gebhart/patrepeval huggingface dataset:
Dispersal and Development of Powdery Mildew Disease Caused by Oidiopsis haplophylli on Ornamental Plants (Nasturtium) Tropaeolum majus L. in Baghdad (2014)

This study wass carried out to investigate the incedence of powdery mildew disease on ornamental plants (Nasturtium) Tropaeolum majus L. caused by Oidiopsis haplophylli in some nurseries of Baghdad area and in fields at college of Agriculture /University of Baghdad. This study was conducted in tow succesive seasons of 2011-2012 (April and May). The survey indicated that the Mildew disease existe in the following nurseries (Al-Adhamiya 97.5% ,Palestine street 93.8%, Zayouna 86.0%, and 100% in two fields at college of Agriculture. It has been found that the disease severity was developed in Agriculture college fields successively from 12-4-2011 to 20-5-2011 and from 12-4-2012 to 20-5-2012 (18.0–98.0 % and 22.7–96.0% )for the two seasons respectively. The records were followed for six times at interval of 7 days.
Characterization of major peptides in Creutzfeldt-Jakob disease and scrapie. (1986)

In Creutzfeldt-Jakob disease three major peptides cosediment with the infectious agent. These distinct peptides are not present in identical fractions from uninfected brain, and bind to polyclonal antibodies raised against "prion protein" purified by protease treatment. Three similar distinct peptides are also found in scrapie-infected brain fractions purified without the use of proteases. To clarify the relationships between these distinct peptides and prion protein, peptides were analyzed on immunoblots after cleavage with various glycosidases. There are two different 34-kDa peptides. One binds to ricin and cannot be detected by nonequilibrium pH gradient electrophoresis, presumably due to its highly acidic or basic pI. A second basic 34-kDa glycopeptide (Gp34) contains multiple terminal sialic acid residues responsible for charge heterogeneity (pI values, 7.2-7.8) and is reduced to a single spot with a pI value of 7.8 after neuraminidase treatment. After (but not before) neuraminidase treatment, secondary D-galactose-like sugars are detectable on Gp34, and a small number of N-acetylglucosamine residues probably represent the third sugar residue in an N-linked chain. When virtually all sugar residues are removed with endoglycosidase H the molecular weight of Gp34 is reduced by only approximately equal to 2 kDa. The residual peptide strongly binds antibody. A third acidic 24- to 26-kDa species (p26) also binds polyclonal antibodies but, in contrast to Gp34, was unaffected by any glycosidase treatment. Protease-treated peptides showed a very broad array of pI spots, consistent with a heterogeneous protein origin. None of the nonproteolyzed peptides show a clear relationship to prion protein. The number of sugar residues on Gp34 is not consistent with those estimated for prion protein. Although p26 could be the source of the "prion sequence," p26 does not appear to be glycosylated. Regardless, it is likely that all the major peptides described thus far are accumulated or modified normal gene products and are not integral components of the infectious agent.
Blood Gene Expression Profiling of Neurologic Diseases (2005)

Blood gene expression profiling can provide surrogate markers for neurologic diseases without obvious blood phenotypes.
Geometric Computation for Machine Vision (1993)

Abstract Machine vision is the study of how to build intelligent machines which can understand the environment by vision. Among many existing books on this subject, this book is unique in that the entire volume is devoted to computational problems, which most books do not deal with. One of the main subjects of this book is the mathematics underlying all vision problems - projective geometry, in particular. Since projective geometry has been developed by mathematicians without any regard to machine vision applications, our first attempt is to `tune' it into the form applicable to machine vision problems. The resulting formulation is termed computational projective geometry and applied to 3-D shape analysis, camera calibration, road scene analysis, 3-D motion analysis, optical flow analysis, and conic image analysis. A salient characteristic of machine vision problems is that data are not necessarily accurate. Hence, computational procedures defined by using exact relationships may break down if blindly applied to inaccurate data. In this book, special emphasis is put on robustness, which means that the computed result is not only exact when the data are accurate but also is expected to give a good approximation in the prescence of noise. The analysis of how the computation is affected by the inaccuracy of the data is also crucial. Statistical analysis of computations based on image data is also one of the main subjects of this book.
MMSE-based design of scaled and offset BP-based decoding algorithms on the fast Rayleigh fading channel (2006)

