gebhart/patrepeval huggingface dataset:
RNA interference: A novel tool for plant disease management (2013)

Plant diseases pose a huge threat to crop production globally. Variations in their genomes cause selection to favor those who can survive pesticides and Bacillus thuringiensis (Bt) crops. Though plant breeding has been the classical means of manipulating the plant genome to develop resistant cultivar for controlling plant diseases, the advent of genetic engineering provides an entirely new approach being pursued to render plants resistant to fungi, bacteria, viruses and nematodes. RNA interference (RNAi) technology has emerged to be a promising therapeutic weapon to mitigate the inherent risks such as the use of a specific transgene, marker gene, or gene control sequences associated with development of traditional transgenics. Silencing specific genes by RNAi is a desirable natural solution to this problem as disease resistant transgenic plants can be produced within a regulatory framework. Recent studies have been successful in producing potent silencing effects by using target double-stranded RNAs through an effective vector system. Transgenic plants expressing RNAi vectors, as well as, dsRNA containing crop sprays have been successful for efficient control of plant pathogens affecting economically important crop species. The present paper discusses strategies and applications of this novel technology in plant disease management for sustainable agriculture production.

	 

	Key words: Plant disease, RNA interference, transgene, management.
Growth stimulation of colorectal carcinoma cells via the c-kit receptor is inhibited by TGF-β1 (1997)

Activation of the receptor tyrosine kinase c-kit by the kit-ligand, also known as stem cell factor (SCF), is essential to melanocyte and germ cell development and during the early stages of hematopoiesis. Deregulated expression of c-kit has been reported in malignancies affecting these lineages, i.e., myeloid leukemias, melanomas, and germ cell tumors. In addition, c-kit and SCF are coexpressed in some breast and colorectal cancer (CRC) cells, raising the question of whether c-kit serves an autocrine role in normal or malignant epithelial tissues. In this study, we demonstrate that human colorectal carcinomas, but not normal colorectal mucosa cells, coexpress SCF and c-kit in situ. Expression of c-kit was also observed in mucosa adjacent to colorectal tumor tissue. Consistent with a growth-regulatory role of SCF in CRC cells, exogenous SCF stimulated anchorage-dependent and anchorage-independent growth in four out of five CRC cell lines. Exogenous transforming growth factor (TGF)-beta 1 added at nanomolar concentrations to HT-29 CRC cells, which express the type I, II, and III TGF-beta receptors, downregulated c-kit expression to background levels and inhibited c-kit-dependent proliferation. Similarly, TGF-beta 1 inhibited SCF-dependent proliferation of three first-passage CRC cell lines. In summary, expression of the potential autocrine SCF/ c-kit axis is a tumor-associated phenomenon in colorectal cancer that can be suppressed by TGF-beta 1 in TGF-beta-responsive CRC cells.
Molecular cloning of the human XRCC1 gene, which corrects defective DNA strand break repair and sister chromatid exchange. (1990)

We describe the cloning and function of the human XRCC1 gene, which is the first mammalian gene isolated that affects cellular sensitivity to ionizing radiation. The CHO mutant EM9 has 10-fold-higher sensitivity to ethyl methanesulfonate, 1.8-fold-higher sensitivity to ionizing radiation, a reduced capacity to rejoin single-strand DNA breaks, and a 10-fold-elevated level of sister chromatid exchange compared with the CHO parental cells. The complementing human gene was cloned from a cosmid library of a tertiary transformant. Two cosmid clones produced transformants that showed approximately 100% correction of the repair defect in EM9 cells, as determined by the kinetics of strand break repair, cell survival, and the level of sister chromatid exchange. A nearly full-length clone obtained from the pcD2 human cDNA expression library gave approximately 80% correction of EM9, as determined by the level of sister chromatid exchange. Based on an analysis of the nucleotide sequence of the cDNA insert compared with that of the 5' end of the gene from a cosmid clone, the cDNA clone appeared to be missing approximately 100 bp of transcribed sequence, including 26 nucleotides of coding sequence. The cDNA probe detected a single transcript of approximately 2.2 kb in HeLa polyadenylated RNA by Northern (RNA) blot hybridization. From the open reading frame and the positions of likely start sites for transcription and translation, the size of the putative XRCC1 protein is 633 amino acids (69.5 kDa). The size of the XRCC1 gene is 33 kb, as determined by localizing the endpoints on a restriction endonuclease site map of one cosmid clone. The deduced amino acid sequence did not show significant homology with any protein in the protein sequence data bases examined.
Collagen Matrix in Spinal Cord Injury (2006)

