gebhart/patrepeval huggingface dataset:
Inhibition of Adhesion, Invasion, and Metastasis by Antibodies Targeting CEACAM6 (NCA-90) and CEACAM5 (Carcinoembryonic Antigen) (2005)

CEACAM5 and CEACAM6 are overexpressed in many cancers and are associated with adhesion and invasion. The effects of three monoclonal antibodies targeting different epitopes on these antigens (NH2-terminal [MN-3] and A1B1 domains [MN-15] shared by CEACAM5 and CEACAM6 and the A3B3 domain [MN-14] restricted to CEACAM5) were evaluated in migration, invasion, and adhesion assays in vitro using a panel of human pancreatic, breast, and colonic cancer cell lines, and in the GW-39 human colonic micrometastasis model in vivo. MN-3 Fab' and MN-15 Fab' were both effective at inhibiting cell migration. MN-15 Fab' treatment inhibited invasion, reducing cell penetration through an extracellular matrix (ECM). MN-3 Fab' also decreased invasion but was less effective than MN-15 Fab' in four of five cell lines. All three monoclonal antibody (mAb) Fabs decreased adhesion of tumor cells to endothelial cells by 49% to 58%. MN-15 Fab' but not MN-3 or MN-14 Fabs induced a decrease in adhesion of three of six cell lines to the ECM protein, fibronectin, but adhesion to vitronectin, laminin, collagen-I, and collagen-IV was not affected. In vivo studies showed that treatment with MN-3 Fab' or MN-15 Fab' of mice implanted with GW-39 human colonic cancer cells increased their survival (P < 0.025 and P < 0.01, respectively). These studies show that antibody Fabs that target either CEACAM5 or CEACAM6 affect cell migration, cell invasion, and cell adhesion in vitro, and that MN-15 and MN-3 Fabs have antimetastatic effects in vivo, resulting in improved survival of mice with metastases. Thus, blocking the N and A1B1 domains of CEACAM5/CEACAM6 can impede the metastatic process.
Extracellular matrix and integrin signalling: the shape of things to come (1999)

The extracellular matrix (ECM) and integrins collaborate to regulate gene expression associated with cell growth, differentiation and survival. Biochemical and molecular analyses of integrin signalling pathways have uncovered several critical cytoplasmic proteins that link the ECM and integrins to intracellular pathways that may contribute to anchorage-dependent growth. A large body of evidence now indicates that the non-receptor protein kinases focal adhesion kinase (FAK) and specific members of the mitogen-activated protein kinases (MAPKs), including the extracellular-signal-regulated kinases (ERKs), mediate these ECM- and integrin-derived signalling events. However, little is known about how FAK and MAPKs contribute to biological processes other than cell proliferation or migration. In addition, remarkably little is known concerning the signalling events that occur in cells that adhere to complex multivalent extracellular matrices via multiple integrin receptors. Given the stringent requirement for attaining a proper morphology in ECM/integrin-directed cell behaviour, it is still not clear how cell shape and tissue architecture impact upon intracellular signalling programmes involving FAK and MAPKs. However, the recent discovery that members of the Rho family of small GTPases are able to regulate ECM/integrin pathways that modulate both cell shape and intracellular signalling provides new insights into how cell morphology and signal transduction become integrated, especially within three-dimensional differentiated tissues.
Proliferation-dependent cytotoxicity of anticancer agents: a review. (1975)

One of the factors of importance in determining the killing of mammalian cells following exposure to a variety of anticancer agents is the proliferative state of the cell population. Generally, proliferating cells are much more sensitive to anticancer agents than are nonproliferating cells. In this review, the cellular aspects of this differential sensitivity are discussed with the hemopoietic stem cell population and tissue culture cells as the focus for the analysis. This phenomenon is not only of concern to the cell biologist but also has implications with regard to scheduling of anticancer agents against human tumors.
Cyclic Variation of DNA Synthesis in Human Breast Epithelium (1977)

DNA synthesis in normal breast epithelium from premenopausal women was assessed by use of autoradiography. In parous women the labeling indexes decreased during the follicular phase of the menstrual cycle and increased to a significantly higher level during the luteal phase.
<title>Three-dimensional approach to lung nodule detection in helical CT</title> (1999)

