gebhart/patrepeval huggingface dataset:
Biochemical Modulation of Radiation-Induced Apoptosis in Murine Lymphoma Cells (1993)

Considerable effort in our laboratory has been directed toward characterizing the role of apoptosis as a mode of cell death in model tumors irradiated in vivo. These studies have shown that apoptosis is an important response in some tumors, correlating with tumor growth delay and tumor cure. However, the response is heterogeneous among both the various tumors examined and the cells in a given tumor, suggesting that the propensity for cells to undergo apoptosis upon irradiation is regulated by unknown factors in tumors. To develop a model system for investigating these regulatory pathways in vitro at the molecular and biochemical levels, we have established cells from a tumor that displays a dramatic apoptotic response in vivo, the TH lymphoma, in cell culture. In this article, we review some of the results of our studies using this model system. To date, we have shown that the dose-response relationship and kinetics of the development of apoptosis for these cells in culture are similar to what we observed for the tumor response in vivo. Moreover, the roles of calcium and signal transduction pathways as important regulatory factors in radiation-induced apoptosis have been defined in this system. Ultimately such investigations may yield the insight necessary for designing protocols to modulate apoptosis biochemically in irradiated normal and tumor tissues to therapeutic advantage.
Persistent homology of directed networks (2016)

While persistent homology has been successfully used to provide topological summaries of point cloud data, the question of computing persistent homology of graphs or networks remains unclear. In particular, the existing literature does not provide a treatment of persistent homology for directed networks that is sensitive to asymmetry. We study a method for constructing simplicial complexes from weighted, directed networks that captures directionality information, and we are able to prove that the persistent homology of such complexes is stable with respect to a certain notion of network distance. We illustrate our construction on a database of simulated hippocampal networks.
Impact of <i>FLT3</i> mutations and promyelocytic leukaemia‐breakpoint on clinical characteristics and prognosis in acute promyelocytic leukaemia (2005)

In the present study 170 newly diagnosed acute promyelocytic leukaemia patients (M3: n = 121; M3v: n = 49) were molecularly characterised with respect to PML breakpoint and additional molecular mutations. In total, 83 patients were positive for bcr1 (49%), five for bcr2 (3%) and 82 for bcr3 (48%). Bcr3 was more frequent in M3v (65.3%) compared with M3 (41.3%) (P = 0.005). Cases with bcr3 showed a significantly higher white blood cell count (median: 3.65 x 10(9)/l vs. 1.59 x 10(9)/l, P = 0.003), as well as a higher PML-RARAABL expression ratio (14.8% vs. 72.7%, P < 0.005) compared with bcr1. FLT3-length-mutations were detected more frequently together with bcr3 compared with bcr1 (56.5% vs. 19.4%, P < 0.001) and in M3v compared with M3 (64.5% vs. 24.1%, P < 0.005). FLT3 tyrosine kinase mutations were found in eight cases (6.4%) and were distributed equally within the total group. Analysis for further mutations revealed no MLL-PTD and KIT mutations and only two cases of 99 analysed (2%) with NRAS mutations. FLT3-mutations were detected in 62 of 139 cases (44.6%) and associated with a significant lower overall survival (P = 0.0339). In addition, cases with bcr3 showed a tendency for a worse event-free survival (P = 0.0795) compared with the bcr1 group.
Spam Detection Using Feature Selection and Parameters Optimization (2010)

