gebhart/patrepeval huggingface dataset:
Antioxidant effects of aminosalicylates and potential new drugs for inflammatory bowel disease: assessment in cell‐free systems and inflamed human colorectal biopsies (1999)

The antioxidant effects of compounds varies between cell-free systems and inflamed colorectal biopsies. The effect of drugs on the chemiluminescence produced by these two assay systems is useful for screening potentially new antioxidant treatments for inflammatory bowel disease. Ascorbate seems worth further study as a novel therapy.
Tissue Specific DNA Methylation in Normal Human Breast Epithelium and in Breast Cancer (2014)

Cancer is a heterogeneous and tissue-specific disease. Thus, the tissue of origin reflects on the natural history of the disease and dictates the therapeutic approach. It is suggested that tissue differentiation, mediated mostly by epigenetic modifications, could guide tissue-specific susceptibility and protective mechanisms against cancer. Here we studied breast specific methylation in purified normal epithelium and its reflection in breast cancers. We established genome wide methylation profiles of various normal epithelial tissues and identified 110 genes that were differentially methylated in normal breast epithelium. A number of these genes also showed methylation alterations in breast cancers. We elaborated on one of them, TRIM29 (ATDC), and showed that its promoter was hypo-methylated in normal breast epithelium and heavily methylated in other normal epithelial tissues. Moreover, in breast carcinomas methylation increased and expression decreased whereas the reverse was noted for multiple other carcinomas. Interestingly, TRIM29 regulation in breast tumors clustered according to the PAM50 classification. Thus, it was repressed in the estrogen receptor positive tumors, particularly in the more proliferative luminal B subtype. This goes in line with previous reports indicating tumor suppressive activity of TRIM29 in estrogen receptor positive luminal breast cells in contrast to oncogenic function in pancreatic and lung cancers. Overall, these findings emphasize the linkage between breast specific epigenetic regulation and tissue specificity of cancer.
Neuropeptides and neural cell adhesion molecule (NCAM) in CSF from patients with ALS (1989)

In 10 patients with amyotrophic lateral sclerosis (ALS), the CSF content of the neuropeptides vasoactive intestinal polypeptide (VIP) and cholecystokinin (CCK) as well as neural cell adhesion molecule (NCAM) was investigated. Compared with normal controls, no deviations were found in CCK or NCAM, while the values of VIP were significantly lower in ALS patients. This finding may reflect a loss of motor neurons.
Studies on the Constituents of Aloe arborescens MILL. var. natalensis BERGER. II. The Structures of Two New Aloesin Esters (1974)

Two new aloesin esters were isolated from the fresh leaves of Aloe arborescens MILL. var. natalensis BERGER and their structures were established to be 2"-O-p-coumaroylaloesin and 2"-O-feruloylaloesin on the basis of chemical and spectral evidences. These esters are the first naturally occurring 2"-O-acylated C-glucosyl compounds.
Virtual machines with sharable operating system (2011)

Virtualization technologies commonly known as Cloud model enable the execution of multiple virtual machine instances (VMs) with different operating systems (OSs) on the same physical host. Each VM instance functions independently as an isolated system with its own physical resources, OS copy and applications. There is only a limited number of currently available and widely used OSs used by most of the running VM instances; it is wasteful to store all the VM images with virtually the same common OS code. It is also inefficient in terms of performance and system resources utilization to virtually clone the entire image each time a new VM instance is provisioned. In addition, performing OS updates and patches are complicated, tedious and error prone since not only the stored images need to be updated, all the running VM instances must be properly refreshed. More importantly, faster provisioning of VM instances in respond to workload changes is critical to the successful operation of Cloud service providers. In this paper, we show our exploration work to address these performance issues by using a common, sharable operating system approach which provides run-time on-demand operating system components to individual VM instances in Cloud environment. This new approach allows optimized VM image storage, faster VM provisioning and efficient OS updates with minimum interruption.
<title>Content-based image retrieval on mobile devices</title> (2005)

