gebhart/patrepeval huggingface dataset:
Emergence of a New Cucurbit-Infecting Begomovirus Species Capable of Forming Viable Reassortants with Related Viruses in the Squash leaf curl virus Cluster (2002)

ABSTRACT Cucurbit leaf curl virus (CuLCV), a whitefly-transmitted geminivirus previously partially characterized from the southwestern United States and northern Mexico, was identified as a distinct bipartite begomovirus species. This virus has near sequence identity with the previously partially characterized Cucurbit leaf crumple virus from California. Experimental and natural host range studies indicated that CuLCV has a relatively broad host range within the family Cucurbitaceae and also infects bean and tobacco. The genome of an Arizona isolate, designated CuLCV-AZ, was cloned and completely sequenced. Cloned CuLCV-AZ DNA A and B components were infectious by biolistic inoculation to pumpkin and progeny virus was transmissible by the whitefly vector, Bemisia tabaci, thereby completing Koch's postulates. CuLCV-AZ DNA A shared highest nucleotide sequence identity with Squash leaf curl virus-R (SLCV-R), SLCV-E, and Bean calico mosaic virus (BCaMV) at 84, 83, and 80%, respectively. The CuLCV DNA B component shared highest nucleotide sequence identity with BCaMV, SLCV-R, and SLCV-E at 71, 70, and 68%, respectively. The cis-acting begomovirus replication specificity element, GGTGTCCTGGTG, in the CuLCV-AZ origin of replication is identical to that of SLCV-R, SLCV-E, and BCaMV, suggesting that reassortants among components of CuLCV-AZ and these begomoviruses may be possible. Reassortment experiments in pumpkin demonstrated that both reassortants of CuLCV-AZ and SLCV-E A and B components were viable. However, for CuLCV-AZ and SLCV-R, only one reassortant (SLCV-R DNA A/CuLCV-AZ DNA B) was viable on pumpkin, even though the cognate component pairs of both viruses infect pumpkin. These results demonstrate that reassortment among sympatric begomovirus species infecting cucurbits are possible, and that, if generated in nature, could result in begomoviruses bearing distinct biological properties.
Substitutions Near the Receptor Binding Site Determine Major Antigenic Change During Influenza Virus Evolution (2013)

The molecular basis of antigenic drift was determined for the hemagglutinin (HA) of human influenza A/H3N2 virus. From 1968 to 2003, antigenic change was caused mainly by single amino acid substitutions, which occurred at only seven positions in HA immediately adjacent to the receptor binding site. Most of these substitutions were involved in antigenic change more than once. Equivalent positions were responsible for the recent antigenic changes of influenza B and A/H1N1 viruses. Substitution of a single amino acid at one of these positions substantially changed the virus-specific antibody response in infected ferrets. These findings have potentially far-reaching consequences for understanding the evolutionary mechanisms that govern influenza viruses.
Write Control Method For High Density Magneto-optical Dim System (1993)

Toward the product of first generation magnet-optical disk, the recording technique using the mark position recording method has been developed, by which the density of 400Mb/in² is attained. In order to increase the density.the technique combined with the mark edge recording method and zoned CAV method is suitable. In the write-once optical disk system of 12" size this technique has been first adopted and the density of 550Mb/in² is realized[l]. In the case of magnet-optical media the control of recording mark edge position and shape which is important for the mark edge recording method is hardly realized because of its higher thermal conductivity. Moreover, this characteristics is sensitive against the environmental temperature.
Development of the precerebellar nuclei in the rat: I. The precerebellar neuroepithelium of the rhombencephalon (1987)