The fibrous scar that develops after central nervous system (CNS) injury is considered a major impediment for axonal regeneration. It consists of a dense collagen IV meshwork, which serves as a binding matrix for numerous other extracellular matrix components and inhibitory molecules like proteoglycans and semaphorins, but also growth-promoting factors. Inhibition of collagen matrix formation in brain and spinal cord lesions leads to axonal regeneration and functional recovery, although collagen IV per se is not inhibitory for axonal outgrowth. This review focuses on the molecular properties of the collagen IV matrix and its interactions with various molecules that are expressed after CNS lesion. Moreover, studies on collagen expression and matrix formation after injury of regenerating versus non-regenerating nervous systems are reviewed. Major differences in collagen deposition in the CNS and the peripheral nervous system (PNS) and differences in specific cell responses to extracellular matrix deposition in the lesion area are discussed. Therapeutic treatments aiming at suppression of fibrous scarring have been shown to promote axon regeneration in various lesion paradigms of the mammalian CNS.
Threading dislocation reduction via laterally overgrown nonpolar (1120) a-plane GaN (2002)

Threading dislocation density reduction of nonpolar (112̄0) a-plane GaN films was achieved by lateral epitaxial overgrowth (LEO). We report on the dependence of morphology and defect reduction on crystallographic stripe orientation. Stripes aligned along [0001] and [1̄100], the most favorable a-plane GaN LEO stripe orientations, possessed well-behaved, symmetric morphologies. Threading dislocation reduction via mask blocking was observed by transmission electron microscopy for [1̄100] stripes which had optimal rectangular cross-sections. Cathodoluminescence studies showed increased light emission for the overgrown regions in comparison to the window regions. The extent of lateral overgrowth of these stripes was asymmetric due to the opposing polarities of the vertical c-plane sidewalls. Conversely, threading dislocations propagated into the symmetric overgrown regions of [0001] stripes which possessed coexisting inclined and vertical {101̄0} facets.
Miniaturized flow-through PCR with different template types in a silicon chip thermocycler (2001)

Flow-through chip thermocyclers can be used in miniaturized rapid polymerase chain reaction (PCR) despite their high surface to volume ratio of samples. We demonstrated that a thermocycler made of silicon and glass chips and containing thin film transducers for heating and temperature control can be adapted to the amplification of various DNA templates of different sources and properties. Therefore, the concept of serial flow in a liquid/liquid two-phase system was combined with a surface management of inner side walls of the microchannel and an adaptation of PCR mixture composition. In addition, the process temperatures and the flow rates were optimized. Thus, a synthetic template originating from investigations on nucleic acid evolution with 106 base pairs [cooperative amplification of templates by cross hybridization (CATCH)], a house keeping gene with 379 base pairs [glutaraldehyde 3-phosphate dehydrogenase (GAPDH)] and a zinc finger protein relevant in human pathogenesis with 700 base pairs [Myc-interacting zinc finger protein-1, knock-out (Miz1-KO)] were amplified successfully. In all three cases the selectivity of priming and amplification could be shown by gel electrophoresis. The typical amplification time was 1 min per temperature cycle. So, the typical residence time of a sample volume inside the 25 cycle device amounts to less then half an hour. The energy consumption of the PCR chip for a 35 min PCR process amounts to less than 0.012 kW h.
Monoclonal antibodies capable of binding SARS-CoV-2 spike protein receptor-binding motif specifically prevent GM-CSF induction (2021)

