gebhart/patrepeval huggingface dataset:
Genome of Horsepox Virus (2006)

Here we present the genomic sequence of horsepox virus (HSPV) isolate MNR-76, an orthopoxvirus (OPV) isolated in 1976 from diseased Mongolian horses. The 212-kbp genome contained 7.5-kbp inverted terminal repeats and lacked extensive terminal tandem repetition. HSPV contained 236 open reading frames (ORFs) with similarity to those in other OPVs, with those in the central 100-kbp region most conserved relative to other OPVs. Phylogenetic analysis of the conserved region indicated that HSPV is closely related to sequenced isolates of vaccinia virus (VACV) and rabbitpox virus, clearly grouping together these VACV-like viruses. Fifty-four HSPV ORFs likely represented fragments of 25 orthologous OPV genes, including in the central region the only known fragmented form of an OPV ribonucleotide reductase large subunit gene. In terminal genomic regions, HSPV lacked full-length homologues of genes variably fragmented in other VACV-like viruses but was unique in fragmentation of the homologue of VACV strain Copenhagen B6R, a gene intact in other known VACV-like viruses. Notably, HSPV contained in terminal genomic regions 17 kbp of OPV-like sequence absent in known VACV-like viruses, including fragments of genes intact in other OPVs and approximately 1.4 kb of sequence present only in cowpox virus (CPXV). HSPV also contained seven full-length genes fragmented or missing in other VACV-like viruses, including intact homologues of the CPXV strain GRI-90 D2L/I4R CrmB and D13L CD30-like tumor necrosis factor receptors, D3L/I3R and C1L ankyrin repeat proteins, B19R kelch-like protein, D7L BTB/POZ domain protein, and B22R variola virus B22R-like protein. These results indicated that HSPV contains unique genomic features likely contributing to a unique virulence/host range phenotype. They also indicated that while closely related to known VACV-like viruses, HSPV contains additional, potentially ancestral sequences absent in other VACV-like viruses.
The Primary Structure of Staphylococcal Enterotoxin B (1970)

Abstract Oxidized and reduced carboxymethylated enterotoxin B was digested with chymotrypsin. The peptides were fractionated on AG1-X2 and Dowex 50W-X2, and further purified by paper chromatography and electrophoresis. A total of 67 pure peptides was isolated and their sequences were determined completely or partially. These peptides provide important overlaps of tryptic peptides previously isolated and sequenced. Since most of the overlaps involve only a single residue, the complete primary structure of enterotoxin B could not be elucidated.
Epothilone A induces apoptosis in neuroblastoma cells with multiple mechanisms of drug resistance (1997)

Epothilone A, a novel macrolide antibiotic, is produced by the myxobacterium Sorangium cellulosum. Similarly to paclitaxel (Taxol), epothilone A inhibits cell proliferation and induces apoptosis by binding to tubulin and stabilizing of microtubuli. Like paclitaxel, epothilone A induced apoptosis in neuroblastoma cells which exhibit constitutive cytoplasmic sequestration of p53 and, hence, an impaired DNA-damage-dependent apoptosis. However, in contrast to paclitaxel, epothilone A was also effective against a constitutively Pgp-expressing, multidrug resistant neuroblastoma cell line (SK-N-SH). Moreover, the efficacy of epothilone A was not impaired even though the Pgp level was further increased during treatment with the drug.
Excessive intake of zinc impairs immune responses (1984)

The effect of administration of large amounts of zinc on immune response and serum lipoproteins was examined. Eleven healthy adult men ingested 150 mg of elemental zinc twice a day for six weeks. This was associated with a reduction in lymphocyte stimulation response to phytohemagglutinin as well as chemotaxis and phagocytosis of bacteria by polymorphonuclear leukocytes. Serum high-density lipoprotein concentration decreased significantly and low-density lipoprotein level increased slightly. The common food fad of zinc supplementation with resultant excessive intake could have deleterious effects in healthy persons. (<i>JAMA</i>1984;252:1443-1446)
RecA binding to bulge- and mismatch-containing DNAs. Certain single base mismatches provide strong signals for RecA binding equal to multiple base bulges (1993)