Short-survival thymidine radiograms from rat embryos aged 13-19 days were analyzed to delineate the precerebellar neuroepithelium of the rhombencephalon. The original definition of the term "rhombencephalon" was modified to refer only to the unique dorsal portion (surface plate) of the medulla and pons where the neural groove fails to fuse and, instead, the medullary velum covers the rhomboid lumen of the fourth ventricle. Initially, the neuroepithelial tissue of the rhombencephalon consists of a pair of rostral and caudal bridgeheads: the former the primary neuroepithelium of the cerebellum and the latter the primary neuroepithelium of the octavo-precerebellar system. The spatial relationship between the cerebellar and precerebellar neuroepithelia soon changes as a result of ongoing morphogenetic events, such that the cerebellar primordium assumes a dorsal position and the precerebellar primordium a ventral position, and the distance between the two decreases. Concurrently the tela choroidea invaginates into the fourth ventricle and a secondary precerebellar neuroepithelium develops. The rostral portion of the secondary precerebellar neuroepithelium grows forward along the choroid plexus and forms the medial recess of the anterior fourth ventricle, while its caudal portion grows in the opposite direction beneath the medullary velum and forms the rostral wall of the posterior fourth ventricle. Evidence will be presented in the succeeding papers that the primary precerebellar neuroepithelium first generates the neurons of the inferior olive that migrate by a circumferential intramural (parenchymal) route to their destination. Next, the neurons of the lateral reticular and external cuneate nuclei are generated. These migrate by a posterior extramural (superficial) route and settle contralaterally. Subsequently, the primary precerebellar neuroepithelium produces the neurons of the nucleus reticularis tegmenti pontis and these form the anterior extramural migratory stream and settle ipsilaterally. Finally, the secondary precerebellar neuroepithelium produces the latest generated neurons of the basal pontine gray that follow the anterior extramural stream and settle ipsilaterally.
Unusual Naphthoquinone Derivatives from the Twigs of Avicennia marina (2007)

In a continuing search for novel bioactive compounds from marine mangrove plants, seven new naphthoquinone derivatives were isolated from Avicennia marina, namely, avicennone A (1), avicennone B (2), avicennone C (3), avicennone D (4), avicenone E (5), avicennone F (6), and avicennone G (7), along with the known compounds avicequinone A (8), stenocarpoquinone B (9), avicequinone C (10), avicenol A (11), and avicenol C (12). The chemical structures of 1-7 were elucidated by spectroscopic methods. Compounds 8-10, and a mixture of 4 and 5, which all contain a 4,9-dione group, showed strong antiproliferative and moderate cytotoxic activities, as well as antibacterial effects.
Role of Supplemental Calcium in the Recurrence of Colorectal Adenomas: A Metaanalysis of Randomized Controlled Trials (2005)

This systematic review and meta-analysis suggest that calcium supplementation prevents recurrent colorectal adenomas.
Phenotypic correction and long-term expression of factor VIII in hemophilic mice by immunotolerization and nonviral gene transfer using the Sleeping Beauty transposon system (2004)

Hemophilia A is a lead candidate for treatment by gene therapy because small increments in the missing secreted protein product, coagulation factor VIII (FVIII), would result in substantial clinical amelioration. Clinically relevant therapy might be achieved by stably delivering a human FVIII cDNA to correct the bleeding disorder. We used the Sleeping Beauty (SB) transposon, delivered as naked plasmid DNA by tail-vein injection, to integrate B-domain-deleted FVIII genes into the chromosomes of hemophilia A mice and correct the phenotype. Since FVIII protein is a neoantigen to these mice, sustaining therapeutic plasma FVIII levels was problematic due to inhibitory antibody production. We circumvented this problem by tolerizing 82% of neonates by a single facial-vein injection of recombinant FVIII within 24 hours of birth (the remaining 18% formed inhibitors). Achievement of high-level (10%-100% of normal) FVIII expression and phenotypic correction required co-injection of an SB transposase-expressing plasmid to facilitate transgene integration in immunotolerized animals. Linker-mediated polymerase chain reaction was used to clone FVIII transposon insertion sites from liver genomic DNA, providing molecular evidence of transposition. Thus, SB provides a nonviral means for sustained FVIII gene delivery in a mouse model of hemophilia A if the immune response is prevented.
Semantics + filtering + search = twitcident. exploring information in social web streams (2012)

Automatically filtering relevant information about a real-world incident from Social Web streams and making the information accessible and findable in the given context of the incident are non-trivial scientific challenges. In this paper, we engineer and evaluate solutions that analyze the semantics of Social Web data streams to solve these challenges. We introduce Twitcident, a framework and Web-based system for filtering, searching and analyzing information about real-world incidents or crises. Given an incident, our framework automatically starts tracking and filtering information that is relevant for the incident from Social Web streams and Twitter particularly. It enriches the semantics of streamed messages to profile incidents and to continuously improve and adapt the information filtering to the current temporal context. Faceted search and analytical tools allow people and emergency services to retrieve particular information fragments and overview and analyze the current situation as reported on the Social Web.
The NsrR regulon in nitrosative stress resistance of Salmonella enterica serovar Typhimurium (2012)