A severe acute respiratory syndrome (SARS)-like coronavirus 2 (SARS-CoV-2) has recently caused a pandemic COVID-19 disease that infected approximately 94 million and killed more than 2,000,000 people worldwide. Like the SARS-CoV, SARS-CoV-2 also employs a receptor-binding motif (RBM) of its envelope spike protein for binding the host angiotensin-converting enzyme 2 (ACE2) to gain viral entry. Currently, extensive efforts are being made to produce vaccines against a surface fragment of a SARS-CoV-2, such as the spike protein, in order to boost protective antibodies that can inhibit virus-ACE2 interaction to prevent viral entry. It was previously unknown how spike protein-targeting antibodies would affect innate inflammatory responses to SARS-CoV-2 infections. Here we generated a highly purified recombinant protein corresponding to the RBM of SARS-CoV-2, and used it to screen for cross-reactive monoclonal antibodies (mAbs). We found two RBM-binding mAbs that competitively inhibited its interaction with human ACE2, and specifically blocked the RBM-induced GM-CSF secretion in both human peripheral blood mononuclear cells and murine macrophage cultures. Our findings have suggested a possible strategy to prevent SARS-CoV-2-elicited "cytokine storm," and revealed a potentially anti-inflammatory and protective mechanism for SARS-CoV-2 spike-based vaccines.
A Pilot Study of Circulating miRNAs as Potential Biomarkers of Early Stage Breast Cancer (2010)

Our observations from this pilot study suggest that the altered levels of circulating miRNAs might have great potential to serve as novel, noninvasive biomarkers for early detection of breast cancer.
Synthesis and duplex stability of oligonucleotides containing cytosine-thymine analogues (1989)

The synthesis of the deoxynucleoside derived from the base P, 6H,8H-3,4-dihydro-pyrimido[4,5-c] [4,5-c] [1,2]oxazin-7-one, 2, and its introduction by established phosphoramidite and H-phosphonate chemistry into oligonucleotides is described. The melting transition temperatures (Tm) of a range of heptadecamer duplexes containing P/A and P/G base-pairs are compared with corresponding ones having N4-methoxycytosine (M) 1 and mismatched normal bases. P/A and P/G pairs allow closely similar duplex stabilities and have the potential to reduce the multiplicity of probes and primers based on amino acid sequences by removing the T/C degeneracy.
Pexophagy: The Selective Degradation of Peroxisomes (2012)

Peroxisomes are single-membrane-bounded organelles present in the majority of eukaryotic cells. Despite the existence of great diversity among different species, cell types, and under different environmental conditions, peroxisomes contain enzymes involved in β-oxidation of fatty acids and the generation, as well as detoxification, of hydrogen peroxide. The exigency of all eukaryotic cells to quickly adapt to different environmental factors requires the ability to precisely and efficiently control peroxisome number and functionality. Peroxisome homeostasis is achieved by the counterbalance between organelle biogenesis and degradation. The selective degradation of superfluous or damaged peroxisomes is facilitated by several tightly regulated pathways. The most prominent peroxisome degradation system uses components of the general autophagy core machinery and is therefore referred to as "pexophagy." In this paper we focus on recent developments in pexophagy and provide an overview of current knowledge and future challenges in the field. We compare different modes of pexophagy and mention shared and distinct features of pexophagy in yeast model systems, mammalian cells, and other organisms.
Abstract B124: Preclinical development of a novel therapeutic antibody to treat pancreas and colorectal cancers (2009)