Studies from several laboratories have demonstrated that RecA protein can recognize a variety of perturbations in the DNA helix. Here, using a nitrocellulose filter binding assay, it was observed that RecA bound to bulge-containing DNAs more effectively than non-bulged DNA. The degree of binding of RecA protein to bulged DNA was dependent on the conformation of the bulged bases and the kinking angles produced by the bulges as determined by the type and number of bases in the bulge. Although a single base mismatch does not kink DNA, RecA protein showed preferential binding to DNAs containing certain single base mismatches. An A.C mismatch flanked by A.T base pairs in a 28-base pair (bp) DNA facilitated the binding of RecA protein to the same high level as when the 28-bp DNA contained a 4-base cytosine bulge. Chemical probing techniques were used to examine the structure of DNA within the RecA filament. It was found that upon binding of RecA protein, the DNA helix becomes accessible over at least 14 bp, and the degree of sensitivity agrees with the binding efficiency of RecA protein.
Isolation and Characterization of a 14500 Molecular Weight Protein from Brains and Tissue Cultures Persistently Infected with Borna Disease Virus (1985)

A protein with an apparent molecular weight of 14500 (14.5K) was extractable from homogenates of Borna disease virus-infected brains and tissue cultures using high concentrations of detergent and salt and by differential centrifugation procedures. The protein, present in an aggregated form, was remarkably resistant to proteinase K. Specific antibodies prepared in the homologous system (rat) recognized the 14.5K protein from various sources (infected brain of rat, mouse or chicken, and tissue cultures), but did not neutralize infectivity nor stain Borna disease virus-specific antigens from in vitro or in vivo preparations. Post-infection immune sera from different animal species did not detect the protein. This 14.5K protein was infection-specific but not disease-specific, and is inferred to be part of an internal virion component.
Generation of monodisperse gel emulsions in a microfluidic device (2006)

We demonstrate that high dispersed phase volume fraction emulsions (i.e., gel emulsions) can be prepared in situ for microfluidic applications. Previously, the production of gel-like emulsions in microfluidic devices, where the droplet size is less than the length-scale of the channel, required multistep splitting of larger droplets in a branched microchannel network. Instead, we employ an abrupt change in the aspect ratio of a single microchannel to rapidly destabilize a confined coflowing stream, forming highly monodisperse droplets (coefficient of variance &amp;lt;1.5%). Using this emulsification mechanism, gel emulsions can be prepared in a single production step.
Intact motility as a Salmonella typhi invasion-related factor (1988)

Invasiveness of Salmonella typhi was investigated. At first, we introduced Tn5 into the chromosome of a wild-type S. typhi strain, GIFU 10007, and screened the independent Tn5 insertion mutants for noninvasive (Inv-) strains. During the first half of this work, we obtained 4 Inv- strains from 1,338 independent Tn5 mutants. The four were either nonflagellate (Fla-), nonmotile (Mot-), or nonchemotactic (Che-). We then isolated more Fla-, Mot-, or Che- mutants and examined the invasiveness of these mutants. Sixty-three spontaneous or Tn5 insertion motility mutants, i.e., Fla-, Mot-, or Che-, were independently isolated from the wild-type strain GIFU 10007; all of them were noninvasive. Motile revertants isolated from some of these mutants showed the same invasiveness as the parent strain. P22-mediated transductional crosses were carried out between some of the motility mutants (as the recipients) and the Fla- reference strains of S. typhimurium with known deletion sites on the genome (as the donors). The mutational sites of the S. typhi mutants were assigned almost evenly to the three flagellar gene regions (regions I, II, and III) of S. typhimurium. The invasiveness of the motile recombinants obtained from the transduction assays was examined. The restoration of intact motility resulted in the restoration of invasiveness. Thus, we conclude that intact motility is an invasion-related factor of S. typhi. The relationship of Vi antigen to the invasiveness of S. typhi was also studied. Vi-negative mutants with intact motility remained invasive, whereas all 63 Inv- spontaneous or Tn5 mutants were Vi positive. Therefore, Vi antigen was not related to the invasiveness of S. typhi.
‘Mixed’ β‐peptides: A unique helical secondary structure in solution. Preliminary communication (1997)

