gebhart/patrepeval huggingface dataset:
A Microscopic Characterization of the Infection of Green and Red Pepper Fruits by an Isolate of Colletotrichum gloeosporioides (1998)

Abstract Colletotrichum gloeosporioides is a common pathogenic fungus in many plants. To investigate the specificity of the isolate C. gloeosporioides to green fruits, fungal behaviours and anthracnose development on green and red pepper fruits were compared using light and stereo microscopic techniques. When the isolate of C. gloeosporioides was inoculated on both green and red fruits, conidial germination, appressoria, and infection hyphae were observed on both fruits within 24 h after inoculation. The fungal invasion and colonization continued to the epidermal cells of green fruits, but not to those of red ones. Initial anthracnose symptoms were detected only on green fruits at 2 days after inoculation resulting in typical sunken necrosis within 5 days after inoculation. Thus the specificity of the isolate to green fruits may be due to successful invasion and colonization of the infection hyphae from appressoria into the epidermal cells through epicuticular layers of green pepper fnats, but not on red ones.
Suppression of diabetes in nonobese diabetic mice by oral administration of porcine insulin. (1991)

Nonobese diabetic (NOD) mice spontaneously develop an autoimmune form of diabetes associated with insulitis. A number of immunomodulatory therapies have been investigated as a treatment for the disease process. Oral administration of the autoantigens myelin basic protein and collagen type II suppresses experimental models of encephalomyelitis and arthritis. We have now found that oral administration of insulin delays the onset and reduces the incidence of diabetes in NOD mice over a 1-year period in animals administered 1 mg of porcine insulin orally twice a week for 5 weeks and then weekly until 1 year of age. As expected, orally administered insulin had no metabolic effect on blood glucose levels. The severity of lymphocytic infiltration of pancreatic islets was also reduced by oral administration of insulin. Furthermore, splenic T cells from animals orally treated with insulin adoptively transfer protection against diabetes, demonstrating that oral insulin administration generates active cellular mechanisms that suppress disease. These results show that oral insulin affects diabetes and the pancreatic cellular inflammatory process in the NOD mouse and raise the possibility that oral administration of insulin or other pancreatic autoantigens may provide a new approach for the treatment of autoimmune diabetes.
Charge Effects on the Formation of Multilayers Containing Strong Polyelectrolytes (2003)

The effect of polymer charge density, polyelectrolyte concentration, and ionic strength on the formation of multilayer films by sequential adsorption of a polyanion (poly(styrene sulfonate), PSS) and a cationic statistical copolymer poly(diallyl-dimethyl-ammoniumchloride-stat-N-methyl-N-vinylacetamide), P(DADMAC-stat-NMVA) is investigated. The degree of charge (DC) of the polycation is controlled through the ratio of cationic DADMAC and neutral NMVA within the copolymer. The resulting polymer films are characterized by ellipsometry and by scanning force microcopy (SFM). For the present system, a minimum DC of about 68% is needed for the formation of stable films. It is proposed that this abrupt change in adsorption behavior at a DC around 68% is related to a threshold of charge reversal, which is necessary for the formation of a multilayer system. Above a DC of 75% the film thickness decreases slightly because of changes in polymer conformation. This results in a thickness maximum the position of which is shifted with varying polymer concentration. The ionic strength has a pronounced effect on the thickness above the charge reversal threshold, that is, where multilayers are formed. With increasing ionic strength, the chains undergo a transition from an extended to a coiled conformation, which leads to an increase in film thickness. Such conformational changes of the polyelectrolytes are indicated by changes in roughness as derived from SFM images. It is concluded that multilayer formation in the present system is electrostatically driven.
Prefetching links on the WWW (2002)

In this paper, we study prefetch techniques in the WWW, in which we predict which files will be needed in the near future and download some of them before they are requested by the user. Our prefetch scheme includes two algorithms: the prediction algorithm and the threshold algorithm. The prediction algorithm estimates the probability with which each file will be requested in the near future. The threshold algorithm computes the prefetch threshold for each server. An important contribution of this paper is a formula we derived to determine the prefetch threshold dynamically based on the system load capacity and the cost of time and system resources to the user. Simulations driven by trace files show that using access information from the client can achieve high successful prediction rates, while using that from the server can result in more hits in general. We have also developed a prefetch program at the client site which assists users in browsing faster and more efficiently.
The Macrophage at the Crossroads of Insulin Resistance and Atherosclerosis (2007)