Content-based image retrieval possesses a tremendous potential for exploration and utilization equally for researchers and people in industry due to its promising results. Expeditious retrieval of desired images requires indexing of the content in large-scale databases along with extraction of low-level features based on the content of images contained in these databases. With the advancement in wireless communication technology and availability of multimedia capable phones it has become vital to query image databases and retrieve results based on the content of query. Our implemented System, “Mobile MUVIS”, based on contemporary MUVIS, aims to bring the capability of content-based query to any device supporting Java platform. It consists of a light-weight client application running on a Java enabled phone and a server containing a servlet running inside a web server. The server responds to image query using efficient native code from selected MUVIS database. The client application, running on mobile phone, is able to form query request which is parsed by servlet for finding closest match to the queried image. The query response is retrieved over GPRS/HSCSD network and images are displayed on the mobile phone. We are able to conclude that such system is feasible but with limited results due to resource constraint on hand-held devices and reduced network bandwidth available in mobile environments.
The Chitinase-Like Protein YKL-40 Modulates Cystic Fibrosis Lung Disease (2011)

The chitinase-like protein YKL-40 was found to be increased in patients with severe asthma and chronic obstructive pulmonary disease (COPD), two disease conditions featuring neutrophilic infiltrates. Based on these studies and a previous report indicating that neutrophils secrete YKL-40, we hypothesized that YKL-40 plays a key role in cystic fibrosis (CF) lung disease, a prototypic neutrophilic disease. The aim of this study was (i) to analyze YKL-40 levels in human and murine CF lung disease and (ii) to investigate whether YKL-40 single-nucleotide polymorphisms (SNPs) modulate CF lung disease severity. YKL-40 protein levels were quantified in serum and sputum supernatants from CF patients and control individuals. Levels of the murine homologue BRP-39 were analyzed in airway fluids from CF-like βENaC-Tg mice. YKL-40SNPs were analyzed in CF patients. YKL-40 levels were increased in sputum supernatants and in serum from CF patients compared to healthy control individuals. Within CF patients, YKL-40 levels were higher in sputum than in serum. BRP-39 levels were increased in airways fluids from βENaC-Tg mice compared to wild-type littermates. In both CF patients and βENaC-Tg mice, YKL-40/BRP-39 airway levels correlated with the severity of pulmonary obstruction. Two YKL-40 SNPs (rs871799 and rs880633) were found to modulate age-adjusted lung function in CF patients. YKL-40/BRP-39 levelsare increased in human and murine CF airway fluids, correlate with pulmonary function and modulate CF lung disease severity genetically. These findings suggest YKL-40 as a potential biomarker in CF lung disease.
Sister chromatid fusion initiates amplification of the dihydrofolate reductase gene in Chinese hamster cells. (1993)

We have utilized a dihydrofolate reductase (DHFR) probe in combination with selected probes from other positions along the 2q chromosome arm in a two-color fluorescence in situ hybridization analysis of early DHFR gene amplification events in CHO cells. These studies show clearly that the most frequent initiating event is the formation of a giant inverted duplication, resulting from chromosome breakage and terminal fusion or a reverse unequal sister chromatid exchange. The dicentric chromosomes thus formed initiate bridge/breakage/fusion cycles that appear to mediate subsequent amplification steps to higher copy number.
Continuous Polony Gels for Tissue Mapping with High Resolution and RNA Capture Efficiency (2021)

Abstract Current technologies for acquiring spatial transcript information from tissue sections rely on either RNA probes or spatial barcodes. The former methods require a priori knowledge for probeset formulation; the latter have yet to achieve single cell resolution and/or transcript capture efficiencies approaching dissociative, single-cell methods. Here, we describe a novel spatial transcriptome assay called p olony (or DNA cluster)- i nde xe d l ibrary-sequencing (PIXEL-seq). It improves upon other spatial barcoding methods by employing “continuous” polony oligos arrayed across a customized gel surface. In terms of assay performance, PIXEL-seq attains ≤ 1 µm resolution and captures &gt;1,000 unique molecular identifiers/10×10 µm 2 . In other words, this global, naive platform achieves subcellular spatial transcriptome mapping while maintaining high transcript capture efficiencies.
ACTION OF SYNTHETIC DETERGENTS ON THE METABOLISM OF BACTERIA (1941)