We are developing an automated method for the detection of lung nodules in helical computed tomography (CT) images. This technique incorporates 2D and 3D analyses to exploit the volumetric image data acquired during a CT examination. Gray-level thresholding is used to segment the lungs within the thorax. A rolling ball algorithm is applied to more accurately define the segmented lung regions. The set of segmented CT sections, which represents the complete lung volume, is iteratively thresholded, and a 10-point connectivity scheme is used to identify contiguous 3D structures. Structures with volumes less than a predefined maximum value comprise the set of nodule candidates, which is then subjected to 2- and 3-D feature analysis. To distinguish between candidates representing nodule and non- nodule structures, the values of the features are merged through linear discriminant analysis. When applied to a database of 17 helical thoracic CT cases, gray-level thresholding combined with the volume criterion detected 82% of the lung nodules. Linear discriminant analysis yielded an area under the receiver operating characteristic curve of 0.93 in the task of distinguishing between nodule and non- nodule structures within this set of nodule candidates.
Identification of a carbonic anhydrase-like domain in the extracellular region of RPTP gamma defines a new subfamily of receptor tyrosine phosphatases. (1993)

The tyrosine phosphatase RPTP gamma is a candidate tumor suppressor gene since it is located on human chromosome 3p14.2-p21 in a region frequently deleted in certain types of renal and lung carcinomas. In order to evaluate its oncogenic potential and to explore its normal in vivo functions, we have isolated cDNAs and deduced the complete sequences of both human and murine RPTP gamma. The murine RPTP gamma gene has been localized to chromosome 14 to a region syntenic to the location of the human gene. Northern (RNA) blot analysis reveals the presence of two major transcripts of 5.5 and 8.5 kb in a variety of murine tissues. In situ hybridization analysis reveals that RPTP gamma mRNA is expressed in specific regions of the brain and that the localization of RPTP gamma changes during brain development. RPTP gamma is composed of a putative extracellular domain, a single transmembrane domain, and a cytoplasmic portion with two tandem catalytic tyrosine phosphatase domains. The extracellular domain contains a stretch of 266 amino acids with striking homology to the zinc-containing enzyme carbonic anhydrase (CAH), indicating that RPTP gamma and RPTP beta (HPTP zeta) represent a subfamily of receptor tyrosine phosphatases. We have constructed a model for the CAH-like domain of RPTP gamma based upon the crystal structure of CAH. It appears that 11 of the 19 residues that form the active site of CAH are conserved in RPTP gamma. Yet only one of the three His residues that ligate the zinc atom and are required for catalytic activity is conserved. On the basis of this model we propose that the CAH-like domain of RPTP gamma may have a function other than catalysis of hydration of metabolic CO2.
Data weighted vs. non-data weighted dual energy reconstructions for X-ray tomography (2002)

X-ray transmission tomography is useful for estimation of attenuation correction for simultaneously obtained emission tomography images. Moreover, X-ray attenuation coefficients can be combined with emission measurements in order to create combined anatomical-functional images. It is imperative, then, that as low X-ray dosage as possible be used. At those fluxes implementation of iterative algorithms becomes desirable. However, that was not the case in clinical practice where X-ray fluxes used are high enough and noniterative algorithms give good results. In order to use the acquired data in a statistically efficient manner an appropriate model has to be employed. Also an efficient algorithm has to be used to solve the objective function. In this paper it is shown that at low fluxes an appropriate weighting becomes a crucial part of the model. Results are presented first for the single energy case and then for the dual energy case.
The ubiquitin system, disease, and drug discovery (2008)