Spam is no more garbage but risk since it recently includes virus attachments and spyware agents which make the recipients’ system ruined, therefore, there is an emerging need for spam detection. Many spam detection techniques based on machine learning algorithms have been proposed. As the amount of spam has been increased tremendously using bulk mailing tools, spam detection techniques should deal with it. For spam detection, parameters optimization and feature selection have been proposed to reduce processing overheads with guaranteeing high detection rates. However, the previous approaches have not taken into account variable importance and optimal number of features and there are no approaches using both of them together so far. In this paper, we propose an optimal spam detection model based on Random Forests (RF) which enables parameters optimization and feature selection. We optimize two parameters of RF to maximize the detection rates. We provide the variable importance of each feature so that it is easy to eliminate the irrelevant features. Furthermore, we decide an optimal number of selected features using two methods; (i) only one parameters optimization during overall feature selection, (ii) parameters optimization in every feature elimination phase. We carry out experiments on the Spambase dataset and show the feasibility of our approach.
ADVANCED IMAGE ANALYSIS BASED SYSTEM FOR AUTOMATIC DETECTION AND CLASSIFICATION OF MALARIAL PARASITE IN BLOOD IMAGES (2014)

ABSTRACT: This paper investigates the possibility of rapid and accurate automated diagnosis of red blood cell disorders and describes a method to detect and classify malarial parasites in blood sample images acquired from light microscopes. As malaria is an infectious disease which is mainly diagnosed by visual microscopical evaluation of Giemsa stained blood smears. As it poses a serious global health problem, automation of the evaluation process is of high importance. The image classification system is designed to positively identify malaria parasite in thin blood smears. Morphological and novel threshold selection techniques are used to identify erythrocytes (red blood cell) and possible parasites present on microscopic slides. Image features based on colour, texture and the geometry of the cells and parasites are generated, as well as features that make use of a priori knowledge of the classification problem and mimic features used by human technicians. Classifier using back propagation feed forward neural network distinguishes between parasite infected and non-infected blood images.
Microlens array for stacked laser diode beam collimation (2005)

To collimate effectively the beam emitted from the stacked laser diode in which the lasing surfaces of the diode bars are not located in a plane, a new type of fast-axis collimator, refractive cylindrical microlens array with tunable focal lengths, is presented in this paper. Each lens of the array has the same diameter of 300μm but different focal lengths, ranged from 430μm to 540μm. By means of the mask moving lithography and replication technology, the microlens array was successfully fabricated. The measured fast-axis divergence of the stacked laser diode beam after the collimator was 25mrad, about half of the one (40mrad) for the microlens array with common focal lengths of 400μm.
Evidence of IgG Autoantibodies Against Human Proinsulin in Patients With IDDM Before Insulin Treatment (1988)

IgG proinsulin autoantibodies (IgG-PAAs) have been found in a fraction of sera from patients with newly diagnosed insulin-dependent diabetes mellitus (IDDM) before onset of insulin treatment. Only sera lacking insulin antibodies have been analyzed, to avoid interference. Competitive inhibition studies provide specificity for human proinsulin but not for insulin. IgG-PAAs largely cross-react with human C-peptide. Precursors of insulin thus are involved in the immune process of IDDM.
Human Tremor: Origins, Detection and Quantification (2013)

The human tremor is one of the most common movement disorders, which is characterized by repetitive and stereotyped movements. The origins of tremor are still not clear, however tremor can be associated with physiological phenomena, such as ageing, and with neurological disorders, for instance, Parkinson’s disease. The first type of tremor is referred to as physiological tremor, whereas the latter as pathological tremor.
Subdivisions of <i>n</i>-dimensional spaces and <i>n</i>-dimensional generalized maps (1989)

This paper deals with the modeling of n-dimensional objects, more precisely with the modeling of subdivisions of n-dimensional topological spaces. We here study the notions of:
Optimizing anaerobic growth rate and fermentation kinetics in Saccharomyces cerevisiae strains expressing Calvin-cycle enzymes for improved ethanol yield (2018)