A study of the effects of synthetic detergents and wetting agents on respiration and glycolysis of Gram-positive and Gram-negative microorganisms has led to the following conclusions. 1. All the cationic detergents studied are very effective inhibitors of bacterial metabolism at 1:3000 concentration, and several are equally active at 1:30,000. Few of the anionic detergents inhibit as effectively as the cationic compounds. 2. Gram-positive and Gram-negative microorganisms are equally sensitive to the action of the cationic detergents. On the other hand, all the anionic detergents included in our studies selectively inhibit the metabolism of Gram-positive microorganisms. 3. The inhibitory action of both types of detergents is influenced markedly by hydrogen ion concentration. Cationic detergents exhibit their maximum activity in the alkaline pH range, and the anionic, in the acid range. 4. Studies of homologous series of straight chain alkyl sulfates and sulfoacetates (C(8) to C(18)) demonstrate that maximum inhibition is exerted by the 12, 14, and 16 carbon compounds (lauryl, myristyl, and cetyl). 5. It has been observed that three lauryl esters of amino acids are powerful inhibitors of bacterial metabolism. To our knowledge, the effects on bacterial metabolism of such cationic detergents (without the quaternary ammonium structure) have not been studied previously. Our results demonstrate that other cationic detergents can exhibit an inhibitory activity comparable to quaternary ammonium compounds. 6. Certain detergents stimulate bacterial metabolism at concentrations lower than the inhibiting values. This effect has been found more frequently among the anionic detergents.
A systems approach to clinical oncology: Focus on breast cancer (2006)

During the past decade, genomic microarrays have been applied with some success to the molecular profiling of breast tumours, which has resulted in a much more detailed classification scheme as well as in the identification of potential gene signature sets. These gene sets have been applied to both the prognosis and prediction of outcome to treatment and have performed better than the current clinical criteria. One of the main limitations of microarray analysis, however, is that frozen tumour samples are required for the assay. This imposes severe limitations on access to samples and precludes large scale validation studies from being conducted. Quantitative reverse transcriptase polymerase chain reaction (qRT-PCR), on the other hand, can be used with degraded RNAs derived from formalin-fixed paraffin-embedded (FFPE) tumour samples, the most important and abundant source of clinical material available. More recently, the novel DASL (cDNA-mediated Annealing, Selection, extension and Ligation) assay has been developed as a high throughput gene expression profiling system specifically designed for use with FFPE tumour tissue samples. However, we do not believe that genomics is adequate as a sole prognostic and predictive platform in breast cancer. The key proteins driving oncogenesis, for example, can undergo post-translational modifications; moreover, if we are ever to move individualization of therapy into the practical world of blood-based assays, serum proteomics becomes critical. Proteomic platforms, including tissue micro-arrays (TMA) and protein chip arrays, in conjunction with surface-enhanced laser desorption ionization time-of-flight mass spectrometry (SELDI-TOF/MS), have been the technologies most widely applied to the characterization of tumours and serum from breast cancer patients, with still limited but encouraging results. This review will focus on these genomic and proteomic platforms, with an emphasis placed on the utilization of FFPE tumour tissue samples and serum, as they have been applied to the study of breast cancer for the discovery of gene signatures and biomarkers for the early diagnosis, prognosis and prediction of treatment outcome. The ultimate goal is to be able to apply a systems biology approach to the information gleaned from the combination of these techniques in order to select the best treatment strategy, monitor its effectiveness and make changes as rapidly as possible where needed to achieve the optimal therapeutic results for the patient.
Illumination estimation and cast shadow detection through a higher-order graphical model (2011)