The macrophage has emerged as an important player in the pathogenesis of both atherosclerosis and insulin resistance. Cross-talk between inflammatory macrophages and adipocytes may be involved in insulin resistance in peripheral tissues. Defective insulin signaling in cells of the arterial wall including macrophages may promote the development of atherosclerosis. Insulin resistant macrophages are more susceptible to endoplasmic reticulum stress and apoptosis in response to various stimuli such as nutrient deprivation, free cholesterol loading, and oxidized LDL. Increased apoptosis of insulin resistant macrophages and impaired phagocytic clearance of apoptotic cells by insulin resistant macrophages in atherosclerotic lesions may lead to enhanced postapoptotic necrosis, larger lipid-rich cores, increased inflammation, and more complex vulnerable plaques.
Renal cell carcinoma and normal kidney protein expression (1997)

Renal cell carcinoma (RCC), a human kidney cancer from the proximal tubular epithelium, accounts for about 3% of adult malignancies. Molecular and cytogenetic analysis have highlighted deletions, translocations, or loss of heterozygosity in the 3p21-p26, a putative RCC locus, as well as in 6q, 8p, 9pq, and 14pq. Studies on phenotypic expression of human kidney tissue and on post-translational modifications in RCC have not yet provided a marker for early renal cell carcinoma diagnosis. Current diagnostic methods do not help to detect the tumor before advanced stages. We therefore used two-dimensional polyacrylamide gel electrophoresis (2-D PAGE) to study normal and tumor kidney tissues in ten patients suffering from RCC. A human kidney protein map in the SWISS-2DPAGE database accessible through the ExPASy WWW Molecular Biology Server was established. Of 2789 separated polypeptides, 43 were identified by gel comparison, amino acid analysis, N-terminal sequencing, and/or immunodetection. The comparison between normal and tumor kidney tissues showed four polypeptides to be absent in RCC. One of them was identified as ubiquinol cytochrome c reductase (UQCR), whose locus has elsewhere been tentatively assigned to chromosome 19p12 or chromosome 22. A second polypeptide was identified as mitochondrial NADH-ubiquinone oxido-reductase complex I whose locus is located on chromosome 18p11.2 and chromosome 19q13.3. These result suggest that the lack of UQCR and of mitochondrial NADH-ubiquinone oxidoreductase complex I expression in RCC may be caused by unknown deletions, or by changes in gene transcription or translation. It might indicate that mitochondrial disfunction plays a major role in RCC genesis or evolution.
Catecholaminergic cell lines from the brain and adrenal glands of tyrosine hydroxylase-SV40 T antigen transgenic mice (1993)

Brain (CATH.a) and adrenal (PATH.1 and PATH.2) cell lines have been established that synthesize abundant dopamine and norepinephrine and express the appropriate catecholaminergic biosynthetic enzymes, tyrosine hydroxylase (TH) and dopamine beta-hydroxylase. The lines were derived from TH-positive tumors in transgenic mice carrying the SV40 T antigen oncogene under the transcriptional control of 773 base pairs of 5' flanking sequences from the rat TH gene. Although the lines continue to express T antigen, they exhibit neuronal properties such as neurofilaments and synaptophysin and lack glial intermediate filaments. Although in vivo TH is only expressed in postmitotic neurons in the CNS, the CATH.a line demonstrates that TH expression and continued cell division are not incompatible after oncogenic transformation.
FGFR1 is amplified during the progression of in situto invasive breast carcinoma (2012)

Amplification of HER2, C-MYC and CCND1 seems to play a role in the early development of breast cancer, but not in its progression. However, the increased frequency of FGFR1 amplification in invasive carcinomas compared with pure DCIS and in the invasive components of individual tumors, and its association with decreased disease-free survival, suggests a role for FGFR1 amplification in the progression of breast cancer including in situ-to-invasive transition, as well as initiation.
MICROBIAL BIOFILMS (1995)

