gebhart/patrepeval huggingface dataset:
Automatic text extraction and character segmentation using maximally stable extremal regions (2016)

Text detection and segmentation is an important prerequisite for many content based image analysis tasks. The paper proposes a novel text extraction and character segmentation algorithm using Maximally Stable Extremal Regions as basic letter candidates. These regions are then subjected to thresholding and thereafter various connected components are determined to identify separate characters. The algorithm is tested along a set of various JPEG, PNG and BMP images over four different character sets; English, Russian, Hindi and Urdu. The algorithm gives good results for English and Russian character set; however character segmentation in Urdu and Hindi language is not much accurate. The algorithm is simple, efficient, involves no overhead as required in training and gives good results for even low quality images. The paper also proposes various challenges in text extraction and segmentation for multilingual inputs.
Characterization of the Mycobacterium tuberculosis phagosome and evidence that phagosomal maturation is inhibited. (1995)

We have used the cryosection immunogold technique to study the composition of the Mycobacterium tuberculosis phagosome. We have used quantitative immunogold staining to determine the distribution of several known markers of the endosomal-lysosomal pathway in human monocytes after ingestion of either M. tuberculosis, Legionella pneumophila, or polystyrene beads. Compared with the other phagocytic particles studied, the M. tuberculosis phagosome exhibits delayed clearance of major histocompatibility complex (MHC) class I molecules, relatively intense staining for MHC class II molecules and the endosomal marker transferrin receptor, and relatively weak staining for the lysosomal membrane glycoproteins, CD63, LAMP-1, and LAMP-2 and the lysosomal acid protease, cathepsin D. In contrast to M. tuberculosis, the L. pneumophila phagosome rapidly clears MHC class I molecules and excludes all endosomal-lysosomal markers studied. In contrast to both live M. tuberculosis and L. pneumophila phagosomes, phagosomes containing either polystyrene beads or heat-killed M. tuberculosis stain intensely for lysosomal membrane glycoproteins and cathepsin D. These findings suggest that (a) M. tuberculosis retards the maturation of its phagosome along the endosomal-lysosomal pathway and resides in a compartment with endosomal, as opposed to lysosomal, characteristics; and (b) the intraphagosomal pathway, i.e., the pathway followed by several intracellular parasites that inhibit phagosome-lysosome fusion, is heterogeneous.
Impaired Functional Recovery After Stroke in the Stroke-Prone Spontaneously Hypertensive Rat (2004)

SHRSP exhibit impaired functional recovery after stroke compared with WKY.
Early-onset Amyloid Deposition and Cognitive Deficits in Transgenic Mice Expressing a Double Mutant Form of Amyloid Precursor Protein 695 (2001)

We have created early-onset transgenic (Tg) models by exploiting the synergistic effects of familial Alzheimer's disease mutations on amyloid beta-peptide (Abeta) biogenesis. TgCRND8 mice encode a double mutant form of amyloid precursor protein 695 (KM670/671NL+V717F) under the control of the PrP gene promoter. Thioflavine S-positive Abeta amyloid deposits are present at 3 months, with dense-cored plaques and neuritic pathology evident from 5 months of age. TgCRND8 mice exhibit 3,200-4,600 pmol of Abeta42 per g brain at age 6 months, with an excess of Abeta42 over Abeta40. High level production of the pathogenic Abeta42 form of Abeta peptide was associated with an early impairment in TgCRND8 mice in acquisition and learning reversal in the reference memory version of the Morris water maze, present by 3 months of age. Notably, learning impairment in young mice was offset by immunization against Abeta42 (Janus, C., Pearson, J., McLaurin, J., Mathews, P. M., Jiang, Y., Schmidt, S. D., Chishti, M. A., Horne, P., Heslin, D., French, J., Mount, H. T. J., Nixon, R. A., Mercken, M., Bergeron, C., Fraser, P. E., St. George-Hyslop, P., and Westaway, D. (2000) Nature 408, 979-982). Amyloid deposition in TgCRND8 mice was enhanced by the expression of presenilin 1 transgenes including familial Alzheimer's disease mutations; for mice also expressing a M146L+L286V presenilin 1 transgene, amyloid deposits were apparent by 1 month of age. The Tg mice described here suggest a potential to investigate aspects of Alzheimer's disease pathogenesis, prophylaxis, and therapy within short time frames.
Infinite Images: Creating and Exploring a Large Photorealistic Virtual Space (2010)