The metabolic engineering strategy presented here enables an almost complete elimination of glycerol production in anaerobic, glucose-grown batch cultures of <i>S. cerevisiae</i>, with an associated increase in ethanol yield, while retaining near wild-type growth rates and a capacity for glycerol formation under osmotic stress. Using current genome-editing techniques, the required genetic modifications can be introduced in one or a few transformations. Evaluation of this concept in industrial strains and conditions is therefore a realistic next step towards its implementation for improving the efficiency of first- and second-generation bioethanol production.
Separation of oxygen and nitrogen due to the controlled pore-opening size of chemically vapor deposited zeolite A (1991)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSeparation of oxygen and nitrogen due to the controlled pore-opening size of chemically vapor deposited zeolite AMiki Niwa, Kiyoshi Yamazaki, and Yuichi MurakamiCite this: Ind. Eng. Chem. Res. 1991, 30, 1, 38–42Publication Date (Print):January 1, 1991Publication History Published online1 May 2002Published inissue 1 January 1991https://pubs.acs.org/doi/10.1021/ie00049a006https://doi.org/10.1021/ie00049a006research-articleACS PublicationsRequest reuse permissionsArticle Views447Altmetric-Citations31LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
NMR studies of changes in subcellular water compartmentation in parenchyma apple tissue during drying and freezing (1997)

Abstract The potential of Nuclear Magnetic Resonance (NMR) and Magnetic Resonance Imaging (MRI) for non-invasively monitoring the subcellular and intercellular redistribution of water in cellular tissue during drying and freezing processes is assessed and it is concluded that despite exciting advances in NMR micro-imaging and NMR microscopy, nonspatially resolved NMR relaxation and diffusion techniques still provide the best probes of subcellular water compartmentation in tissue. The power of the NMR relaxation technique is illustrated by using the changes in the distribution of NMR water proton transverse relaxation times to monitor the subcellular compartmentation of water and ice during the drying and freezing of parenchyma apple tissue. The NMR drying data are analysed with a numerical model of the cell and show that mild air-drying in a fluidized bed results in loss of water from the vacuolar compartment, but not from the cytoplasm or cell wall regions. The loss of vacuolar water is associated with overall shrinkage of the cell and only a slight increase in air space. During freezing the vacuolar compartment is found to be the first to freeze, with the cytoplasmic and cell wall compartments only freezing at much lower temperatures. Freeze-drying apple tissue gives much lower water contents than fluidized bed drying, but the NMR data confirms that it destroys membrane integrity and causes cell wall collapse.
16S rRNA Gene Sequences from Bacteria Associated with Adult Anopheles darlingi (Diptera: Culicidae) Mosquitoes (2008)

The microbial flora associated with Anopheles darlingi Root (Diptera: Culicidae), a major Neotropical malaria vector, was investigated for the development of a paratransgenesis-based approach to control malaria transmission in Brazil. Female mosquitoes were collected using human land catches and captured insects provided a bloodmeal. The controlled blood feeding resulted in increased detection of mosquito bacterial population because it was possible to retrieve bacterial DNA from all blood-fed mosquitoes. The 16S sequences of bacteria recovered, include some closely related to those found in other vector mosquitoes, including Aeromonas, Pantoea and Pseudomonas species.
The synthesis and transition temperatures of some ferroelectric host materials based on 4- and 4′-( <i>trans</i> -4-alkylcyclohexylmethoxy)-2,3-difluorobiphenyls (1994)

Abstract A range of 2,3-difluoro-substituted biphenyls incorporating a cyclohexylmethoxy unit as one terminal chain has been prepared and these materials are compared to the analogous compounds already reported with a dimethylene linking group. Related, directly-linked cyclohexylbiphenyls and some open-chain analogues have also been prepared which add to the diversity of the compounds reported. These were prepared as host materials of low birefringence for ferroelectric (S∗c) mixtures and in general, the compounds have quite high Sc phase stability. Metallation procedures have been used to prepare arylboronic acids which were employed in palladium-catalysed cross-coupling reactions to provide good yields of liquid crystal materials. The synthesis and transition temperatures of these compounds are discussed and compared with each other and with other selected ortho-difluoro-substituted systems.
The quest for bacterial allergens (2018)