Direct observations have clearly shown that biofilm bacteria predominate, numerically and metabolically, in virtually all nutrient-sufficient ecosystems. Therefore, these sessile organisms predominate in most of the environmental, industrial, and medical problems and processes of interest to microbiologists. If biofilm bacteria were simply planktonic cells that had adhered to a surface, this revelation would be unimportant, but they are demonstrably and profoundly different. We first noted that biofilm cells are at least 500 times more resistant to antibacterial agents. Now we have discovered that adhesion triggers the expression of a sigma factor that derepresses a large number of genes so that biofilm cells are clearly phenotypically distinct from their planktonic counterparts. Each biofilm bacterium lives in a customized microniche in a complex microbial community that has primitive homeostasis, a primitive circulatory system, and metabolic cooperativity, and each of these sessile cells reacts to its special environment so that it differs fundamentally from a planktonic cell of the same species.
Distance-Dependent Emission from Dye-Labeled Oligonucleotides on Striped Au/Ag Nanowires:  Effect of Secondary Structure and Hybridization Efficiency (2006)

When fluorescently tagged oligonucleotides are located near metal surfaces, their emission intensity is impacted by both electromagnetic effects (i.e., quenching and/or enhancement of emission) and the structure of the nucleic acids (e.g., random coil, hairpin, or duplex). We present experiments exploring the effect of label position and secondary structure in oligonucleotide probes as a function of hybridization buffer, which impacts the percentage of double-stranded probes on the surface after exposure to complementary DNA. Nanowires containing identifiable patterns of Au and Ag segments were used as the metal substrates in this work, which enabled us to directly compare different dye positions in a single multiplexed experiment and differences in emission for probes attached to the two metals. The observed metal-dye separation dependence for unstructured surface-bound oligonucleotides is highly sensitive to hybridization efficiency, due to substantial changes in DNA extension from the surface upon hybridization. In contrast, fluorophore labeled oligonucleotides designed to form hairpin secondary structures analogous to solution-phase molecular beacon probes are relatively insensitive to hybridization efficiency, since the folded form is quenched and therefore does not appreciably impact the observed distance-dependence of the response. Differences in fluorescence patterning on Au and Ag were noted as a function of not only chromophore identity but also metal-dye separation. For example, emission intensity for TAMRA-labeled oligonucleotides changed from brighter on Ag for 24-base probes to brighter on Au for 48-base probes. We also observed fluorescence enhancement at the ends of nanowires and at surface defects where heightened electromagnetic fields affect the fluorescence.
Updated Guidelines for The Diagnosis and Treatment of Gastroesophageal Reflux Disease (1999)

DeVault, Kenneth R MD, FACG; Castell, Donald O MD, FACG The Practice Parameters Committee of the American College of Gastroenterology Author Information
Toward a Maillard reaction theory of aging. (1989)

The inescapable chronic exposure of cellular and extracellular matrix molecules to reducing sugars which can initiate the Maillard reaction in vivo suggests that the fundamental aging process might be mediated by the Maillard reaction. An attempt to explain aging on the basis of the Maillard reaction, however, raises a number of conceptual questions. These questions are formulated below as a basis for a theory of aging based on the Maillard reaction.
Assessment of bacterial viability status by flow cytometry and single cell sorting (1998)