We present a system for generating “infinite” images from large collections of photos by means of transformed image retrieval. Given a query image, we first transform it to simulate how it would look if the camera moved sideways and then perform image retrieval based on the transformed image. We then blend the query and retrieved images to create a larger panorama. Repeating this process will produce an “infinite” image. The transformed image retrieval model is not limited to simple 2-D left/right image translation, however, and we show how to approximate other camera motions like rotation and forward motion/zoom-in using simple 2-D image transforms. We represent images in the database as a graph where each node is an image and different types of edges correspond to different types of geometric transformations simulating different camera motions. Generating infinite images is thus reduced to following paths in the image graph. Given this data structure we can also generate a panorama that connects two query images, simply by finding the shortest path between the two in the image graph. We call this option the “image taxi.” Our approach does not assume photographs are of a single real 3-D location, nor that they were taken at the same time. Instead, we organize the photos in themes, such as city streets or skylines and synthesize new virtual scenes by combining images from distinct but visually similar locations. There are a number of potential applications to this technology. It can be used to generate long panoramas as well as content aware transitions between reference images or video shots. Finally, the image graph allows users to interactively explore large photo collections for ideation, games, social interaction, and artistic purposes.
Supramolecular Ordering in Oligothiophene−Fullerene Monolayers (2009)

Scanning tunneling microscopy (STM) of monolayers comprising oligothiophene and fullerene molecular semiconductors reveals details of their molecular-scale phase separation and ordering with potential implications for the design of organic electronic devices, in particular future bulk heterojunction solar cells. Prochiral terthienobenzenetricarboxylic acid (TTBTA) self-assembles at the solution/graphite interface into either a porous chicken wire network linked by dimeric hydrogen bonding associations of COOH groups (R(2)(2) (8)) or a close-packed network linked in a novel hexameric hydrogen bonding motif (R(6)(6) (24)). Analysis of high-resolution STM images shows that the chicken wire phase is racemically mixed, whereas the close-packed phase is enantiomerically pure. The cavities of the chicken wire structure can efficiently host C60 molecules, which form ordered domains with either one, two, or three fullerenes per cavity. The observed monodisperse filling and long-range co-alignment of fullerenes is described in terms of a combination of an electrostatic effect and the commensurability between the graphite and molecular network, which leads to differentiation of otherwise identical adsorption sites in the pores.
Conserving disk energy in network servers (2003)

In this paper we study four approaches to conserving disk energy in high-performance network servers. The first approach is to leverage the extensive work on laptop disks and power disks down during periods of idleness. The second approach is to replace high-performance disks with a set of lower power disks that can achieve the same performance and reliability. The third approach is to combine high-performance and laptop disks, such that only one of these two sets of disks is powered on at a time. This approach requires the mirroring (and coherence) of all disk data on the two sets of disks. Finally, the fourth approach is to use multi-speed disks, such that each disk is slowed down for lower energy consumption during periods of light load. We demonstrate that the fourth approach is the only one that can actually provide energy savings for network servers. In fact, our results for Web and proxy servers show that the fourth approach can provide energy savings of up to 23%, in comparison to conventional servers, without any degradation in server performance.
Diffuse radiation in the Galaxy (1941)

Observations have been obtained to verify the existence of diffuse interstellar radiation. A Fabry photometer, attached to the 40-inch refractor at the Yerkes Observatory, was used to measure the brightness of regions over a wide range of galactic latitude. The intensities in the photographic region of the spectrum were calibrated by means of the Polar Sequence stars. The mean of four such runs across the Milky Way, on circles of nearly constant longitude, l = 40°, shows a maximum of brightness of 80 stars of the tenth magnitude per square degree for the diffuse extra-terrestrial radiation. The mean of three runs near l = 140° shows a maximum of 35 in the same units. It is shown that the observed intensity of diffuse light may be explained as scattered stellar radiation if the phase function governing the scattering of starlight by the interstellar matter is strongly forward-throwing. The concentration of the diffuse light toward the galactic circle is also in agreement with this property of the phase function. The observations also indicate that the scattering efficiency, or albedo, of the particles is greater than 0.3
RAPSearch2: a fast and memory-efficient protein similarity search tool for next-generation sequencing data (2011)