Abstract NPC-1C is a chimeric monoclonal antibody being developed as a novel biological treatment for pancreatic and colorectal cancers. This antibody was selected from a panel of hybridomas generated from mice immunized with semi-purified membrane-associated proteins derived from biologically screened, pooled human allogeneic colon cancer tissues. NPC-1C appears to recognize an aberrantly expressed form of MUC5AC expressed specifically by human colon and pancreatic tumor tissues and cell lines. NPC-1C does not cross-react with normal human tissues (and with MUC5AC from other type of cancers), however, except for occasional, weak binding to certain GI tract tissues, which may indicate a pre-malignant state. In vitro, the NPC-1C antibody exhibits specific ADCC activity against human colon and pancreatic tumor cells, but not against control tumor cell lines. In vivo, the anti-tumor efficacy of NPC-1C was tested using preestablished subcutaneous human pancreatic tumor xenograft models. The data showed significant, and reproducible, anti-tumor action, including some complete tumor regressions. The clinical application for this antibody was bolstered by several examples of human tumor tissues were stained with biotin-conjugated NPC-1C which show a strong correlation of NPC-1C staining against pancreatic and colon tumors, with approximately 45% of tumors staining strongly positive. The staining pattern was typical of mucin expression, but also showed cytoplasmic and cell membrane staining. The pre-clinical toxicity profile of NPC-1C in normal BALB/c mice demonstrated little, if any, toxicity following single or multiple intravenous injections of 10 mg/kg, 50 mg/kg, or 100 mg/kg of clinical-grade NPC-1C antibody. Toxicity parameters measured include body weight, food consumption, complete blood analysis, serum chemistries, gross pathology, and microscopic histopathology. The bio-distribution of radio-labeled NPC-1C in mice with pre-established subcutaneous human tumors revealed specific accumulation of NPC-1C at the tumor site, with little or no binding or accumulation in several major organ systems. Finally, we studied the cytokine and antibody responses to NPC-1C in the pre-clinical mouse model. Although anti-NPC-1C antibodies were detected (as expected) in a time-dependent fashion, we did not detect changes in Type I (IL-2 or g-IFN) and Type II (IL-4 or IL-5) cytokines in response to up to 100 mg/kg of NPC-1C either 3 days or 14 days after intravenous administration. The pre-clinical development of NPC-1C indicates that it is safe and efficacious, and suggest that it should be well-tolerated and may have clinical activity in patients whose tumor expresses the altered MUC5AC epitope. The FDA has approved the Investigational New Drug (IND) application to initiate a Phase I clinical trial with NPC-1C for patients with advanced pancreatic and colorectal cancer. Citation Information: Mol Cancer Ther 2009;8(12 Suppl):B124.
<title>Flow and congestion control for Internet media streaming applications</title> (1997)

The emergence of streaming multimedia players provides users with low latency audio and video content over the Internet. Providing high-quality, best-effort, real-time multimedia content requires adaptive delivery schemes that fairly share the available network bandwidth with reliable data protocols such as TCP. This paper proposes a new flow and congestion control scheme, SCP (streaming control protocol), for real- time streaming of continuous multimedia data across the Internet. The design of SCP arose from several years of experience in building and using adaptive real-time streaming video players. SCP addresses two issues associated with real- time streaming. First, it uses a congestion control policy that allows it to share network bandwidth fairly with both TCP and other SCP streams. Second, it improves smoothness in streaming and ensures low, predictable latency. This distinguishes it from TCP's jittery congestion avoidance policy that is based on linear growth and one-half reduction of its congestion window. In this paper, we present a description of SCP, and an evaluation of it using Internet- based experiments.
Site-directed Mutagenesis of Vacuolar H+-pyrophosphatase (1995)

A characteristic feature of the vacuolar H(+)-translocating inorganic pyrophosphatase (V-PPase) of plant cells is its high sensitivity to irreversible inhibition by N-ethylmaleimide (NEM) and other sulfhydryl reagents. Previous investigations in this laboratory have demonstrated that the primary site for substrate-protectable covalent modification of the V-PPase by 14C-labeled NEM maps to a single M(r) 14,000 V8 protease fragment (V8(14)K) (Zhen, R.-G., Kim, E. J., and Rea, P. A. (1994) J. Biol. Chem. 269, 23342-23350). Here, we describe site-directed mutagenesis of the cDNA encoding the V-PPase from Arabidopsis thaliana, its heterologous expression in Saccharomyces cerevisiae and single substitution of all 9 conserved Cys residues to either Ser or Ala. In all cases, except one, Cys mutagenesis exerts little or no effect on either the catalytic activity or susceptibility of the enzyme to inhibition by NEM. By contrast, and in complete agreement with the results of peptide mapping experiments, substitution of Cys634, the sole conserved cysteine residue encompassed by V8(14)K, with Ser or Ala generates enzyme that is insensitive to NEM but active in both PPi hydrolysis and PPi-dependent H+ translocation. The specific requirement for Cys634 for inhibition by NEM and the dispensability of all of the conserved Cys residues, including Cys634, for V-PPase function indicate that the inhibitory action of maleimides reflects steric constraints imposed by the addition of a substituted alkyl group to the side chain of Cys634 rather than direct participation of this amino acid residue in catalysis.
Nitric oxide synthase is expressed in the lymphomononuclear cells of synovial fluid in patients with rheumatoid arthritis. (1999)