Nitric oxide (NO·) is an important mediator of innate immunity. The facultative intracellular pathogen Salmonella has evolved mechanisms to detoxify and evade the antimicrobial actions of host-derived NO· produced during infection. Expression of the NO·-detoxifying flavohaemoglobin Hmp is controlled by the NO·-sensing transcriptional repressor NsrR and is required for Salmonella virulence. In this study we show that NsrR responds to very low NO· concentrations, suggesting that it plays a primary role in the nitrosative stress response. Additionally, we have defined the NsrR regulon in Salmonella enterica sv. Typhimurium 14028s using transcriptional microarray, qRT-PCR and in silico methods. A novel NsrR-regulated gene designated STM1808 has been identified, along with hmp, hcp-hcr, yeaR-yoaG, ygbA and ytfE. STM1808 and ygbA are important for S. Typhimurium growth during nitrosative stress, and the hcp-hcr locus plays a supportive role in NO· detoxification. ICP-MS analysis of purified STM1808 suggests that it is a zinc metalloprotein, with histidine residues H32 and H82 required for NO· resistance and zinc binding. Moreover, STM1808 and ytfE promote Salmonella growth during systemic infection of mice. Collectively, these findings demonstrate that NsrR-regulated genes in addition to hmp are important for NO· detoxification, nitrosative stress resistance and Salmonella virulence.
RETRACTED: Identification of a coronary vascular progenitor cell in the human heart (2009)

Primitive cells capable of generating small resistance arterioles and capillary structures in the injured myocardium have been identified repeatedly. However, these cells do not form large conductive coronary arteries that would have important implications in the management of the ischemic heart. In the current study, we determined whether the human heart possesses a class of progenitor cells that regulates the growth of endothelial cells (ECs) and smooth muscle cells (SMCs) and vasculogenesis. The expression of vascular endothelial growth-factor receptor 2 (KDR) was used, together with the stem cell antigen c-kit, to isolate and expand a resident coronary vascular progenitor cell (VPC) from human myocardial samples. Structurally, vascular niches composed of c-kit-KDR-positive VPCs were identified within the walls of coronary vessels. The VPCs were connected by gap junctions to ECs, SMCs, and fibroblasts that operate as supporting cells. In vitro, VPCs were self-renewing and clonogenic and differentiated predominantly into ECs and SMCs and partly into cardiomyocytes. To establish the functional import of VPCs, a critical stenosis was created in immunosuppressed dogs, and tagged human VPCs were injected in proximity to the constricted artery. One month later, there was an increase in coronary blood flow (CBF) distal to the stenotic artery, resulting in functional improvement of the ischemic myocardium. Regenerated large, intermediate, and small human coronary arteries and capillaries were found. In conclusion, the human heart contains a pool of VPCs that can be implemented clinically to form functionally competent coronary vessels and improve CBF in patients with ischemic cardiomyopathy.
Aspartyl protease from Trichoderma harzianum CECT 2413: cloning and characterization The GenBank/EMBL/DDBJ accession number for the sequence reported in this paper is AJ276388. (2002)

A gene that encodes an extracellular aspartyl protease from Trichoderma harzianum CECT 2413, papA, has been isolated and characterized. Based on several conserved regions of other fungal acid proteases, primers were designed to amplify a probe that was used to isolate the papA gene from a genomic library of T. harzianum. papA was an intronless ORF which encoded a polypeptide of 404 aa, including a prepropeptide at the N-terminal region formed by one putative signal peptide, a second peptide which could be cleaved to activate the enzyme and the active protease of calculated 36·7 kDa and pI 4·35. Northern experiments indicated that papA gene was pH regulated, repressed by ammonium, glucose and glycerol, and induced by organic nitrogen sources. The promoter possessed potential AreA, PacC and MYC sites for nitrogen, pH and mycoparasitism regulation respectively, but lacked potential CreA sites for carbon regulation. IEF and zymograms indicated that PAPA was a pepstatin-sensitive aspartyl protease of pI 4·5. Transformants from T. harzianum CECT 2413 cultivated in yeast extract-supplemented medium overexpressed papA and had a fourfold increase in protease activity compared to the wild-type, while transformants that overexpressed the β-1,6-glucanase gene bgn16.2 and papA had an additional 30% increase in β-1,6-glucanase activity compared to bgn16.2 single transformants. Overexpression of both genes in ammonium-supplemented medium did not result in higher levels of PAPA and/or BGN16.2 proteins. These results indicated that both PAPA and β-1,6-glucanase undergo proteolysis in ammonium-supplemented medium but PAPA is not responsible for β-1,6-glucanase degradation.
Semi-synthesis of Polymyxin B (2-10) and Colistin (2-10) Analogs Employing the Trichloroethoxycarbonyl (Troc) Group for Side Chain Protection of .ALPHA.,.GAMMA.-Diaminobutyric Acid Residues (2007)