Available at the RAPSearch2 website.
Oxidative damage to methyl-CpG sequences inhibits the binding of the methyl-CpG binding domain (MBD) of methyl-CpG binding protein 2 (MeCP2) (2004)

Cytosine methylation in CpG dinucleotides is believed to be important in gene regulation, and is generally associated with reduced levels of transcription. Methylation-mediated gene silencing involves a series of DNA-protein and protein-protein interactions that begins with the binding of methyl-CpG binding proteins (MBPs) followed by the recruitment of histone-modifying enzymes that together promote chromatin condensation and inactivation. It is widely known that alterations in methylation patterns, and associated gene activities, are often found in human tumors. However, the mechanisms by which methylation patterns are altered are not currently understood. In this paper, we investigate the impact of oxidative damage to a methyl-CpG site on MBP binding by the selective placement of 8-oxoguanine (8-oxoG) and 5-hydroxymethylcytosine (HmC) in a MBP recognition sequence. Duplexes containing these specific modifications were assayed for binding to the methyl-CpG binding domain (MBD) of one member of the MBP family, methyl-CpG binding protein 2 (MeCP2). Our results reveal that oxidation of either a single guanine to 8-oxoG or of a single 5mC to HmC, significantly inhibits binding of the MBD to the oligonucleotide duplex, reducing the binding affinity by at least an order of magnitude. Oxidative damage to DNA could therefore result in heritable, epigenetic changes in chromatin organization.
Cell-free fetal DNA and non-invasive prenatal diagnosis (2009)

Currently in the UK, prenatal diagnosis of genetic conditions and Down's syndrome requires invasive diagnostic tests such as amniocentesis and chorionic villus sampling (CVS). Procedural related miscarriage rates of about 1% have been quoted for these tests which are not usually done before 11 weeks' gestation.1 Annually in the UK, 32 000 women have an invasive diagnostic test as a result of other screening tests, indicating that they are at increased risk for their children having Down's syndrome. Around a further 1500 pregnant women have an invasive test because the fetus is at high risk of a genetic condition.

An area that has generated much interest in recent years has been in isolating fetal genetic material present in maternal blood as a target for non-invasive prenatal diagnosis (NIPD). In 1997 Lo et al 2 identified cell-free fetal DNA in the maternal circulation. This finding has generated research in the development of clinical applications based on analysing this fetal genetic material for NIPD. Cell-free fetal DNA represents extracellular DNA which originates from trophoblastic cells.3 However, the vast majority of cell-free DNA in maternal blood originates from the mother, with cell-free fetal DNA representing only 3% of the total cell-free circulating DNA in early pregnancy rising to 6% in late pregnancy.4

After delivery, cell-free fetal DNA is rapidly cleared from the maternal circulation, making it specific to that pregnancy. As the fetal DNA is swamped by the presence of cell-free maternal DNA, the challenge has been to separate the fetal from the maternal cell-free DNA. Various methods have been used for this, including using methods based on the fact that the fetal DNA is shorter than maternal DNA. However, it is still not possible to extract pure fetal DNA and so currently prenatal diagnosis using cell-free fetal DNA is …
Fatty acid synthesis is essential in embryonic development: Fatty acid synthase null mutants and most of the heterozygotes die in utero (2003)

In animals, including humans, the source of long-chain saturated fatty acids is de novo synthesis, which is mediated by fatty acid synthase (FAS), ingested food, or both. To understand the importance of de novo fatty acid synthesis, we generated FAS knockout mice. The heterozygous FAS mutants (Fasn+/-) are ostensibly normal. In Fasn+/- mice the levels of FAS mRNA and the FAS activity are approximately 50% and 35% lower, respectively, than those of WT mice; hence, FAS levels are affected by gene dosage. When the Fasn+/- mutant mice were interbred, Fasn-/- mice were not produced; thus, FAS is essential during embryonic development. Furthermore, the number of Fasn+/- progeny obtained was 70% less than predicted by Mendelian inheritance, indicating partial haploid insufficiency. Even when one of the parents was WT, the estimated loss of heterozygous progeny was 60%. This loss of Fasn+/- pups appeared to be strain-specific and became more pronounced as the heterozygous females produced more litters. Most of the Fasn-/- mutant embryos died before implantation and the Fasn+/- embryos died at various stages of their development. Feeding the breeders a diet rich in saturated fatty acids did not prevent the loss of homoor heterozygotes. These observations are very important in considering teratogenic consequences of drugs aimed at inhibiting FAS activity, to reduce either obesity or the growth of cancerous tissues.
Combining two strategies to improve perfusion and drug delivery in solid tumors (2013)