SF mononuclear cells from patients with RA express iNOS and are involved in NO production in the joint. The number of positive cells is correlated with CRP concentration, suggesting the implication of NO production in the inflammatory process.
Strong TCR Ligation Without Costimulation Causes Rapid Onset of Fas-Dependent Apoptosis of Naive Murine CD4+ T Cells (1999)

Activation-induced cell death of T cells typically occurs late in the primary response after a prior proliferative response. Here, we describe a novel form of cell death in which purified naive murine CD4+ cells undergo apoptosis within 18 h in vitro after strong TCR ligation. Such rapid-onset TCR-mediated death of T cells does not involve cell division and is Fas-dependent, inhibited by CD28 (and IL-6) costimulation and enhanced by IL-4 and IL-7; by contrast, spontaneous death of CD4+ cells cultured alone is Fas-independent and inhibited by IL-4 and IL-7. TCR-mediated Fas-dependent death of CD4+ cells is prevented by combined TCR/Fas ligation and by drugs that inhibit calcineurin-dependent signaling and mitogen-activated protein kinase MEK1 activation.
IDH2 mutations are frequent in angioimmunoblastic T-cell lymphoma (2012)

Mutations in isocitrate dehydrogenase 1 (IDH1) and isocitrate dehydrogenase 2 (IDH2) occur in most grade 2 and 3 gliomas, secondary glioblastomas, and a subset of acute myelogenous leukemias but have not been detected in other tumor types. The mutations occur at specific arginine residues and result in the acquisition of a novel enzymatic activity that converts 2-oxoglutarate to D-2-hydroxyglutarate. This study reports IDH1 and IDH2 genotyping results from a set of lymphomas, which included a large set of peripheral T-cell lymphomas. IDH2 mutations were identified in approximately 20% of angioimmunoblastic T-cell lymphomas (AITLs), but not in other peripheral T-cell lymphoma entities. These results were confirmed in an independent set of AITL patients, where the IDH2 mutation rate was approximately 45%. This is the second common genetic lesion identified in AITL after TET2 and extends the number of neoplastic diseases where IDH1 and IDH2 mutations may play a role.
Intestinal Infection of Neonatal Dogs with Canine Coronavirus 1-71: Studies by Virologic, Histologic, Histochemical, and Immunofluorescent Techniques (1976)

Enteritis induced in neonatal dogs by oral inoculation of coronavirus 1-71 was studied by virologic, histologic, histochemical, and immunofluorescent antibody methods. The enteritis, accompanied by diarrhea, developed in 4 to 7 days and was characterized by atrophy and fusion of intestinal villi and deepening of crypts, increase in cellularity of the lamina propria, flattening of epithelial cells, and discharge of goblet cells. Intra-epithelial enzyme activities generally were depressed. Specific immunofluorescent antibody reactions were present in villous epithelium of the duodenum starting on postinoculation day 2 and of the ileum on day 4. Epiehtlium of the colon showed no reaction. Virus was present in the feces for 6 to 9 days and was recovered from the small and large intestines from day 2 through day 10. The infection was not fatal and was self limiting; the diarrhea stopped between 1 and 2 weeks. The intestinal mucosa also started recovering by the end of week 1, proceeding caudally from the duodenum.
A NUMERICAL STUDY ON TIME- REVERSAL ELECTROMAGNETIC WAVE FOR INDOOR ULTRA-WIDEBAND SIGNAL TRANSMISSION (2007)

In this paper, the propagation of ultra-wideband (UWB) pulse based on time reversal (TR) technique is studied by finitedifferent time-domain method in indoor environment. Time compression and spatial focusing of TR waveform are simulated and the propagation of multi-waveform string is analyzed. Then UWB wireless signal transmission based on TR concept is studied numerically. The studied results indicate that the UWB communication based on TR technique can obtain better Inter-Symbol Interference (ISI) and Co-Channel Interference (CCI) performance than traditional one because of its unique property.