noise in dynamical systems (1983)

The functional renormalization group is used to show that a wide class of dynamical systems displays spectra with a $\frac{1}{{f}^{\ensuremath{\delta}}}$ divergence. Cutoffs introduced by stochastic or deterministic perturbations have universal features as well. Numerical support is presented.
PINHOLE CONTACT LENSES (1952)

Chicago College of Optometry Chicago, Illinois *Read before the annual meeting of the American Academy of Optometry, New York, New York, December 9, 1951. For publication in the July, 1952, issue of the American Journal of Optometry and Archives of American Academy of Optometry. †Optometrist. Ph.D. Dean of College. Fellow, American Academy of Optometry.
A nanomaterial-based breath test for distinguishing gastric cancer from benign gastric conditions (2013)

The preliminary results of this pilot study could open a new and promising avenue to diagnose GC and distinguish it from other gastric diseases. It should be noted that the applied methods are complementary and the potential marker compounds identified by gas-chromatography/mass spectrometry are not necessarily responsible for the differences in the sensor responses. Although this pilot study does not allow drawing far-reaching conclusions, the encouraging preliminary results presented here have initiated a large multicentre clinical trial to confirm the observed patterns for GC and benign gastric conditions.
Theta‐type DNA replication stimulates homologous recombination in the <i>Bacillus subtilis</i> chromosome (1996)

To test the effects of theta-type replication on homologous DNA recombination, we integrated in the chromosome of Bacillus subtilis a structure comprising a conditional replication region and direct repeats of approximately 4 kb. The replicon was derived from a broad-host-range plasmid, pAM beta 1, which replicates by a unidirectional theta mechanism and its thermosensitive. The direct repeats were derived from plasmid pBR322 and flanked the chloramphenicol-resistance gene of plasmid pC194. Recombination between the repeats could therefore lead to a loss of the resistance gene or the appearance of additional repeats. The integrated replicon was active at the permissive temperature, and approximately 25% of the integrated plasmids could be isolated as Y-shaped molecules after restriction, having a branch at the replication origin. Replicon activity stimulated recombination four- to fivefold, as estimated from the proportion of chloramphenicol-sensitive cells at the restrictive and permissive temperature, and also led to the appearance of additional direct repeats. We conclude that theta-type replication stimulates homologous recombination and suggest that many or even most recombination events between long homologous sequences present in a bacterial genome may be the consequence of DNA replication.
MHC imbalance and metastatic spread in Lewis lung carcinoma clones (1983)

Imbalance in the Kb and Db region encoded molecules is observed in Lewis lung carcinoma clones. The uncloned metastatic population and the D122 high-metastatic clone show no expression of H-2Kb products, while the nonmetastatic A9 clone expresses Kb products. Twenty-nine new subclones of 3LL and A9 were analyzed for D-end and K-end membrane expression, primary growth rate and metastatic spread. We show that the imbalance in H-2Kb to H-2Db is correlated with metastatic properties of a given clone, but local tumor growth is not. A "low Kb/low Db" phenotype is nonmetastatic as is a "high Kb/high Db" phenotype; a "low Kb/high Db" is highly metastatic and a "medium Kb/high Db" is moderately metastatic. We find support for this notion of imbalance in experiments on MHC modulation by interferon and retinoic acid. Interferon increases both Kb and Db expression of A9 and D122 clones yet the net increase of Db was greater than Kb. This was associated with an increase in metastasis formation. Retinoic acid increases the expression of the Db gene product on the nonmetastatic A9, clone, without apparent changes in Kb expression. This treatment shifts the A9 to a high-metastatic phenotype. The significance of this imbalance to the tumor--host relationship is discussed.
Pathological Basis of Retrolental Fibroplasia (1954)

SINCE the pathological picture of the final stage of retrolental fibroplasia is not of a specific character, no important advance in our understanding of the disease was to be expected until the distinctive histological features of its earliest phases became known. Following a report on the clinical appear- ances of the developing disease (Owens and Owens, 1949), there soon appeared a number of careful microscopical studies which provided a clear concept of its pathogenesis; from the histological evidence accumulated in the works of Heath (1950a, b; 1951), Tyner and Frayer (1951), Reese and Blodi (1951), and Reese and others (1952), it became abundantly clear that the primary pathological change is angioblastic in nature and presents as an overgrowth of the developing retinal vessels. Some of the conclusions reached in these studies, however, differ in detail from our own and, while it is no longer necessary to present a detailed study of the histology of this condition, it would appear desirable to report upon the pathology of a few representative cases from our own material and to discuss it in relation to the observations already in the literature.
A novel design concept for small-skew clock LSIs with the self-delay-adjustment (2002)

A novel concept for +or-50-ps-skew clock distribution LSIs for use in large computers is presented. The keys for obtaining this are the separated distribution of the frequency and phase of the master clock, and the detailed design of self-phase-adjustment circuits. The basic idea of the method is described, with emphasis on design formulae for clock signal delay times. Bipolar clock LSIs have been designed and tested. A clock skew time of +or-50 ps has been obtained with an adjustable phase range of 3.7 ns.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
The RESID Database of Protein Modifications as a resource and annotation tool (2004)

The RESID Database of Protein Modifications is a comprehensive collection of annotations and structures for protein modifications and cross-links including pre-, co-, and post-translational modifications. The database provides: systematic and alternate names, atomic formulas and masses, enzymatic activities that generate the modifications, keywords, literature citations, Gene Ontology (GO) cross-references, protein sequence database feature table annotations, structure diagrams, and molecular models. This database is freely accessible on the Internet through resources provided by the European Bioinformatics Institute (http://www.ebi.ac.uk/RESID), and by the National Cancer Institute--Frederick Advanced Biomedical Computing Center (http://www.ncifcrf.gov/RESID). Each RESID Database entry presents a chemically unique modification and shows how that modification is currently annotated in the protein sequence databases, Swiss-Prot and the Protein Information Resource (PIR). The RESID Database provides a table of corresponding equivalent feature annotations that is used in the UniProt project, an international effort to combine the resources of the Swiss-Prot, TrEMBL and PIR. As an annotation tool, the RESID Database is used in standardizing and enhancing modification descriptions in the feature tables of Swiss-Prot entries. As an Internet resource, the RESID Database assists researchers in high-throughput proteomics to search monoisotopic masses and mass differences and identify known and predicted protein modifications.
Limbus Damage in Ocular Graft-versus-Host Disease (2010)

Graft-versus-host disease (GVHD) is the major cause of morbidity and mortality among patients undergoing allogeneic hematopoietic stem cell transplantation. Although animal models have been clearly established for the study of skin, liver, and gut, currently there is no equivalent experiemental model for analyzing ocular involvement, which is rather common, especially among patients diagnosed with chronic GVHD. In the current study we have developed a murine model of ocular GVHD and, for the first time, we describe the histopathologic features involving cornea and limbus, which could play a role in the physiopathology of the disease at the ocular level. Our results represent a major finding that allows us to define a model for evaluating new therapeutic strategies for treating ocular GVHD prior to their use in clinical setting.