Blood perfusion in tumors can be significantly lower than that in the surrounding normal tissue owing to the leakiness and/or compression of tumor blood vessels. Impaired perfusion reduces oxygen supply and results in a hypoxic microenvironment. Hypoxia promotes tumor progression and immunosuppression, and enhances the invasive and metastatic potential of cancer cells. Furthermore, poor perfusion lowers the delivery of systemically administered drugs. Therapeutic strategies to improve perfusion include reduction in vascular permeability by vascular normalization and vascular decompression by alleviating physical forces (solid stress) inside tumors. Both strategies have shown promise, but guidelines on how to use these strategies optimally are lacking. To this end, we developed a mathematical model to guide the optimal use of these strategies. The model accounts for vascular, transvascular, and interstitial fluid and drug transport as well as the diameter and permeability of tumor vessels. Model simulations reveal an optimal perfusion region when vessels are uncompressed, but not very leaky. Within this region, intratumoral distribution of drugs is optimized, particularly for drugs 10 nm in diameter or smaller and of low binding affinity. Therefore, treatments should modify vessel diameter and/or permeability such that perfusion is optimal. Vascular normalization is more effective for hyperpermeable but largely uncompressed vessels (e.g., glioblastomas), whereas solid stress alleviation is more beneficial for compressed but less-permeable vessels (e.g., pancreatic ductal adenocarcinomas). In the case of tumors with hyperpermeable and compressed vessels (e.g., subset of mammary carcinomas), the two strategies need to be combined for improved treatment outcomes.
Reversible Inhibitors of the Gastric (H+/K+)-ATPase. 5. Substituted 2,4-Diaminoquinazolines and Thienopyrimidines (1995)

Quinazolines bearing a secondary 4-(arylamino) substituent demonstrate an SAR for inhibition of the gastric (H+/K+)-ATPase different from the previously described 3-acylquinolines, suggesting that, although these compounds are also K(+)-competitive, they probably bind to the enzyme in a different orientation. Compounds bearing a tertiary 4-(arylamino) substituent, however, in particular 4-(N-methylarylamino), appear to possess an SAR quite similar to the 3-acylquinolines. We show that this arises from the effect of the N-methylation, which is to orientate the 4-(arylamino) substituent syn to C5, analogous to the 3-acylquinolines. Compounds possessing both a 4-(N-methylarylamino) substituent and a 2-(arylamino) substituent proved to be very potent, K(+)-competitive inhibitors of K(+)-stimulated ATPase activity with Ki values down to 12 nM. Some compounds also proved to be effective inhibitors of stimulated acid secretion in both the rat and dog when dosed intravenously. However, although a number of these demonstrated activity after oral administration in the dog, the level and variability precluded further evaluation.
The Alzheimer's Disease Neuroimaging Initiative 3: Continued innovation for clinical trial improvement (2016)

ADNI-3 will aim to inform AD treatment trials and facilitate development of AD disease-modifying treatments.
Reexpression of RAG-1 and RAG-2 Genes in Activated Mature Mouse B cells (1996)

Recombination activating genes (RAG-1 and RAG-2), involved in V(D)J rearrangement of immunoglobulin genes, have been thought to be expressed only in immature stages of B-cell development. However, RAG-1 and RAG-2 transcripts were found to be reexpressed in mature mouse B cells after culture with interleukin-4 in association with several different co-stimuli. Reexpression was also detected in draining lymph nodes from immunized mice. RAG-1 and RAG-2 proteins could be detected by immunofluorescence microscopy in the nuclei of B cells cultured in vitro and in the germinal centers of draining lymph nodes. These findings suggest that RAG gene products play a heretofore unsuspected role in mature B cells.
THE ROLE OF MACROPHAGES AND EICOSANOIDS IN THE PATHOGENESIS OF EXPERIMENTAL ALLERGIC NEURITIS (1988)

