gebhart/patrepeval huggingface dataset:
Genetic Evidence for an Interferon-Antagonistic Function of Rift Valley Fever Virus Nonstructural Protein NSs (2001)

Rift Valley fever virus (RVFV), a phlebovirus of the family Bunyaviridae, is a major public health threat in Egypt and sub-Saharan Africa. The viral and host cellular factors that contribute to RVFV virulence and pathogenicity are still poorly understood. All pathogenic RVFV strains direct the synthesis of a nonstructural phosphoprotein (NSs) that is encoded by the smallest (S) segment of the tripartite genome and has an undefined accessory function. In this report, we show that MP12 and clone 13, two attenuated RVFV strains with mutations in the NSs gene, were highly virulent in IFNAR(-/-) mice lacking the alpha/beta interferon (IFN-alpha/beta) receptor but remained attenuated in IFN-gamma receptor-deficient mice. Both attenuated strains proved to be excellent inducers of early IFN-alpha/beta production. In contrast, the virulent strain ZH548 failed to induce detectable amounts of IFN-alpha/beta and replicated extensively in both IFN-competent and IFN-deficient mice. Clone 13 has a defective NSs gene with a large in-frame deletion. This defect in the NSs gene results in expression of a truncated protein which is rapidly degraded. To investigate whether the presence of the wild-type NSs gene correlated with inhibition of IFN-alpha/beta production, we infected susceptible IFNAR(-/-) mice with S gene reassortant viruses. When the S segment of ZH548 was replaced by that of clone 13, the resulting reassortants became strong IFN inducers. When the defective S segment of clone 13 was exchanged with the wild-type S segment of ZH548, the reassortant virus lost the capacity to stimulate IFN-alpha/beta production. These results demonstrate that the ability of RVFV to inhibit IFN-alpha/beta production correlates with viral virulence and suggest that the accessory protein NSs is an IFN antagonist.
Cdc7 Kinase Inhibitors: Pyrrolopyridinones as Potential Antitumor Agents. 1. Synthesis and Structure–Activity Relationships (2008)

Cdc7 kinase is an essential protein that promotes DNA replication in eukaryotic organisms. Genetic evidence indicates that Cdc7 inhibition can cause selective tumor-cell death in a p53-independent manner, supporting the rationale for developing Cdc7 small-molecule inhibitors for the treatment of cancers. In this paper, the synthesis and structure-activity relationships of 2-heteroaryl-pyrrolopyridinones, the first potent Cdc7 kinase inhibitors, are described. Starting from 2-pyridin-4-yl-1,5,6,7-tetrahydro-pyrrolo[3,2-c]pyridin-4-one, progress toward a simple scaffold, tailored for Cdc7 inhibition, is reported.
Segmentation of the cardiovascular tree in 4D from PC-MRI images (2013)

Investigating the dynamics of blood flow is essential to understanding the cardiovascular system and its pathologies. Phase Contrast Magnetic Resonance Imaging (PC-MRI) enables acquisition of 4-dimensional time resolved velocity experiments. Slice-by-slice analysis of the data is time consuming and cumbersome. In this master thesis a simple but eective algorithm for fully automatic visualization of the entire cardiovascular tree based on 4D PC-MRI velocity data. The achieved visualization portrays the cardiovascular vessel tree.The purposed segmentation algorithm is implemented in MATLAB and combined with the existing software Segment and Fourflow for visualization. Clinical data shows very promising visualization of the cardiovascular tree.
The preparation of polyamide-oligonucleotide probes containing multiple non-radioactive labels (1990)

Oligonucleotide probes containing multiple non-radioactive labels have been prepared by utilising and extending the methods used to prepare polyamide-oligonucleotide conjugates. The probes were prepared by incorporating suitable amino acid residues, such as lysines, in the polyamide, which were then used as sites for the attachment of the non-radioactive labels. The procedures developed give control over the distance of the label from the oligonucleotide, and also the inter-label distance. The labels can be conveniently introduced while the substrate is still on the solid support. Even though fluorescent oligonucleotide probes prepared in this way carrying multiple carboxyfluorescein labels gave low levels of fluorescence due to quenching, the probes containing ten biotin labels gave a detection sensitivity of approximately 5 attomole (3 million molecules).
Anti-Complement Autoantibodies in Membranoproliferative Glomerulonephritis and Dense Deposit Disease (2011)