Abstract β‐Hexapeptides 1–5 and a β‐dodecapeptide 6 with sequences containing two different types of β‐amino acids (aliphatic proteinageous side chains in the 2‐ or in the 3‐position) have been prepared. CD ( Fig. 1 ) and NMR measurements indicate that, with one exception, the secondary structures formed by these new β‐peptides differ from those of isomers studied previously. Detailed NMR analysis of the β‐hexapeptide 5 (with alternating β 2 ,β 3 ‐building blocks) and molecular‐dynamics simulations have produced a minimum energy conformation ( Fig. 2,b )which might be described as a novel irregular helix containing ten‐ and twelve‐membered H‐bonded rings. This demonstrates the great structural variability of β‐peptides, since three different helical secondary structures have been discovered to date.
Genetics and malignant progression of human brain tumours. (1995)

Progression of gliomas to more malignant phenotypes involves numerous molecular genetic alterations. The genes affected by these alterations, the steps in malignant progression for which they are responsible, their normal function in controlling diverse cellular functions such as differentiation, signal transduction, cell cycle progression and angiogenesis and how they may act in concert with other tumour suppressor genes or oncogenes are some of the questions finally coming into focus and being studied. As other genes are discovered, their association with tumour progression can be assessed, coupled with current histopathology and used to determine more accurately patient prognosis and strategies for intervention. With the generation of specific reagents, such as monoclonal antibodies directed to glioma derived antigens or emerging gene therapy techniques designed to deliver toxic, antisense or reconstituting genes specifically to tumour tissue, new approaches will be devised that may finally be used to treat these tumours effectively.
Rho-Kinase Phosphorylates COOH-terminal Threonines of Ezrin/Radixin/Moesin (ERM) Proteins and Regulates Their Head-to-Tail Association (1998)

The ezrin/radixin/moesin (ERM) proteins are involved in actin filament/plasma membrane interaction that is regulated by Rho. We examined whether ERM proteins are directly phosphorylated by Rho-associated kinase (Rho-kinase), a direct target of Rho. Recombinant full-length and COOH-terminal half radixin were incubated with constitutively active catalytic domain of Rho-kinase, and approximately 30 and approximately 100% of these molecules, respectively, were phosphorylated mainly at the COOH-terminal threonine (T564). Next, to detect Rho-kinase-dependent phosphorylation of ERM proteins in vivo, we raised a mAb that recognized the T564-phosphorylated radixin as well as ezrin and moesin phosphorylated at the corresponding threonine residue (T567 and T558, respectively). Immunoblotting of serum-starved Swiss 3T3 cells with this mAb revealed that after LPA stimulation ERM proteins were rapidly phosphorylated at T567 (ezrin), T564 (radixin), and T558 (moesin) in a Rho-dependent manner and then dephosphorylated within 2 min. Furthermore, the T564 phosphorylation of recombinant COOH-terminal half radixin did not affect its ability to bind to actin filaments in vitro but significantly suppressed its direct interaction with the NH2-terminal half of radixin. These observations indicate that the Rho-kinase-dependent phosphorylation interferes with the intramolecular and/ or intermolecular head-to-tail association of ERM proteins, which is an important mechanism of regulation of their activity as actin filament/plasma membrane cross-linkers.
Lipase-mediated formation of peroxycarboxylic acids used in catalytic epoxidation of alkenes (1990)

Epoxidation of alkenes was achieved under extremely mild conditions by employing peroxycarboxylic acids formed continuously in situ by lipase-catalysed perhydrolysis of the corresponding carboxylic acids.
Transforming Growth Factor .BETA.1 Selectively Increases Gene Expression of the Serine/Threonine Kinase Receptor 1 (SKR1) in Human Hepatoma Cell Lines. (1994)