In this paper, we propose a novel framework to jointly recover the illumination environment and an estimate of the cast shadows in a scene from a single image, given coarse 3D geometry. We describe a higher-order Markov Random Field (MRF) illumination model, which combines low-level shadow evidence with high-level prior knowledge for the joint estimation of cast shadows and the illumination environment. First, a rough illumination estimate and the structure of the graphical model in the illumination space is determined through a voting procedure. Then, a higher order approach is considered where illumination sources are coupled with the observed image and the latent variables corresponding to the shadow detection. We examine two inference methods in order to effectively minimize the MRF energy of our model. Experimental evaluation shows that our approach is robust to rough knowledge of geometry and reflectance and inaccurate initial shadow estimates. We demonstrate the power of our MRF illumination model on various datasets and show that we can estimate the illumination in images of objects belonging to the same class using the same coarse 3D model to represent all instances of the class.
Learning flexible concepts from streams of examples: FLORA2 (1992)

FLORA2 is a program for supervised learning of concepts that are subject to concept drift. The learning process is incremental in that the examples are processed one by one. A special feature of our program consists in keeping in memory a subset of examples -- a window. In time, new examples are being added to the window while other ones are considered outdated and are forgotten. In order to track the concept drift, the system keeps in memory not only valid descriptions of the concepts as they are derived from the objects currently present in the window, but also `candidate descriptions&amp;apos; that may turn into valid descriptions in the future. 1 Introduction One of the key tasks of the Machine Learning discipline is to find powerful methods for abstracting concepts out of a set of objects. Basically, two subproblems of this task exist: supervised learning and unsupervised learning. The former assumes that a set of preclassified examples (positive and negative) of some concept(s) are avail...
Potato plants expressing antisense and sense S‐adenosylmethionine decarboxylase (SAMDC) transgenes show altered levels of polyamines and ethylene: antisense plants display abnormal phenotypes (1996)

A molecular approach has been used to study the role of polyamines in plant development by manipulating the expression of the S‐adenosylmethionine decarboxylase (SAMDC) gene. SAMDC is a key enzyme involved in the biosynthesis of the polyamines spermidine and spermine and is also known to influence the rate of biosynthesis of ethylene. Previously, a cDNA clone of the SAMDC gene of potato has been isolated and characterized. This cDNA clone has been used to make antisense and sense SAMDC constructs under the control of the 35S CaMV or tetracycline‐inducible promoters. Agrobacterium ‐mediated transformation has been used to produce transgenic potato plants with the engineered antisense and sense SAMDC genes in order to downregulate or overexpress the SAMDC transcript, respectively. Decreases or increases in the level of SAMDC transcript in the antisense and sense transgenic plants were observed, respectively. Antisense transgenic plants which expressed the engineered SAMDC gene constitutively under the control of the 35S CaMV promoter with a duplicated enhancer region showed a range of stunted phenotypes with highly branched stems, short internodes, small leaves and inhibited root growth. The abnormal characteristics of the antisense plants correlated with the altered levels of SAMDC transcript, SAMDC activity, polyamine content and rate of ethylene evolution. Attempts to produce sense transgenic plants with the 35S SAMDC sense construct were unsuccessful indicating that a constitutive overexpression of the engineered SAMDC is lethal to the plants. When antisense and sense SAMDC transgenes were expressed under the control of a tetracycline‐inducible promoter a number of transgenic plants were produced. In these antisense and sense plants, significant changes in the level of SAMDC transcript, SAMDC activity and free polyamine content were observed on tetracycline‐induction of detached leaves.
Surfactant proteins A and D inhibit the growth of Gram-negative bacteria by increasing membrane permeability (2003)