The ubiquitin system of protein modification has emerged as a crucial mechanism involved in the regulation of a wide array of cellular processes. As our knowledge of the pathways in this system has grown, so have the ties between the protein ubiquitin and human disease. The power of the ubiquitin system for therapeutic benefit blossomed with the approval of the proteasome inhibitor Velcade in 2003 by the FDA. Current drug discovery activities in the ubiquitin system seek to (i) expand the development of new proteasome inhibitors with distinct mechanisms of action and improved bioavailability, and (ii) validate new targets. This review summarizes our current understanding of the role of the ubiquitin system in various human diseases ranging from cancer, viral infection and neurodegenerative disorders to muscle wasting, diabetes and inflammation. I provide an introduction to the ubiquitin system, highlight some emerging relationships between the ubiquitin system and disease, and discuss current and future efforts to harness aspects of this potentially powerful system for improving human health. PUBLICATION HISTORY : Republished from Current BioData's Targeted Proteins database (TPdb; http://www.targetedproteinsdb.com).
Restriction analysis and homology studies of the bovine adenovirus 7 genome (1984)

We located the cleavage sites for restriction endonucleases EcoRI, HindIII, and BamHI on the genome of bovine adenovirus 7. Cross-hybridization at reduced stringency revealed two regions of homology shared by the DNA of human adenovirus 2 and bovine adenoviruses 7 and 3. These regions correspond to the hexon and the IVa2 protein genes of the human adenovirus. Another region of homology shared only by the human adenovirus and bovine adenovirus 7 corresponded to the penton or the polypeptide IIIa genes. These results allowed us to align the restriction map of bovine adenovirus 7 with respect to the other adenoviruses.
Electrical characteristics dependence on the channel fin aspect ratio of multi-fin field effect transistors (2009)

In this work we investigate the impact of the fin number and structure on device dc and dynamic behaviors of multi-fin field effect transistor (FET) circuits. Based on the same channel volume, multi-fin FETs with different fin aspect ratio (AR ≡ fin height/fin width) are explored using an experimentally validated three-dimensional device simulation. The multi-fin FinFET (AR = 2) has a better channel controllability than the tri-gate (AR = 1) and the quasi-planar (AR = 0.5) FETs. Besides, the 6T SRAM with triple-fin FinFETs provides the largest static noise margin because of the largest transconductance. Notably, though the FinFETs are with a large effective fin width and driving current, the larger gate capacitance may limit the intrinsic device gate delay. The transient characteristics of multi-fin inverters are further examined with different load capacitance (Cload). As Cload is increased, the impact of the device intrinsic gate capacitance on transient characteristcs is decreased and the delay time compared with that of single-fin inverters is smaller due to being dominated by the driving current of the transistor. Consequently, the multi-fin FinFET circuits exhibit a smallest delay time. The results of the study provide an insight into the dc and transient characteristics of multi-fin transistors and associated digital circuits.
Zebrafish primary neurons initiate expression of the LIM homeodomain protein Isl-1 at the end of gastrulation (1993)

ABSTRACT Isl-1 has previously been established as the earliest marker of developing chicken spinal motor neurons where it is regulated by inductive signals from the floorplate and notochord. We now report that, in zebrafish, the expression of Isl-1 is initiated in Rohon-Beard cells, primary motor neurons, interneurons and cranial ganglia, hours before the neural tube itself is formed. The expression is initiated simultaneously in the RohonBeard cells and the primary motor neurons, at the axial level of the presumptive first somite. The Isl-1-expressing motor neurons appear on either side of the ventral midline whereas the interneurons and Rohon-Beard cells initiate expression while located at the edge of the germinal shield. Isl-1 expression is initiated in these cells before the formation of a differentiated notochord. Isl-1 is expressed in the various functional classes of primary neurons at 24 hours postfertilization. This selective expression of a homeodomain protein in the primary neurons implies that these neurons share a common program of early development and that they have evolved and been selected for as a coordinated system. One of the functions of the primary neurons is to send long axons which pioneer the major axon tracts in the zebrafish embryo. An evolutionary conserved functional role for Isl-1 in the expression of the pioneering phenotype of the primary neurons is suggested.
DIMENSION REDUCTION, FEATURE EXTRACTION AND INTERPRETATION OF DATA WITH NETWORK COMPUTING (1996)