Improved strategies for the chemical conversion of natural polymyxin B and colistin to their N-terminal analogs are reported. First, the protection of the side chains of five L-alpha,gamma-diaminobutyric acid (Dab) residues in natural polymyxin B and colistin was achieved with trichloroethoxycarbonyl (Troc), then the resulting pentakis(N gamma-Troc)-polymyxin B and pentakis(N gamma)Troc)-colistin were treated with trifluoroacetic acid (TFA) : methanesulfonic acid (MSA) : dimethylformamide (DMF) : H2O (10 : 30 : 55 : 5) at 40 degrees C in order to remove N alpha-alkanoyl-Dab(Troc)-OH selectively. The new key compounds, tetrakis(N gamma-Troc)-polymyxin B (2-10) and tetrakis(N gamma-Troc)-colistin (2-10), were obtained in 19% and 15% yields, respectively, which is higher than previous reports using trifluoroacetyl (Tfa) for tetrakis(N gamma-Tfa)-polymyxin B (2-10) and tetrakis(N gamma-Tfa)-colistin (2-10), respectively. Acylation of tetrakis(N gamma-Troc)-polymyxin B (2-10) and tetrakis(N gamma-Troc)-colistin (2-10) with various hydrophobic acids bearing aliphatic or aromatic ring structures, followed by the deprotection of Troc by Zn in AcOH, produced polymyxin B (2-10) and colistin (2-10) analogs which were used for structure-activity relationship studies. It was found that cyclohexylbutanoyl-, 4-biphenylacetyl-, and 1-adamantaneacetyl-polymyxin B (2-10) showed potent antimicrobial activity equal to that of polymyxin B against three Gram-negative bacterial strains. The lipopolysacharide (LPS) binding activity of cyclohexylbutanoyl-, 4-biphenylacetyl-, and cyclododecanecarbonyl-polymyxin B (2-10) increased greatly in comparison with that of polymyxin B (2-10). The various N alpha-acylated polymyxin B (2-10) analogs showed slightly higher antimicrobial and LPS binding activities than the corresponding N alpha-acylated colistin (2-10) analogs.
[In vitro study of the cefamandole-fosfomycin combination against methicillin-resistant staphylococci]. (1984)

In vitro antibacterial activity of cefamandole-fosfomycin (CFM-FOS) combination was studied on 50 methicillin-resistant staphylococci strains. Anti-bacterial effects were evaluated with a bactericidal microtiter checkerboard method. CFM-FOS was compared with other combinations known to be potent against staphylococci. Synergy was consistently recorded with CFM-FOS. Mean MBC of CFM combined with FOS was 1 microgram/ml. Vancomycin-fosfomycin combination was infrequently synergistic (20%). Rifampin-fosfomycin, cefamandole-fusidic acid, and cloxacillin-fusidic acid combinations were usually antagonistic at bactericidal levels. Rifampicin-fusidic acid combination usually yielded additive effects. CFM-FOS killed most methicillin-resistant staphylococci studied at therapeutic concentrations.
Aneuploidy and cancer (2000)

Numeric aberrations in chromosomes, referred to as aneuploidy, is commonly observed in human cancer. Whether aneuploidy is a cause or consequence of cancer has long been debated. Three lines of evidence now make a compelling case for aneuploidy being a discrete chromosome mutation event that contributes to malignant transformation and progression process. First, precise assay of chromosome aneuploidy in several primary tumors with in situ hybridization and comparative genomic hybridization techniques have revealed that specific chromosome aneusomies correlate with distinct tumor phenotypes. Second, aneuploid tumor cell lines and in vitro transformed rodent cells have been reported to display an elevated rate of chromosome instability, thereby indicating that aneuploidy is a dynamic chromosome mutation event associated with transformation of cells. Third, and most important, a number of mitotic genes regulating chromosome segregation have been found mutated in human cancer cells, implicating such mutations in induction of aneuploidy in tumors. Some of these gene mutations, possibly allowing unequal segregations of chromosomes, also cause tumorigenic transformation of cells in vitro. In this review, the recent publications investigating aneuploidy in human cancers, rate of chromosome instability in aneuploidy tumor cells, and genes implicated in regulating chromosome segregation found mutated in cancer cells are discussed.
Synthesis of biologically active novel bis Schiff bases, bis hydrazone and bis guanidine derivatives (2009)