In this paper, we use the minimum mean square error (MMSE) criterion to design the scaled and offset belief propagation (BP)-based decoding algorithms for short low-density parity-check (LDPC) codes on the fast Rayleigh fading channel. Based on the MMSE criterion, the theoretical formulas and numerical calculations on the optimum factors for these two improved BP-based algorithms are provided. The simulation results for several short (Chen et al., 2005 and Gallager, 1962) regular LDPC codes on the fast Rayleigh fading channel demonstrate that the scaled and offset BP-based algorithms with our proposed factors can achieve the performance better than that of the BP algorithm.
Frequent alteration of CDKN2 (p16(INK4A)/MTS1) expression in human primary prostate carcinomas. (1997)

CDKN2 (p16(INK4A)/MTS1) is found to be mutated in a variety of human tumor types. To explore the involvement of CDKN2 in prostate carcinogenesis, alterations of CDKN2 were examined in 116 human prostate tissues and cell lines and xenografts. Markedly reduced expression of CDKN2 mRNA was found in 43% (26 of 60) of untreated primary carcinomas, whereas no alteration was observed in 10 benign prostatic hyperplasias. In 17 matched sets from individual patients, 41% of cancerous tissues in contrast to 6% of noncancerous tissues expressed low levels of CDKN2 mRNA, supporting the role of CDKN2 as a tumor suppressor in prostate cancer. Alteration of CDKN2 was observed in each prostate tumor cell line, including one with a missense mutation, and in one of three xenograft tumor tissues derived from primary carcinomas. Two cell lines (PC-3 and TSU-Pr1) expressed only CDKN2 E1beta transcripts, indicating that the expression of CDKN2 E1alpha and E1beta are under separate control in the prostate. A high level of CDKN2 expression was related to abnormal RB1 in one primary tumor and in the DU145 cell line, which expressed the mutated CDKN2 allele. Analysis of genomic DNA indicated that altered CDKN2 expression in primary carcinomas of the prostate was more frequently due to down-regulation of transcription (five of seven) than deletion of the gene (two of seven). Additionally, CDKN2 mRNA was induced in nonexpressor cell lines by treatment with 5-aza-2'-deoxycytidine. This study demonstrates that alteration of CDKN2 is one of the most frequent genetic abnormalities in prostate cancer and may contribute to prostate carcinogenesis.
Mucosal and systemic adjuvant activity of alphavirus replicon particles (2006)

Vaccination represents the most effective control measure in the fight against infectious diseases. Local mucosal immune responses are critical for protection from, and resolution of, infection by numerous mucosal pathogens. Antigen processing across mucosal surfaces is the natural route by which mucosal immunity is generated, as peripheral antigen delivery typically fails to induce mucosal immune responses. However, we demonstrate in this article that mucosal immune responses are evident at multiple mucosal surfaces after parenteral delivery of Venezuelan equine encephalitis virus replicon particles (VRP). Moreover, coinoculation of null VRP (not expressing any transgene) with inactivated influenza virions, or ovalbumin, resulted in a significant increase in antigen-specific systemic IgG and fecal IgA antibodies, compared with antigen alone. Pretreatment of VRP with UV light largely abrogated this adjuvant effect. These results demonstrate that alphavirus replicon particles possess intrinsic systemic and mucosal adjuvant activity and suggest that VRP RNA replication is the trigger for this activity. We feel that these observations and the continued experimentation they stimulate will ultimately define the specific components of an alternative pathway for the induction of mucosal immunity, and if the activity is evident in humans, will enable new possibilities for safe and inexpensive subunit and inactivated vaccines.
Animal Models of Pulmonary Fibrosis (2005)