Human hepatoma cell lines (Hep 3B-TS, PLC/PRF/5, and Hep G2), sensitive to growth inhibition by transforming growth factor beta 1 (TGF-beta 1), express TGF-beta receptors type I, type II, and type III. We report that TGF-beta 1 protein selectively increased steady-state levels of the mRNA for the serine/threonine kinase receptor 1 (SKR1), a member of the TGF-beta superfamily receptor genes in these cells, whereas TGF-beta 1 had little effect on expression of the TGF-beta receptor type II gene. This increase of SKR1 mRNA in Hep 3B-TS cells could be detected by Northern blot analysis within 3 h of addition of TGF-beta 1 to the cells, and enhanced message levels peaked at 12 h as long as TGF-beta 1 was present in the culture medium. Hep 3B-TR cells which were resistant to TGF-beta 1 due to lack of both TGF-beta receptors type I and type II, expressed SKR1 mRNA, but it was not induced by TGF-beta 1 protein. The increased expression of SKR1 mRNA in the cells was actinomycin D-sensitive and was not dependent on new protein synthesis. The results indicate that TGF-beta 1 selectively induces SKR1 message at a transcriptional level by a positive regulator.
Growth Kinetics of ZnS Thin Films from a High-Rate Chemical Bath Deposition with Trisodium-Nitrilotriacetate Complexing (2018)

In this study, a quartz crystal microbalance was used to perform in-situ study of ZnS growth using a chemical bath with Trisodium-nitrilotriacetate Complexing. In contrast to ex-situ studies, three deposition regions can be distinctly observed from the first twenty minute of growth curves based on in-situ measurements. The activation energy, as determined by the Arrhenius equation was found to be 66.22 kJ mol−1 and 36.32 kJ mol−1 for the first and second growth regions respectively. The growth curves suggest that ZnS film growth is initiated by an ion-by-ion reaction mechanism followed by a cluster-by-cluster deposition in the second growth region, and then is terminated by a terminal growth region where the deposition rate gradually slows down and eventually stops due to depletion of reactive species. An empirical rate equation describing ZnS thin film growth kinetics for the linear portion of the cluster-by-cluster growth region was obtained by fitting the growth rates as a function of the precursor concentrations. The improved understanding of growth mechanism and reaction kinetics could benefit future work toward designing more efficient chemical bath deposition process to fabricate nanocrystalline ZnS films for different applications.
2'-O-alkyl polynucleotides. I. Novel procedure for the synthesis of 2'-O-alkyl nucleotides (1972)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXT2'-O-alkyl polynucleotides. I. Novel procedure for the synthesis of 2'-O-alkyl nucleotidesI. Tazawa, S. Tazawa, J. L. Alderfer, and P. O. P. Ts'oCite this: Biochemistry 1972, 11, 26, 4931–4937Publication Date (Print):December 19, 1972Publication History Published online1 May 2002Published inissue 19 December 1972https://pubs.acs.org/doi/10.1021/bi00776a009https://doi.org/10.1021/bi00776a009research-articleACS PublicationsRequest reuse permissionsArticle Views146Altmetric-Citations24LEARN 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
Diversity of spore-forming bacteria in cattle manure, slaughterhouse waste and samples from biogas plants (2010)

Biogas is gaining in importance as an energy source and because the residues are used as fertilizers, we needed to study the prevalence of pathogenic bacteria in such material.
Photo-Cross-Linkable Thermoresponsive Star Polymers Designed for Control of Cell-Surface Interactions (2010)

Star polymers with thermoresponsive arms, consisting of 2-(2-methoxyethoxy)ethyl methacrylate (MEO₂MA) and oligo(ethylene glycol) methacrylate with ~4 ethylene oxide units (OEOMA₃₀₀, M(n) = 300), were synthesized via atom transfer radical polymerization (ATRP). 25% of the arms contained benzophenone chain-end functionality at the star periphery. A mixture of linear poly(MEO₂MA-co-OEOMA₃₀₀)-Br macroinitiators without and with benzophenone end-group macroinitiators were (MI and Bzp-MI, respectively) cross-linked with ethylene glycol dimethacrylate to form star polymers. Formation of star polymers was monitored by GPC, and the presence of benzophenone functionality in the stars was confirmed by ¹H NMR. The UV-vis spectroscopy revealed that the star polymers exhibit the low critical solution temperature (LCST) at 27 °C, slightly lower than LCST of either MI or Bzp-MI. Commercially available tissue culture grade polystyrene surface was modified by depositing a thin film of functionalized stars and UV cross-linking (λ = 365 nm). The star polymers covalently attached onto surfaces allowed a control of cell shrinkage and attachment in response to temperature changes.
Synthesis of BN-Fused Polycyclic Aromatics via Tandem Intramolecular Electrophilic Arene Borylation (2011)