A number of bis Schiffs bases 3a-d havc been synthesized by condensation of 2,4,8.10 tetraoxaspiro[5,5]undecane 3,9-dipropanamine 1 with furfural, indole-3-aldehyde, 2-acetylpyridine. 4-acetylpyridine and 5a-c by condensation of 1,4-bis (3-aminopropyl) piperazine 4 with indole-3-aldehyde, 2-acetylpyridine, 4-acetylpyridine, in high yields by using microwave irradiation. Bis hydrazone derivatives 8a-c arc obtained by condensation of 2,6-diacetylpyridine 7 with various arylsulfonylhydrazides using microwave irradiation. A number of bis guanidinc derivatives 11a-j arc synthesized by condensation of 1,3-diaminoguanidine monohydrochloride 10 with various aldehydes 9a-c and ketones 9d-j. The structurcs assigned to these purified compounds i.e 3a-d, 5a-c, 8a-c, and 11a-j, arc supported by correct spectral data and elemental analysis. Anti-inflammatory activities of 3b and 11c arc comparable to standard drug phenyl butazone. Analgesic activities of 11c and 3b arc compared with phenyl butazone and 3b showed better activity then phenyl butazone.
Bitmap Movement Detection: HDR for Dynamic Scenes (2010)

Exposure Fusion and other HDR techniques generate well-exposed images from a bracketed image sequence while reproducing a large dynamic range that far exceeds the dynamic range of a single exposure. Common to all these techniques is the problem that the smallest movements in the captured images generate artefacts (ghosting) that dramatically affect the quality of the final images. This limits the use of HDR and Exposure Fusion techniques because common scenes of interest are usually dynamic. We present a method that adapts Exposure Fusion, as well as standard HDR techniques, to allow for dynamic scene without introducing artefacts. Our method detects clusters of moving pixels within a bracketed exposure sequence with simple binary operations. We show that the proposed technique is able to deal with a large amount of movement in the scene and different movement configurations. The result is a ghost-free and highly detailed exposure fused image at a low computational cost.
Novel in vitro assay for the detection of pharmacologic inducers of fetal hemoglobin (2000)

Current techniques for identifying fetal hemoglobin (HbF) inducers are complex and time consuming. We developed a rapid and efficient method for detecting HbF inducers. Our system uses a recombinant DNA construct in which the coding sequences of 2 different luciferase reporter genes, firefly and renilla, are substituted for those of human γ and β globin genes, respectively. The activity of these genes can be distinguished by a simple, highly sensitive enzymatic assay in cell lysates. GM979 cells stably transfected with the construct are cultured in the presence of compounds, and their effects are determined by measuring the changes in activity of the 2 luciferase genes. Specific γ globin gene inducers are recognized by their ability to increase γ-firefly luciferase (γF) gene activity significantly more than β-renilla luciferase (βR) gene activity, identified by an increased ratio of γ-firefly luciferase activity over total luciferase activity. These results suggest that the use of the 2 luciferase reporter genes provides a simple, highly sensitive, and reproducible system for the detection of compounds that increase γ-globin gene expression. It can therefore be used for the screening of chemical agents that may have γ-globin gene inducibility.
A decomposition model to track gene expression signatures: preview onobserver-independent classification of ovarian cancer (2002)

We present a variational independent component analysis (ICA) method for reducing high dimensional DNA array data to a smaller set of latent variables, each associated with a gene signature. We present the results of applying the method to data from an ovarian cancer study, revealing a number of tissue type-specific and tissue type-independent gene signatures present in varying amounts among the samples surveyed. The observer independent results of such molecular analysis of biological samples could help identify patients who would benefit from different treatment strategies. We further explore the application of the model to similar high-throughput studies.