Anti-Complement Autoantibodies in Membranoproliferative Glomerulonephritis and Dense Deposit Disease
A review of thermal processing in the subsecond range: semiconductors and beyond (2016)

Thermal processing in the subsecond range comprises modern, non-equilibrium annealing techniques which allow various material modifications at the surface without affecting the bulk. Flash lamp annealing (FLA) is one of the most diverse methods for short-time annealing with applications ranging from the classical field of semiconductor doping to the treatment of polymers and flexible substrates. It still continues to extend its use to other material classes and applications, and is becoming of interest for an increasing number of users. In this review we present a short, but comprehensive and consistent picture of the current state-of-the-art of FLA, sometimes also called pulsed light sintering. In the first part we take a closer look at the physical and technological background, namely the electrical and optical specifications of flash lamps, the resulting temperature profiles, and the corresponding implications for process-relevant parameters such as reproducibility and homogeneity. The second part briefly considers the various applications of FLA, starting with the classical task of defect minimization and ultra-shallow junction formation in Si, followed by further applications in Si technology, namely in the fields of hyperdoping, crystallization of thin amorphous films, and photovoltaics. Subsequent chapters cover the topics of doping and crystallization in Ge and silicon carbide, doping of III–V semiconductors, diluted magnetic semiconductors, III–V nanocluster synthesis in Si, annealing of transparent conductive oxides and high-k materials, nanoclusters in dielectric matrices, and the use of FLA for flexible substrates.
Cost-saving process recovers CO/sub 2/ from power-plant flue gas (1982)

Introduces a new technology which features a new alkanolamine-based solvent that is said to be less corrosive at higher concentrations and have greater resistance to oxygen than other CO/sub 2/ stripping solvents. The high-purity CO/sub 2/ will be used for enhanced oil recovery in Texas. Corrosion inhibitors available up till now could not provide adequate protection when oxygen was present in the gas stream. Dow Chemical Co. reports that its new product is stable in the presence of oxygen and provides corrosion protection sufficient to permit the use of mild steel for most of the plant equipment. Diagram shows how an enrichment boiler is used to increase the CO/sub 2/ concentration by combusting some of the oxygen in the flue gas. Presents tabular comparison of both conventional and Procon systems using monoethanolamine (MEA) and Gas/Spec FS-1L. Along with an expected reduction of over 50% in energy requirement compared with a 12% MEA system, the new technology is said to lose only half as much solvent.
Degradation of dicamba by an anaerobic consortium enriched from wetland soil (1993)

The biodegradability of dicamba was investigated under anaerobic conditions with a consortium enriched from wetland soil. Degradation proceeded through an initial demethylation reaction, forming 3,6-dichlorosalicylic acid, followed by reductive dechlorination, forming 6-chlorosalicylic acid. The consortium, consisting of a sulfate reducer, three methanogens, and a fermenter, was unable to mineralize the aromatic ring.
Effects of the A·T/T·A Degeneracy of Pyrrole−Imidazole Polyamide Recognition in the Minor Groove of DNA (1996)