In general, there are two types of animal models: natural and experimental. Because there are no natural models for pulmonary fibrosis, an experimental model that reproduces key aspects of the human disease would be useful for the study of this form of lung disease, the natural history of which is not always known. To date, a variety of animal models have been used to investigate mechanisms of pulmonary and other types of fibrosis, including the intratracheal instillation of bleomycin, fluorescein isothiocyanate, or particulate matter, such as silica and asbestos. This chapter will describe two commonly used techniques, namely bleomycin and silica-induced, which have been developed for the study of pulmonary fibrosis in animal models.
Extremely low frequency electromagnetic fields (ELF‐EMFs) induce in vitro angiogenesis process in human endothelial cells (2008)

Effects of extremely low frequency (ELF) electromagnetic fields (EMFs) on activation of angiogenesis were analysed using cultured umbilical human vein endothelial cells (HUVECs). The cultures were exposed to a sinusoidal EMF to intensity of 1 mT, 50 Hz for up to 12 h. EMFs increased the degree of endothelial cell proliferation and tubule formation, coupled by an acceleration in the process of wound healing. Since this process is physiologically accompanied by a large modification in the structural organization of actin and focal adhesions, we analyzed the rearrangement of some cytoskeleton elements demonstrating a major reorganization of the fibres and of the focal adhesion complexes after EMF exposure. Finally, Western blot analysis revealed a significant increase in phosphorylation as well as the overall expression of VEGF receptor 2 (KDR/Flk-1) suggesting that EMFs may modulate in vitro some endothelial functions correlated to angiogenesis through signal transduction pathways dependent on VEGF.
Mucolipidosis type IV (1998)

Patients with mucolipidosis type IV have characteristic cranial MRI findings that suggest that this disorder causes both developmental and neurodegenerative abnormalities.
Mass spectrometric and capillary electrophoretic investigation of the enzymatic degradation of heparin-like glycosaminoglycans (1998)

Difficulties in determining composition and sequence of glycosaminoglycans, such as those related to heparin, have limited the investigation of these biologically important molecules. Here, we report methodology, based on matrix-assisted laser desorption ionization MS and capillary electrophoresis, to follow the time course of the enzymatic degradation of heparin-like glycosaminoglycans through the intermediate stages to the end products. MS allows the determination of the molecular weights of the sulfated carbohydrate intermediates and their approximate relative abundances at different time points of the experiment. Capillary electrophoresis subsequently is used to follow more accurately the abundance of the components and also to measure sulfated disaccharides for which MS is not well applicable. For those substrates that produce identical or isomeric intermediates, the reducing end of the carbohydrate chain was converted to the semicarbazone. This conversion increases the molecular weight of all products retaining the reducing terminus by the "mass tag" (in this case 56 Da) and thus distinguishes them from other products. A few picomoles of heparin-derived, sulfated hexa- to decasaccharides of known structure were subjected to heparinase I digestion and analyzed. The results indicate that the enzyme acts primarily exolytically and in a processive mode. The methodology described should be equally useful for other enzymes, including those modified by site-directed mutagenesis, and may lead to the development of an approach to the sequencing of complex glycosaminoglycans.
Identification of a peripheral blood transcriptional biomarker panel associated with operational renal allograft tolerance (2007)