Allergies are complex diseases featuring local tissue inflammation, which is characterized by an exaggerated type 2 immune response to environmental compounds known as allergens. Pollens, environmental fungi, and house dust mites are examples of common allergens. Bacteria have a dual role in allergy. Usually, they are associated with protection, however, certain bacterial species promote the development and exacerbation of allergic inflammation. Notably, IgE antibodies specific for bacterial antigens are found in the sera of allergic individuals. This implies that some bacterial factors are allergens, eliciting a specific type 2 immune response. However, to date, only a few of these are molecularly defined. This review summarizes the current knowledge about known bacterial allergens, and it provides an overview of the available techniques for the discovery of new allergens as well as for measuring the immune responses directed against them.
A low cost tail-cuff method for the estimation of mean arterial pressure in conscious rats. (1990)

Methods utilized in the determination of systolic tail-cuff pressure (TCP) in awake rats are aimed at detecting the earliest possible tail pulsations as the cuff is deflated. In the method described in this study, a small, inexpensive electret microphone is used as a sensor, connected to the tail by a piece of rubber tubing. This design provides selective attenuation of tail pulsations appearing as the cuff is deflated between systolic and mean arterial pressures. In this manner, tail pulsations are detected only when the cuff pressure is lowered below the mean arterial pressure, thus providing an estimation of the latter. The method was validated in prewarmed awake normotensive and hypertensive rats by simultaneous comparison with directly measured systolic and mean pressures or with a conventional tail-cuff method. Validation studies were also carried out in anesthetized rats undergoing wide variations of arterial pressure by parenteral injections of norepinephrine or nitroprusside. Close agreement was observed between TCP determined with this method and directly obtained mean, but not systolic, pressure. Thus, the method described in this study constitutes an inexpensive alternative to conventional tail-cuff methods. Mean, rather than systolic pressure, appears to be evaluated in the conscious rat by employing this method.
Pulsed dosed delivery of oxygen in mechanically ventilated pigs with acute lung injury (2013)

We were able to demonstrate that oxygen delivery using a POC in mechanically ventilated pigs with ALI is feasible. We were also able to demonstrate that pulsed dose delivery from a POC is superior to continuous flow oxygen delivery for oxygenation in ALI, when using volume control. We propose that this is a safe alternative to conserve oxygen in the transport of critically ill patients.
Computational approach to radiogenomics of breast cancer: Luminal A and luminal B molecular subtypes are associated with imaging features on routine breast MRI extracted using computer vision algorithms (2015)

Luminal A and luminal B molecular subtype breast cancer are associated with semiautomatically extracted features from routine contrast enhanced breast MRI.
Chemokine receptor CXCR3 and its ligands CXCL9 and CXCL10 are required for the development of murine cerebral malaria (2008)

Cerebral malaria is a significant cause of global mortality, causing an estimated two million deaths per year, mainly in children. The pathogenesis of this disease remains incompletely understood. Chemokines have been implicated in the development of cerebral malaria, and the IFN-inducible CXCR3 chemokine ligand IP-10 (CXCL10) was recently found to be the only serum biomarker that predicted cerebral malaria mortality in Ghanaian children. We show that the CXCR3 chemokine ligands IP-10 and Mig (CXCL9) were highly induced in the brains of mice with murine cerebral malaria caused by Plasmodium berghei ANKA. Mice deficient in CXCR3 were markedly protected against cerebral malaria and had far fewer T cells in the brain compared with wild-type mice. In competitive transfer experiments, CXCR3-deficient CD8(+) T cells were 7-fold less efficient at migrating into the infected brains than wild-type CD8(+) T cells. Adoptive transfer of wild-type CD8(+) effector T cells restored susceptibility of CXCR3-deficient mice to cerebral malaria and also restored brain proinflammatory cytokine and chemokine production and recruitment of T cells, independent of CXCR3. Mice deficient in IP-10 or Mig were both partially protected against cerebral malaria mortality when infected with P. berghei ANKA. Brain immunohistochemistry revealed Mig staining of endothelial cells, whereas IP-10 staining was mainly found in neurons. These data demonstrate that CXCR3 on CD8(+) T cells is required for T cell recruitment into the brain and the development of murine cerebral malaria and suggest that the CXCR3 ligands Mig and IP-10 play distinct, nonredundant roles in the pathogenesis of this disease.
Pseudopalisades in Glioblastoma Are Hypoxic, Express Extracellular Matrix Proteases, and Are Formed by an Actively Migrating Cell Population (2004)