A tandem intramolecular electrophilic arene borylation reaction has been developed for the synthesis of BN-fused polycyclic aromatic compounds such as 4b-aza-12b-boradibenzo[g,p]chrysene (A) and 8b,11b-diaza-19b,22b-diborahexabenzo[a,c,fg,j,l,op]tetracene. These compounds adopt a twisted conformation, which results in a tight and offset face-to-face stacking array in the solid state. Time-resolved microwave conductivity measurements prove that the intrinsic hole mobility of A is comparable to that of rubrene, one of the most commonly used organic semiconductors, indicating that BN-substituted PAHs are potential candidates for organic electronic materials.
Phosphorothioate Oligonucleotides with Low Phosphate Diester Content:  Greater than 99.9% Sulfurization Efficiency with “Aged” Solutions of Phenylacetyl Disulfide (PADS) (2004)

In this report, we describe the design of an efficient and robust sulfurization step in the production process of phosphorothioate (PS) oligonucleotides by solid-phase synthesis. Average stepwise sulfurization efficiencies >99.9% were obtained with “aged” solutions of phenylacetyl disulfide (PADS) in the solvent system acetonitrile/3-picoline (0.2 M, 1:1, v/v). Preparation of the reagent at least 1 day prior to use yields PS-oligonucleotides with low-level phosphate (PO) diester content. The use of freshly prepared PADS solutions gave oligonucleotide products with increased PO-diester content (stepwise sulfurization efficiency 99.5−99.7%). Short aging periods combined with short sulfurization contact times lead to formation of oligonucleotide 4,4‘-dimethoxytrityl-C-phosphonate derivatives. Investigation of reagent stability and sulfurization efficiency revealed significant changes in solution composition over time caused by dissociation of the PADS molecule. The “in situ” formation of a reactive intermediate, presumably a polysulfide, appears to be crucial for optimal synthesis results.
FGFR3–TACC3: A novel gene fusion in cervical cancer (2015)

Cervical cancer epitomizes the success of cancer prevention through the human papillomavirus (HPV) vaccine, but significant challenges remain in the treatment of advanced disease. We report the first three cases of cervical carcinoma harboring an FGFR3-TACC3 fusion, which serves as a novel therapeutic target. The fusion, identified by comprehensive genomic profiling, activates the FGFR pathway that has been implicated in HPV-driven carcinogenesis. One of the patients whose tumor contained the FGFR3-TACC3 fusion was treated with an investigational FGFR tyrosine kinase inhibitor. Concomitant molecular alterations involving the PI3K/AKT/mTOR and RAF/MEK pathways were also identified and suggest other treatment strategies that deserve investigation. This case series highlights the role of comprehensive genomic profiling in the identification of new therapeutic targets and in targeted therapy selection for patients with cervical cancer.
Decoding the Building Blocks of Life from the Perspective of Quantum Information (2013)

Physical theories often start out as theories which only embrace essential features of the macroscopic world, where their predictions depend on certain parameters that have to be either assumed or taken from experiments; as a result these parameters cannot be predicted by such theories. To understand why the parameters have the values they do, we have to go one level deeper—typically to smaller scales where the easiest processes to study are the ones at the lowest level. When the deeper level reduces the number of unknown parameters, we consider the theory to be complete and satisfactory. The level below conventional molecular biology is spanned by atomic and molecular structure and by quantum dynamics. However, it is also true that at the lowest level it becomes very difficult to grasp all the features of the molecular processes that occur in living systems such that the complexity of the numerous parameters that are involved make the endeavour a very intricate one. Information theory provides a powerful framework for extracting essential features of complicated processes of life, and then analyzing them in a systematic manner. In connection to the latter, quantum information biology is a new field of scientific inquiry in which information-theoretical tools and concepts are permitting to get insight into some of the most basic and yet unsolved questions of molecular biology.