Long-term allograft survival generally requires lifelong immunosuppression (IS). Rarely, recipients display spontaneous "operational tolerance" with stable graft function in the absence of IS. The lack of biological markers of this phenomenon precludes identification of potentially tolerant patients in which IS could be tapered and hinders the development of new tolerance-inducing strategies. The objective of this study was to identify minimally invasive blood biomarkers for operational tolerance and use these biomarkers to determine the frequency of this state in immunosuppressed patients with stable graft function. Blood gene expression profiles from 75 renal-transplant patient cohorts (operational tolerance/acute and chronic rejection/stable graft function on IS) and 16 healthy individuals were analyzed. A subset of samples was used for microarray analysis where three-class comparison of the different groups of patients identified a "tolerant footprint" of 49 genes. These biomarkers were applied for prediction of operational tolerance by microarray and real-time PCR in independent test groups. Thirty-three of 49 genes correctly segregated tolerance and chronic rejection phenotypes with 99% and 86% specificity. The signature is shared with 1 of 12 and 5 of 10 stable patients on triple IS and low-dose steroid monotherapy, respectively. The gene signature suggests a pattern of reduced costimulatory signaling, immune quiescence, apoptosis, and memory T cell responses. This study identifies in the blood of kidney recipients a set of genes associated with operational tolerance that may have utility as a minimally invasive monitoring tool for guiding IS titration. Further validation of this tool for safe IS minimization in prospective clinical trials is warranted.
Structural Properties of Chimeric Peptides Containing a T‐cell Epitope Linked to a Fusion Peptide and their Importance for in Vivo Induction of Cytotoxic T‐cell Responses (1997)

We have previously shown that when administered to mice without adjuvant, a chimeric peptide consisting of the fusion peptide F from measles virus protein linked at the C-terminus of a cytotoxic T-cell epitope from the M2 protein of respiratory syncytial virus efficiently primes for an major histocompatibility complex (MHC) class-I restricted cytotoxic T lymphocyte (CTL) response. In this report, we demonstrated by microspectrofluorometry that the fusion-peptide moiety bound to the plasma membrane of living cells. When the fusion peptide was linked to the C-terminus of the CTL epitope, the chimeric peptide (M2-F) adopted a marked beta-sheet conformation. In contrast, when the fusion peptide was linked to the N-terminus of the T-cell epitope (F-M2), the chimeric peptide adopted an alpha-helical conformation in the presence of trifluoroethanol. The immunogenicity of the two chimeric peptides for class-I restricted CTL was also significantly different, the one adopting the alpha-helical conformation being more immunogenic. Probably due to its obvious conversion to an alpha-helical conformation, the F-M2 peptide could have a higher propensity to insert into membranes, as shown by microspectrofluorometry, with a resultant better immunogenicity than the M2-F peptide.
An architecture for building self-configurable systems (2000)

Developing wireless sensor networks can enable information gathering, information processing and reliable monitoring of a variety of environments for both civil and military applications. It is however necessary to agree upon a basic architecture for building sensor network applications. This paper presents a general classification of sensor network applications based on their network configurations and discusses some of their architectural requirements. We propose a generic architecture for a specific subclass of sensor applications which we define as self-configurable systems where a large number of sensors coordinate amongst themselves to achieve a large sensing task. Throughout this paper we assume a certain subset of the sensors to be immobile. This paper lists the general architectural and infra-structural components necessary for building this class of sensor applications. Given the various architectural components, we present an algorithm that self-organizes the sensors into a network in a transparent manner. Some of the basic goals of our algorithm include minimizing power utilization, localizing operations and tolerating node and link failures.
Mutagenesis of a Buried Polar Interaction in an SH3 Domain:  Sequence Conservation Provides the Best Prediction of Stability Effects (1998)

The SH3 domain from the Fyn tyrosine kinase possesses a buried hydrogen bond between the side chains of a glutamate (Glu24) and a serine (Ser41) residue. Multiple amino acid substitutions were made at these positions to determine the role of this interaction in the stability and conformational specificity of the domain and to assess the relationship between the thermodynamic stability of mutants and sequence conservation seen in the SH3 domain family. Analysis of single and double alanine mutations indicated that the Glu24-Ser41 interaction contributes 0.50 kcal/mol to the stability of the domain. However, disruption of the Glu24-Ser41 interaction did not impair peptide binding function, suggesting that the interaction is not critical for conformational specificity. The stability of the domain was not increased by the replacement of these residues with different combinations of hydrophobic residues or with potential salt bridge forming residues. Despite their similar structural roles in the Fyn SH3 domain, the Ser41 position was considerably more tolerant to substitution than was the Glu24 position. An alignment of >350 different SH3 domains has been completed in our laboratory. A statistically significant correlation was found between the conservation data for the Glu24 and Ser41 positions and the thermodynamic stabilities of the mutants constructed at these positions. Surprisingly, our analysis of sequence alignment data provided a more accurate prediction of the stability of mutants than did examination of the three-dimensional structure of the domain.
TRPS1 expression promotes angiogenesis and affects VEGFA expression in breast cancer (2014)