Experimental allergic neuritis (EAN) can be prevented or ameliorated by global blockade of macrophages. How these cells damage peripheral nervous tissue in this autoimmune demyelinating polyneuropathy is not fully understood. Since macrophages exert a number of their inflammatory actions by the release of arachidonic acid-derived eicosanoids, we investigated the possible role of these mediators in the pathogenesis of EAN. Lewis rats with myelin-induced EAN were treated before and after onset of clinical signs. Administration of corticosteroids or of the cyclo-oxygenase inhibitors indomethacin and BW755c before the onset of neurological signs suppressed the disease, as judged by clinical assessment, serial electrophysiological testing and histological examination, while initiation of drug treatment on day 13 postimmunization still markedly attenuated the course of EAN. The selective lipoxygenase blocker nafazatrom had only a slight effect. Determination of the production by macrophages ex vivo of eicosanoids corroborated the predicted site of action of the pharmacological compounds applied. We infer that macrophage-derived proinflammatory arachidonic acid metabolites significantly contribute to functional and tissue damage in EAN. Our results may be relevant to future pharmacological treatment of the acute Guillain-Barré syndrome.
Quantum Dot Peptide Biosensors for Monitoring Caspase 3 Proteolysis and Calcium Ions (2010)

The nanoscale size and unique optical properties of semiconductor quantum dots (QDs) have made them attractive as central photoluminescent scaffolds for a variety of biosensing platforms. In this report we functionalize QDs with dye-labeled peptides using two different linkage chemistries to yield Förster resonance energy transfer (FRET)-based sensors capable of monitoring either enzymatic activity or ionic presence. The first sensor targets the proteolytic activity of caspase 3, a key downstream effector of apoptosis. This QD conjugate utilized carbodiimide chemistry to covalently link dye-labeled peptide substrates to the terminal carboxyl groups on the QD's surface hydrophilic ligands in a quantitative manner. Caspase 3 cleaved the peptide substrate and disrupted QD donor-dye acceptor FRET providing signal transduction of enzymatic activity and allowing derivation of relevant Michaelis-Menten kinetic descriptors. The second sensor was designed to monitor Ca2+ ions that are ubiquitous in many biological processes. For this sensor, Cu+-catalyzed [3 + 2] azide-alkyne cycloaddition was exploited to attach a recently developed azide-functionalized CalciumRuby-Cl indicator dye to a cognate alkyne group present on the terminus of a modified peptide. The labeled peptide also expressed a polyhistidine sequence, which facilitated its subsequent metal-affinity coordination to the QD surface establishing the final FRET sensing construct. Adding exogenous Ca2+ to the sensor solution increased the dyes fluorescence, altering the donor-acceptor emission ratio and manifested a dissociation constant similar to that of the native dye. These results highlight the potential for combining peptides with QDs using different chemistries to create sensors for monitoring chemical compounds and biological processes.
In vitro cytokine profile in childhood alopecia areata and the immunomodulatory effects of AS-101 (2005)

The aim of the present study was to determine the effect of AS-101, a known immunomodulator, on the pattern of cytokine production in children with patchy alopecia areata (PAA). Ten previously untreated children with PAA were compared to 10 healthy age- and sex-matched controls. Peripheral blood mononuclear cells (PBMC) were isolated from all participants. Unstimulated and phytohaemagglutinin (PHA)-stimulated PBMC were tested with and without the addition of AS-101. The production of interferon gamma (IFNgamma), soluble interleukin (IL)-2 receptor (IL-2R), IL-10, IL-5 and IL-6 was determined. The levels of soluble IL-2R, IL-5 and IL-6 were significantly higher in the PAA patients than the controls. AS-101 inhibited the production of IL-10, IFNgamma, IL-2R and IL-5 in both PAA patients and controls, but there was a greater inhibitory effect in children with PAA.
Finding others online (2002)

In this paper, we examine what types of reputation information users find valuable when selecting someone to interact with in online environments. In an online experiment, we asked users to imagine that they were looking for a partner for a social chat. We found that similarity to the user and ratings from the user's friends were the most valuable pieces of reputation information when selecting chat partners. The context in which reputations were used (social chat, game or newsgroup) affected the self-reported utility of the pieces of reputation information
Nanopore base calling on the edge (2021)

Supplementary data are available at Bioinformatics online.