The subject matter of this paper is one of long-standing interest to the Pattern Recognition and Artificial Intelligence research communities, namely that of "feature extraction" for facilitating the task of classification or various other tasks. We show that internal representations of neural networks do not yield unique feature values but can provide the basis for facilitating a number of useful information management tasks, such as memorization, categorization, discovery, associative recall and others. These matters are illustrated with three sets of data, one of a benchmark nature, another of the nature of real-world sensor data, and a third set consisting of semiconductor crystal structure parameters.
Quantification of Polymer Interactions in Bacterial Adhesion (1998)

Adhesion of bacteria to solids is governed by van der Waals, electrostatic, and acid-base (hydrophobic) interactions, which are combined in an extended DLVO model (DLVO-AB) and by interactions of bacterial surface polymers with the solid surfaces. A method to calculate polymer interactions was not available yet, and their existence had been inferred only qualitatively from the deviation of the actual adhesion from DLVO-AB-based expectations. Here, we present attempts (i) to quantify polymer interactions from this deviation and (ii) to calculate them independently as the sum of repulsive and attractive contributions. Repulsion was assumed to result from the resistance of the polymer layer against compression. Its calculation was most sensitive to the packing density of the polymers in the cell envelope. Attraction was assumed to origin from polymer adsorption to the surface and was calculated on the basis of adsorption data of isolated surface polymers. Comparison of total interaction energy curves with adhesion of six Gram-negative bacteria to glass showed that the low adherence of five strains may have resulted from dominant polymer repulsion, i.e., hardly compressible cell envelopes hindered the bacteria to approach the energy minima resulting from DLVO-AB interactions. One strain adhered readily, possibly because polymer repulsion was low and polymer attraction and DLVO-AB forces dominated the overall interaction.
In-Depth. Agustin Huneeus og Quintessa (2003)

Wilson's disease (WD) is a relatively rare autosomal recessive inherited disorder causing copper accumulation in different organs, mainly the liver and brain. Psychiatric disturbances represent a diagnostic and therapeutic issue in WD. A search for relevant articles was carried out on PubMed/Medline, Scopus, and Google Scholar, for papers focused on psychiatric disorders in WD published between 1985-2016. Ninety-two articles were included in this review, showing the findings from 35 observational and case-control studies and 57 case reports. This study discussed the findings on the prevalence of psychiatric symptoms in WD, their impact on the life of those diagnosed, and the efficacy of available treatments on the psychiatric outcomes of WD. Psychiatric disorders are confirmed frequent in WD, with a high prevalence of mood disorders, and contribute to worse Quality-of-Life and psychosocial outcomes. Because specific therapies for WD lead to a good life expectancy, adherence to medicaments and clinical monitoring should be warranted by a multidisciplinary approach, including a hepathologic, neurologic, and psychiatric careful evaluation and education of those affected and their relatives.
The effects of wide-area conditions on WWW server performance (2001)

WWW workload generators are used to evaluate web server performance, and thus have a large impact on what performance optimizations are applied to servers. However, current benchmarks ignore a crucial component: how these servers perform in the environment in which they are intended to be used, namely the wide-area Internet.This paper shows how WAN conditions can affect WWW server performance. We examine these effects using an experimental test-bed which emulates WAN characteristics in a live setting, by introducing factors such as delay and packet loss in a controlled and reproducible fashion. We study how these factors interact with the host TCP implementation and what influence they have on web server performance. We demonstrate that when more realistic wide-area conditions are introduced, servers exhibit very different performance properties and scaling behaviors, which are not exposed by existing benchmarks running on LANs. We show that observed throughputs can give misleading information about server performance, and thus find that maximum throughput, or capacity, is a more useful metric. We find that packet losses can reduce server capacity by as much as 50 percent and increase response time as seen by the client. We show that using TCP SACK can reduce client response time, without reducing server capacity.
Noninvasive imaging of hemoglobin concentration and oxygenation in the rat brain using high-resolution photoacoustic tomography (2006)