Angiogenesis is a hallmark of the malignant process in breast cancer in which vascular endothelial growth factor A (VEGFA) plays an important role. Trichorhinophalangeal syndrome type 1 (TRPS1) is a GATA-type transcription factor and is involved in trichorhinophalangeal syndrome type 1. To investigate the role of TRPS1 in breast cancer angiogenesis, we analyzed the expression of TRPS1 and microvessel density (MVD) marker CD31 by immunohistochemistry in 117 paraffin-embedded breast tissues. TRPS1 expression was positively correlated with CD31. We further investigated whether TRPS1induces human umbilical vein endothelial cell (HUVEC) migration and VEGFA expression of breast cancer cells. The over-expression of TRPS1 induced a significant increase in HUVEC migration accompanied by VEGFA up-regulation in transfected cells. In contrast, knockdown of TRPS1 decreased the induction of HUVEC migration and significantly down-regulated VEGFA expression. Furthermore, endogenous TRPS1 was present in the VEGFA promoter, as determined by chromatin immunoprecipitation assay. Taken together, this study showed that TRPS1 promotes angiogenesis and affects VEGFA expression in breast cancer.
PPFMs and other Covert Contaminants: Is There More to Plant Physiology than just Plant? (1994)

Crop loss due to soil salinization is an increasing threat to agriculture worldwide. This review provides an overview of cellular and physiological mechanisms in plant responses to salt. We place cellular responses in a time- and tissue-dependent context ...Read More
The making of the minibody: An engineered β‐protein for the display of conformationally constrained peptides (1994)

Conformationally constraining selectable peptides onto a suitable scaffold that enables their conformation to be predicted or readily determined by experimental techniques would considerably boost the drug discovery process by reducing the gap between the discovery of a peptide lead and the design of a peptidomimetic with a more desirable pharmacological profile. With this in mind, we designed the minibody, a 61-residue beta-protein aimed at retaining some desirable features of immunoglobulin variable domains, such as tolerance to sequence variability in selected regions of the protein and predictability of the main chain conformation of the same regions, based on the 'canonical structures' model. To test the ability of the minibody scaffold to support functional sites we also designed a metal binding version of the protein by suitably choosing the sequences of its loops. The minibody was produced both by chemical synthesis and expression in E. coli and characterized by size exclusion chromatography, UV CD (circular dichroism) spectroscopy and metal binding activity. All our data supported the model, but a more detailed structural characterization of the molecule was impaired by its low solubility. We were able to overcome this problem both by further mutagenesis of the framework and by addition of a solubilizing motif. The minibody is being used to select constrained human IL-6 peptidic ligands from a library displayed on the surface of the f1 bacteriophage.
MECHANISMS OF INTRAVITREAL TOXICITY OF INDOCYANINE GREEN DYE (2007)

Much evidence supports that ICG dye has a dose-dependent toxic effect on the retina. Therefore, the following recommendations to minimize toxic effects on the retina are proposed: dye injection in concentrations as low as possible; avoidance of repeated ICG injections onto bare retina; dye injection far from the macular hole to prevent direct dye contact with the RPE; short incubation time of ICG in the vitreous cavity to diminish the concentration in contact with the retinal tissue; and the light pipe kept far from the retina throughout the whole surgical procedure.