Rapid bacterial detection and viability measurements have been greatly enhanced by recent advances in the use of fluorescent stains in cytometry. It has previously been shown that four physiological states can be distinguished: reproductively viable, metabolically active, intact and permeabilized. Previous sorting experiments have shown that not all intact cells readily grow, but some intact cells can grow even when they fail to show metabolic activity, as determined by esterase turnover. To circumvent the limitations imposed by active dye extrusion or cell dormancy on viability measurements used to date (e.g., enzyme activity or cell polarization), a fast triple fluorochrome staining procedure has been developed that takes account of these problems. This allows further cellular characterization of intact cells by: active exclusion of ethidium bromide (EB) (metabolically active cells), uptake of EB but exclusion of bis-oxonol (BOX) (de-energized but with a polarized cell membrane) and uptake of both dyes (depolarized). Permeabilized cells were identified by propidium iodide (PI) uptake. The method was validated using an electronically programmable single cell sorter (EPICS Elite) and aged Salmonella typhimurium cells. Reproductive viability was determined by sorting single cells to their staining pattern directly onto agar plates. Most polarized cells could be recovered as well as a significant fraction of the depolarized cells, demonstrating that depolarization is a sensitive measure of cell damage but a poor indicator of cell death.
A Microdevice with Integrated Liquid Junction for Facile Peptide and Protein Analysis by Capillary Electrophoresis/Electrospray Mass Spectrometry (2000)

A novel microfabricated device was implemented for facile coupling of capillary electrophoresis with mass spectrometry (CE/MS). The device was constructed from glass wafers using standard photolithographic/wet chemical etching methods. The design integrated (a) sample inlet ports, (b) the separation channel, (c) a liquid junction, and (d) a guiding channel for the insertion of the electrospray capillary, which was enclosed in a miniaturized subatmospheric electrospray chamber of an ion trap MS. The replaceable electrospray capillary was precisely aligned with the exit of the separation channel by a microfabricated guiding channel. No glue was necessary to seal the electrospray capillary. This design allowed simple and fast replacement of either the microdevice or the electrospray capillary. The performance of the device was tested for CE/MS of peptides, proteins, and protein tryptic digests. On-line tandem mass spectrometry was used for the structure identification of the protein digest products. High-efficiency/high-resolution separations could be obtained on a longer channel (11 cm on-chip) microdevice, and fast separations (under 50 s) were achieved with a short (4.5 cm on-chip) separation channel. In the experiments, both electrokinetic and pressure injections were used. The separation efficiency was comparable to that obtained from conventional capillary electrophoresis.
Magnetic particles derived from iron nitride (1990)

Due to its high saturation magnetization ( sigma /sub s/(0K) approximately=208 emu/g) and to the ease of obtaining it as a particulate material, Fe/sub 4/N could be a suitable magnetic material for replacing highly reactive metallic iron pigments ( sigma /sub s/(0K) approximately=218 emu/g) in high-density recording. Throughout a nitriding process of properly selected precursors Fe/sub 4/N can be obtained in either of two morphologies: acicular or isotropic. Further protection of the magnetic particles can be ensured through coating of the precursor particles prior to thermal decomposition in NH/sub 3//H/sub 2/ atmosphere or through substitutions with selected elements. The obtained passivated nitrides are characterized by high magnetic properties (H/sub c/ approximately=600 Oe; sigma /sub s/ approximately=150 emu/g) and chemical stability well adapted for use as magnetic pigments for high-density recording.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Disease management: a leap of faith to lower-cost, higher-quality health care. (2003)

With managed care's promise to reduce costs and improve quality waning, employers and health plans are exploring more targeted ways to control rapidly rising health costs. Disease management programs, which focus on patients with chronic conditions such as asthma and diabetes, are growing in popularity, according to findings from the Center for Studying Health System Change's (HSC) 2002-03 site visits to 12 nationally representative communities. In addition to condition-based disease management programs, some health plans and employers are using intensive case management services to coordinate care for high-risk patients with potentially costly and complex medical conditions. Despite high expectations, evidence of both disease management and case management programs' success in controlling costs and improving quality remains limited.
Three-dimensional microwave tomography: initial experimental imaging of animals (2002)

The purpose of this study was to construct a microwave tomographic system capable of conducting experiments with whole scale biological objects and to demonstrate the feasibility of microwave tomography for imaging such objects using a canine model. Experiments were conducted using a three-dimensional (3-D) microwave tomographic system with working chamber dimensions of 120 cm in diameter and 135 cm in height. The operating frequency was 0.9 GHz. The object under study was located in the central area of the tomographic chamber filled with a salt solution. Experimentally measured attenuation of the electromagnetic field through the thorax was about -120 dB. To obtain images, we used various two-dimensional and 3-D reconstruction schemes. Images of the canine were obtained. In spite of imperfections, the images represent a significant milestone in the development of microwave tomography for whole body imaging and demonstrate its feasibility.
Characterization of a Gene Family Abundantly Expressed in Oenothera organensis Pollen That Shows Sequence Similarity to Polygalacturonase (1990)