Pairing rules have been developed to predict the sequence specificity of minor groove binding polyamides containing pyrrole (Py) and imidazole (Im) amino acids. An Im/Py pair distinguishes G.C from C.G and both of these from A.T/T.A base pairs. A Py/Py pair appears not to distinguish A.T from T.A base pairs. To test the extent of this degeneracy, the affinity and binding orientation of the hairpin polyamide ImPyPy-gamma-PyPyPy-beta-Dp were measured for eight possible five base pair 5'-TG(A,T)(3)-3' match sites. Affinity cleavage experiments using a polyamide with an EDTA.Fe(II) moiety at the carboxy terminus, ImPyPy-gamma-PyPyPy-beta-Dp-EDTA.Fe(II), are consistent with formation of an oriented 1:1 hairpin polyamide complex at all eight 5'-TG(A,T)(3)-3' binding sites [20 mM HEPES, 200 mM NaCl, 50 mg/ml glycogen, pH 7.0, 22 degrees C, 5 mM DTT, 1 mM Fe(II)]. Quantitative DNase I footprint titration experiments reveal that ImPyPy-gamma-PyPyPy-beta-Dp binds all eight 5'-TG(A,T)(3)-3' target sites with only a 12-fold difference in the equilibrium association constants between the strongest site, 5'-TGTTT-3' (Ka = 2.1 x 10(8) M-1), and the weakest site, 5'-TGAAT-3' (Ka = 1.8 x 10(7) M-1) (10 mM Tris.HCl, 10 mM KCl, 10 mM MgCl2, 5 mM CaCl2, pH 7.0, 22 degrees C). This relatively small range indicates that the Py/Py pair is approximately degenerate for recognition of A,T base pairs, affording generality with regard to targeting sequences of mixed A.T/T.A composition.
Expression of a mouse Zfy-1/lacZ transgene in the somatic cells of the embryonic gonad and germ cells of the adult testis (1994)

The Zfy-1 and Zfy-2 genes, which arose by gene duplication, map to the mouse Y chromosome and encode nearly identical zinc-finger proteins. Zfy-1 is expressed in the genital ridge and adult testis and likely encodes a transcription activator. Although potential roles in sex determination and spermatogenesis have been hotly debated, the biological functions of Zfy-1 remain unknown. To study the gene's regulation, transgenes with 21-28 kb of Zfy-1 5' flanking DNA placed upstream of lacZ were constructed in plasmids or created by homologous recombination of coinjected DNA molecules. The resulting transgenic mice expressed beta-galactosidase in the genital ridge of both males and females starting between embryonic day 10 and 11 (E10-E11), peaking at E12-E13 and then declining to low levels by E15, a pattern that matches Zfy-1 mRNA as detected by RT-PCR. This lacZ expression in genital ridge was confined to somatic cells as demonstrated by its absence from the alkaline phosphatase-positive germ cells. It had been reported previously that Zfy-1 mRNA was absent from the embryonic gonad of homozygous W(e) embryos, which virtually lack germ cells. By contrast, we observed normal expression of the Zfy-1/lacZ transgene when introduced into the W(e) background, suggesting that germ cells are not necessary for expression. In the adult, the Zfy-1/lacZ transgene is expressed abundantly in developing germ cells. Extragonadal (kidney, meninges, arteries, choroid plexus) expression of the transgene was also observed in embryos. A smaller transgene with only 4.3 kb of Zfy-1 5' flanking DNA was expressed only in germ cells of adult mice. These results suggest that an enhancer for germ cell expression in the adult lies near the Zfy-1 promoter and that an enhancer for expression in the somatic cells of the embryonic gonad is located further 5'.
Efficient Generation, Storage, and Manipulation of Fully Flexible Pharmacophore Multiplets and Their Use in 3-D Similarity Searching (2003)