Simultaneous transcranial imaging of two functional parameters, the total concentration of hemoglobin and the hemoglobin oxygen saturation, in the rat brain in vivo is realized noninvasively using laser-based photoacoustic tomography (PAT). As in optical diffusion spectroscopy, PAT can assess the optical absorption of endogenous chromophores, e.g., oxygenated and deoxygenated hemoglobins, at multiple optical wavelengths. However, PAT can provide high spatial resolution because its resolution is diffraction-limited by photoacoustic signals rather than by optical diffusion. Laser pulses at two wavelengths are used sequentially to acquire photoacoustic images of the vasculature in the cerebral cortex of a rat brain through the intact skin and skull. The distributions of blood volume and blood oxygenation in the cerebral cortical venous vessels, altered by systemic physiological modulations including hyperoxia, normoxia, and hypoxia, are visualized successfully with satisfactory spatial resolution. This technique, with its prominent sensitivity to endogenous contrast, can potentially contribute to the understanding of the interrelationship between neural, hemodynamic, and metabolic activities in the brain.
Relationship of Cell-Cycle Expression of Ia-like Antigenic Determinants on Normal and Leukemia Human Granulocyte-Macrophage Progenitor Cells to Regulation In Vitro by Acidic Isoferritins (1982)

An association has been established between human Ia-like (Ia) antigenic determinants, expression during DNA synthesis on granulocyte-macrophage colony forming cells (CFU-GM) and the regulatory action of acidic isoferritins in vitro. Treatment of human bone marrow cells with monoclonal-anti-Ia-like (Ia) plus complement inhibited colony and cluster formation by approximately 50% but did not affect pre-CFU-GM. Reduction of colonies and clusters was similar whether bone marrow cells were exposed to anti-Ia plus complement, high specific activity tritiated thymidine ((3)HTdr) or acidic isoferritins. No further decrease was apparent with (3)HTdr or acidic isoferritins after Ia-antigen(+) CFU-GM were removed, or with anti-Ia plus complement or acidic isoferritins after DNA synthetic phase (S-phase) CFU-GM were removed. Anti-Ia, without complement, did not reduce colony or cluster formation but did block the inhibitory action of acidic isoferritins. A relationship existed between Ia antigens and the activity of acidic isoferritins in the following ways: (a) The apparent loss of Ia-antigens from CFU-GM by 5 h in culture at 37 degrees C, but not at 27 degrees or 4 degrees C, was associated with nonresponsiveness to inhibition with acidic isoferritins, (b) Ia-antigen(-), noncycling pre-CFU-GM that were insensitive to acidic isoferritins could generate a population of Ia-antigen(+) cycling CFU-GM in vitro that were responsive to inhibition by acidic isoferritins, and (c) nondetectability of Ia-antigens on CFU-GM from patients with leukemia was associated with nonresponsiveness to inhibition by acidic isoferritins. These results implicate Ia-antigen(+) progenitor cells in the regulation of myelopoiesis in vitro and demonstrate that absence of Ia-antigens on patient CFU-GM is associated with imbalances in normal regulatory interactions in vitro. These findings may be of relevance to normal regulation and to the progression of leukemia.
DNA Vaccines: Immunology, Application, and Optimization (2000)

The development and widespread use of vaccines against infectious agents have been a great triumph of medical science. One reason for the success of currently available vaccines is that they are capable of inducing long-lived antibody responses, which are the principal agents of immune protection against most viruses and bacteria. Despite these successes, vaccination against intracellular organisms that require cell-mediated immunity, such as the agents of tuberculosis, malaria, leishmaniasis, and human immunodeficiency virus infection, are either not available or not uniformly effective. Owing to the substantial morbidity and mortality associated with these diseases worldwide, an understanding of the mechanisms involved in generating long-lived cellular immune responses has tremendous practical importance. For these reasons, a new form of vaccination, using DNA that contains the gene for the antigen of interest, is under intensive investigation, because it can engender both humoral and cellular immune responses. This review focuses on the mechanisms by which DNA vaccines elicit immune responses. In addition, a list of potential applications in a variety of preclinical models is provided.
Strategic bidding in competitive electricity markets: a literature survey (2002)

Participants in a competitive electricity market develop bidding strategies in order to maximize their own profits. On the other hand, it is necessary for regulators to investigate strategic bidding behavior in order to identify possible market power abuse and to limit such abuse by introducing appropriate market management rules. An interesting body of work has been done on this subject, and this paper presents a literature survey based on more than 30 research publications.