Sherri M. Brown, Martha L. Crouch, Characterization of a Gene Family Abundantly Expressed in Oenothera organensis Pollen That Shows Sequence Similarity to Polygalacturonase, The Plant Cell, Vol. 2, No. 3 (Mar., 1990), pp. 263-274
High Reproducibility using Sodium Hydroxide-Stripped Long Oligonucleotide DNA Microarrays (2005)

Recently, long oligonucleotide (60- to 70-mer) microarrays for two-color experiments have been developed and are gaining widespread use. In addition, when there is limited availability of mRNA from tissue sources, RNA amplification can and is being used to produce sufficient quantities of cRNA for microarray hybridization. Taking advantage of the selective degradation of RNA under alkaline conditions, we have developed a method to "strip" glass-based oligonucleotide microarrays that use fluorescent RNA in the hybridization, while leaving the DNA oligonucleotide probes intact and usable for a second experiment. Replicate microarray experiments conducted using stripped arrays showed high reproducibility, however, we found that arrays could only be stripped and reused once without compromising data quality. The intraclass correlation (ICC) between a virgin array and a stripped array hybridized with the same sample showed a range of 0.90-0.98, which is comparable to the ICC of two virgin arrays hybridized with the same sample. Using this method, once-stripped oligonucleotide microarrays are usable, reliable, and help to reduce costs.
Speech/gesture interface to a visual-computing environment (2000)

We developed a speech/gesture interface that uses visual hand-gesture analysis and speech recognition to control a 3D display in VMD, a virtual environment for structural biology. The reason we used a particular virtual environment context was to set the necessary constraints to make our analysis robust and to develop a command language that optimally combines speech and gesture inputs. Our interface uses: automatic speech recognition (ASR), aided by a microphone, to recognize voice commands; two strategically positioned cameras to detect hand gestures; and automatic gesture recognition (AGR), a set of computer vision techniques to interpret those hand gestures. The computer vision algorithms can extract the user's hand from the background, detect different finger positions, and distinguish meaningful gestures from unintentional hand movements. Our main goal was to simplify model manipulation and rendering to make biomolecular modeling more playful. Researchers can explore variations of their model and concentrate on biomolecular aspects of their task without undue distraction by computational aspects. They can view simulations of molecular dynamics, play with different combinations of molecular structures, and better understand the molecules' important properties. A potential benefit, for example, might be reducing the time to discover new compounds for new drugs.
Vascular Endothelial Growth Factor In Ocular Fluid of Patients with Diabetic Retinopathy and Other Retinal Disorders (1995)

Aiello, L P; Avery, R L; Arrigg, P G; Keyt, B A; Jampel, H D; Shah, S T; Pasquale, L R; Thieme, H; Iwamoto, M A; Park, J E
Chosen-ciphertext secure proxy re-encryption (2007)

In a proxy re-encryption (PRE) scheme, a proxy is given special information that allows it to translate a ciphertext under one key into a ciphertext of the same message under a different key. The proxy cannot, however, learn anything about the messages encrypted under either key. PRE schemes have many practical applications, including distributed storage, email, and DRM. Previously proposed re-encryption schemes achieved only semantic security; in contrast, applications often require security against chosen ciphertext attacks. We propose a definition of security against chosen ciphertext attacks for PRE schemes, and present a scheme that satisfies the definition. Our construction is efficient and based only on the Decisional Bilinear Diffie-Hellman assumption in the standard model. We also formally capture CCA security for PRE schemes via both a game-based definition and simulation-based definitions that guarantee universally composable security. We note that, simultaneously with our work, Green and Ateniese proposed a CCA-secure PRE, discussed herein.