Pharmacophore triplets and quartets have been used by many groups in recent years, primarily as a tool for molecular diversity analysis. In most cases, slow processing speeds and the very large size of the bitsets generated have forced researchers to compromise in terms of how such multiplets were stored, manipulated, and compared, e.g., by using simple unions to represent multiplets for sets of molecules. Here we report using bitmaps in place of bitsets to reduce storage demands and to improve processing speed. Here, a bitset is taken to mean a fully enumerated string of zeros and ones, from which a compressed bitmap is obtained by replacing uniform blocks ("runs") of digits in the bitset with a pair of values identifying the content and length of the block (run-length encoding compression). High-resolution multiplets involving four features are enabled by using 64 bit executables to create and manipulate bitmaps, which "connect" to the 32 bit executables used for database access and feature identification via an extensible mark-up language (XML) data stream. The encoding system used supports simple pairs, triplets, and quartets; multiplets in which a privileged substructure is used as an anchor point; and augmented multiplets in which an additional vertex is added to represent a contingent feature such as a hydrogen bond extension point linked to a complementary feature (e.g., a donor or an acceptor atom) in a base pair or triplet. It can readily be extended to larger, more complex multiplets as well. Database searching is one particular potential application for this technology. Consensus bitmaps built up from active ligands identified in preliminary screening can be used to generate hypothesis bitmaps, a process which includes allowance for differential weighting to allow greater emphasis to be placed on bits arising from multiplets expected to be particularly discriminating. Such hypothesis bitmaps are shown to be useful queries for database searching, successfully retrieving active compounds across a range of structural classes from a corporate database. The current implementation allows multiconformer bitmaps to be obtained from pregenerated conformations or by random perturbation on-the-fly. The latter application involves random sampling of the full range of conformations not precluded by steric clashes, which limits the usefulness of classical fingerprint similarity measures. A new measure of similarity, The Stochastic Cosine, is introduced here to address this need. This new similarity measure uses the average number of bits common to independently drawn conformer sets to normalize the cosine coefficient. Its use frees the user from having to ensure strict comparability of starting conformations and having to use fixed torsional increments, thereby allowing fully flexible characterization of pharmacophoric patterns.
Enhancing polyethylenimine's delivery of plasmid DNA into mammalian cells (2002)

The effect of various chemical modifications of nitrogen atoms on the efficiency of polyethylenimines (PEIs) as synthetic vectors for the delivery of plasmid DNA into monkey kidney cells in vitro has been systematically investigated. The resultant structure-activity relationship has both provided mechanistic insights and led to PEI derivatives with markedly enhanced performance. For example, N-acylation of PEI with the molecular mass of 25 kDa (PEI25, one of the most potent polycationic gene delivery vectors) with alanine nearly doubles its transfection efficiency in the presence of serum and also lowers its toxicity. Furthermore, dodecylation of primary amino groups of 2-kDa PEI yields a nontoxic polycation whose transfection efficiency in the presence of serum is 400 times higher than the parent's and which exceeds 5-fold even that of PEI25.
Theory of sequence effects on DNA translocation through proteins and nanopores (2002)

A general formula for the sequence effects on the average translocation time of a polymer passing through a narrow hole under a chemical potential gradient is provided. The utility of the general expression is illustrated by considering the diblock sequence of a polymer with two kinds of monomers. The experimental conditions required for sufficient discrimination of various sequences are addressed.
Phosphorescent Complexes of Porphyrin Ketones: Optical Properties and Application to Oxygen Sensing (1995)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTPhosphorescent Complexes of Porphyrin Ketones: Optical Properties and Application to Oxygen SensingDmitri B. Papkovsky, Gelii V. Ponomarev, Wolfgang. Trettnak, and Paul. O'LearyCite this: Anal. Chem. 1995, 67, 22, 4112–4117Publication Date (Print):November 15, 1995Publication History Published online1 May 2002Published inissue 15 November 1995https://pubs.acs.org/doi/10.1021/ac00118a013https://doi.org/10.1021/ac00118a013research-articleACS PublicationsRequest reuse permissionsArticle Views1911Altmetric-Citations259LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
[Establishment of PD-L1 transgenic mouse model and recovery of the motion after spinal cord injury]. (2011)

The TgPD-L1 mice whose background are C57BL/6 were established successfully and high expression level of PD-L1 in tissues promotes locomotion recovery after spinal cord injury in TgPD-L1 mice.
Anaerobic Benzene Oxidation in the Fe(III) Reduction Zone of Petroleum-Contaminated Aquifers (1998)