The pulmonary collectins, surfactant proteins A (SP-A) and D (SP-D), have been reported to bind lipopolysaccharide (LPS), opsonize microorganisms, and enhance the clearance of lung pathogens. In this study, we examined the effect of SP-A and SP-D on the growth and viability of Gram-negative bacteria. The pulmonary clearance of Escherichia coli K12 was reduced in SP-A-null mice and was increased in SP-D-overexpressing mice, compared with strain-matched wild-type controls. Purified SP-A and SP-D inhibited bacterial synthetic functions of several, but not all, strains of E. coli, Klebsiella pneumoniae, and Enterobacter aerogenes. In general, rough E. coli strains were more susceptible than smooth strains, and collectin-mediated growth inhibition was partially blocked by coincubation with rough LPS vesicles. Although both SP-A and SP-D agglutinated E. coli K12 in a calcium-dependent manner, microbial growth inhibition was independent of bacterial aggregation. At least part of the antimicrobial activity of SP-A and SP-D was localized to their C-terminal domains using truncated recombinant proteins. Incubation of E. coli K12 with SP-A or SP-D increased bacterial permeability. Deletion of the E. coli OmpA gene from a collectin-resistant smooth E. coli strain enhanced SP-A and SP-D-mediated growth inhibition. These data indicate that SP-A and SP-D are antimicrobial proteins that directly inhibit the proliferation of Gram-negative bacteria in a macrophage- and aggregation-independent manner by increasing the permeability of the microbial cell membrane.
Protein folding includes oligomerization – examples from the endoplasmic reticulum and cytosol (2008)

A correct three-dimensional structure is a prerequisite for protein functionality, and therefore for life. Thus, it is not surprising that our cells are packed with proteins that assist protein folding, the process in which the native three-dimensional structure is formed. In general, plasma membrane and secreted proteins, as well as those residing in compartments along the endocytic and exocytic pathways, fold and oligomerize in the endoplasmic reticulum. The proteins residing in the endoplasmic reticulum are specialized in the folding of this subset of proteins, which renders this compartment a protein-folding factory. This review focuses on protein folding in the endoplasmic reticulum, and discusses the challenge of oligomer formation in the endoplasmic reticulum as well as the cytosol.
Oestrogen Receptors and Selective Oestrogen Receptor Modulators: Molecular and Cellular Pharmacology (2005)

The early termination of the two arms of the Women's Health Initiative Trials has led to an increased interest and demand for selective oestrogen receptor modulators because of their potential to retain the benefits of hormone replacement therapy (oestrogen plus a gestagen) and at the same time avoid most of its severe adverse events. Selective oestrogen receptor modulators are a class of oestrogen receptor binding, small organic molecules that take advantage of the plasticity of the oestrogen receptors (alpha and beta, respectively), modulating the surface conformation of the oestrogen receptors upon binding in the respective ligand binding cavity. By doing so they affect the binding of various co-factors to the surface of the oestrogen receptors that, at least in part, explains why selective oestrogen receptor modulators may mimic the activity of oestrogen in some tissues where so desired, while opposing its activity in tissues where oestrogen-like activity is undesirable. Although selective oestrogen receptor modulators have many properties in common they also display unique activities including oestrogen receptor surface modulation and regulation of target gene expression. Selective oestrogen receptor modulators therefore offer the opportunity to develop pharmaceuticals with very distinct pharmacology and mechanism of action. Furthermore, these modulators offer the advantage of decreased risk for the development of breast and endometrial cancer and circumvent the need for combination with a gestagen. Most selective oestrogen receptor modulators in development bind with roughly equal affinity to both oestrogen receptor alpha and beta (balanced) and our view is that it is unlikely that a balanced selective oestrogen receptor modulator will inherit all desired effects of oestrogen (e.g. 17beta-oestradiol) and at the same time be devoid of all undesired effects. We therefore propose that the development of oestrogen receptor-subtype (alpha and beta, respectively) selective pharmaceuticals for specific applications (designer drugs) would better provide the benefits of hormone replacement therapy without its associated risks.