Necrosis and vascular proliferation are the pathologic features that distinguish the most malignant infiltrative astrocytoma, glioblastoma (GBM), from those of lower grades. In GBM, hypercellular zones called pseudopalisades typically surround necrotic foci. Although these cells are known to secrete high levels of proangiogenic factors that promote tumor growth, their origins are ill defined. We propose that pseudopalisades represent differing stages and histologic samplings of astrocytoma cells migrating away from a hypoxic/anoxic focus, often triggered by a central vaso-occlusive event. This proposition is based on our findings that pseudopalisading cells are 5-50% less proliferative and 6-20 times more apoptotic than adjacent astrocytoma, indicating that cell accumulation does not result from increased proliferation or resistance to apoptosis. Coexisting inflammatory cells account for <2% of pseudopalisading cells and cannot account for hypercellularity. Pseudopalisading cells show nuclear expression of hypoxia-inducible factor 1 alpha, consistent with their hypoxic nature, and hypoxia induces a 20-60% increase in glioma cell migration in vitro. Hypoxic cells in vitro and pseudopalisades in GBM specimens show enhanced gelatinase activity, typical of an invasive phenotype. These results suggest that pseudopalisading cells are migrating at the periphery of a hypoxic center. To uncover a potential source of hypoxia and sequence of structural events leading to pseudopalisade formation, we performed a morphometric analysis of 234 pseudopalisades from 85 pretreatment GBMs. We found distorted, degenerating, or thrombosed blood vessels within the center of more than half the pseudopalisades, suggesting that at least a subset of pseudopalisades are two-dimensional histologic representations of tumor cells migrating away from a vaso-occlusive event.
Exploring Shale Basins using Existing Wells (2012)

Abstract In the search for unconventional shale plays with commercial potential, many operators have properties in petroprovince basins containing wells through potentially productive shale zones. These shales were often encountered as part of exploration or development programs for deeper conventional targets. Often, the overlying shale is known to have had gas or oil shows reported during initial drilling, but little or no additional geological data was acquired at the time. This paper discusses the workflow and method to use the minimal information from these existing wells, and to quantitatively incorporate them into a basin exploration program. The process begins with a single new well, such as a sidetrack from an existing well, which is evaluated with the full array of open hole logging tools. Coring (conventional or sidewall), DFIT tests, and other shale-specific logging tools are performed on this initial well. Pre-existing wells that penetrate the objective shale can also be quantitatively assessed for relevant shale properties by using specialized logging tools, such as a combined through-casing pulsed neutron and sonic tool, to map relevant shale properties. These tools are calibrated to the open hole data to generate a wider distribution of data points containing critical shale properties that can be demonstrated to have a strong relationship with production. After the data acquisition process has been performed, the data are combined with existing seismic and structural information to delineate the best areas for further evaluation. Using modern mapping tools, a basin can be rapidly appraised to identify sweet spots, providing further exploration targets for evaluation drilling. This paper discusses limitations, best practices, workflows, and methods, and includes an example of a European shale evaluation log to demonstrate this exploration technique.
A simplified 3-step fabrication scheme for high mobility AMLCD panels (1994)

A 3 yield-determining mask CdSe TFT process is presented for the fabrication of AMLCD panels. The process comprises non critical processing steps, high mobility TFTs and optimum aperture ratio design