The potential for anaerobic benzene oxidation in the Fe(III)-reduction zone of petroleum-contaminated aquifers was evaluated. Sediments were incubated under strict anaerobic conditions without any amendments in order to simulate in situ conditions. [14C]Benzene was not oxidized to 14CO2 at most sites examined, which is consistent with previous studies that have found that benzene tends to persist in unamended, anaerobic aquifer materials and/or long periods of time are required in order to adapt the microbial population for benzene degradation. However, at one site located in Bemidji, MN, [14C]benzene was oxidized to 14CO2 in unamended sediments without an apparent lag, suggesting that benzene was anaerobically degraded in situ. Benzene was not significantly oxidized in sediments from nearby Fe(III)-reducing sites nor in sediments collected from an uncontaminated background site in the same aquifer. Culturing and 16S rRNA-based molecular studies of the Bemidji aquifer demonstrated that while all sites contained similar numbers of Fe(III)-reducing microorganisms closely related to Geothrix fermentens, the site at which anaerobic benzene degradation was observed was greatly enriched with microorganisms in the family Geobacteraceae. This study provides the first data consistent with in situ anaerobic oxidation of benzene to carbon dioxide in the Fe(III)-reducing zone of a petroleum-contaminated aquifer and suggests that comparative studies on the size of the Geobacteraceae community in petroleum-contaminated aquifers might aid in the location of zones in which benzene degradation coupled to Fe(III) reduction is taking place.
Cytokine gene polymorphisms in inflammatory bowel disease. (1996)

The associations demonstrated are modest: these polymorphisms are unlikely to be important determinants of overall disease susceptibility.
Progressive multifocal leukoencephalopathy: current treatment options and future perspectives (2015)

Progressive multifocal leukoencephalopathy (PML) is a rare but debilitating and frequently fatal viral disease of the central nervous system, primarily affecting individuals with chronically and severely suppressed immune systems. The disease was relatively obscure until the outbreak of HIV/AIDS, when it presented as one of the more frequent opportunistic infections in this immune deficiency syndrome. It attracted additional attention from the medical and scientific community following the discovery of significant PML risk associated with natalizumab, a monoclonal antibody used for treatment of relapsing-remitting multiple sclerosis. This was followed by association of PML with other immunosuppressive or immunomodulating drugs. PML is currently untreatable disease with poor outcomes, so it is a significant concern when developing new immunotherapies. Current prophylaxis and treatment of PML are focused on immune reconstitution, restoration of immune responses to JC virus infection, and eventual suppression of immune reconstitution inflammatory syndrome. This approach was successful in reducing the incidence of PML and improved survival of PML patients with HIV infection. However, the outcome for the majority of PML patients, regardless of their medical history, is still relatively poor. There is a high unmet need for both prophylaxis and treatment of PML. The aim of this review is to discuss potential drug candidates for prophylaxis and treatment of PML with a critical review of previously conducted and completed PML treatment studies as well as to provide perspectives for future therapies.
High sensitivity mass spectrometric methods for obtaining intact molecular weights from gel-separated proteins (1999)

The molecular weight measurement of intact Escherichia coli proteins separated by isoelectric focusing-immobilized pH gradient (IEF-IPG) gels and analyzed by mass spectrometry is presented. Two methods are discussed: (i) electrospray ionization (ESI) mass spectrometry (MS) of extracted proteins, and (ii) matrix-assisted laser desorption/ionization (MALDI)-MS analysis directly from IEF-IPG gels. Both ESI and MALDI methods yield sub-picomole sensitivity and good mass measurement accuracy. The use of an array detector for ESI-MS was essential to discriminate against contaminating background ions and to selectively detect high mass protein ions. MALDI-MS offers high-throughput analysis of one- and potentially two-dimensional (2-D) gels. The "virtual 2-D" gel method with first-dimensional IEF separation and the second dimension as molecular mass determination by MS, is a particularly promising method for protein analysis due to its ultra high sensitivity and correspondence to classical 2-D gels. Further sensitivity enhancements for the MALDI-MS method are provided by post acceleration detection optimized for high mass time-of-flight analysis.