gebhart/patrepeval huggingface dataset:
ANTISENSE RNA CONTROL IN BACTERIA, PHAGES, AND PLASMIDS (1994)

Antisense RNA control is now recognized as an efficient and specific means of regulating gene expression at the posttranscriptional level. Almost all naturally occurring cases have been found in prokaryotes, often in their accessory genetic elements. Several antisense RNA systems are now well-understood, and these display a spectrum of mechanisms of action, binding pathways, and kinetics. This review summarizes antisense RNA control in prokaryotes, emphasizing the biology of the systems involved.
Determinants of Bureaucratic Turnover Intention: Evidence from the Department of the Treasury (2006)

This study employs a novel statistical strategy to examine the determinants of turnover intention in government service. To appropriately measure a main determinant of turnover intention-functional preferences-I estimate an ordinal item response model using data from the Federal Human Capital Survey. The sample is selected to facilitate an important comparison: the Internal Revenue Service (IRS) has undergone significant performancebased pay reforms for supervisors, but not for nonsupervisors, whereas the Office of the Comptroller of the Currency (OCC), also a subunit of the U.S. Treasury, has not. Inferential models of turnover intention reveal among other things that functional and friendship solidary preferences are important determinants of turnover intention, but increased accountability is associated with greater turnover among subordinates. IRS supervisors, who face paybanding, are significantly less likely to consider leaving than their counterparts in the OCC, who do not face such incentives.
MR imaging of splenic metastases: ferrite-enhanced detection in rats (1987)

MR imaging of splenic metastases: ferrite-enhanced detection in ratsR Weissleder, PF Hahn, DD Stark, E Rummeny, S Saini, J Wittenberg and JT FerrucciAudio Available | Share
Activation of Stat5 by interleukin 2 requires a carboxyl-terminal region of the interleukin 2 receptor beta chain but is not essential for the proliferative signal transmission. (1995)

The high-affinity interleukin 2 (IL-2) receptor (IL-2R) consists of three subunits: the IL-2R alpha, IL-2R beta c, and IL-2R gamma c chains. Two members of the Janus kinase family, Jak1 and Jak3, are associated with IL-2R beta c and IL-2R gamma c, respectively, and they are activated upon IL-2 stimulation. The cytokine-mediated Jak kinase activation usually results in the activation of a family of latent transcription factors termed Stat (signal transducer and activator of transcription) proteins. Recently, the IL-2-induced Stat protein was purified from human lymphocytes and found to be the homologue of sheep Stat5/mammary gland factor. We demonstrate that the human Stat5 is activated by IL-2 and that Jak3 is required for the efficient activation. The cytoplasmic region of the IL-2R beta c chain required for activation of Stat5 is mapped within the carboxyl-terminal 147 amino acids. On the other hand, this region is not essential for IL-2-induced cell proliferation.
Activity of Candida rugosa Lipase Immobilized on γ-Fe2O3 Magnetic Nanoparticles (2003)

We report the stability and enzymatic activity of Candida rugosa Lipase (E.C.3.1.1.3) immobilized on gamma-Fe2O3 magnetic nanoparticles. The immobilization strategies were either reacting the enzyme amine group with a nanoparticle surface acetyl, or amine groups. In the former, the enzyme was attached through a C=N bond, while in the latter it was connected using glutaraldehyde. AFM images show an average particle size of 20 +/- 10 nm after deconvolution. The enzymatic activity of the immobilized lipase was determined by following the ester cleavage of p-nitrophenol butyrate. The covalently immobilized enzyme was stabile and reactive over 30 days.
Room-Temperature Synthesis and Characterization of Nanocrystalline CdS, ZnS, and CdxZn1-xS (2002)

A novel and simple chemical reduction route at room temperature is described to synthesize nanocrystalline CdS, ZnS, and CdxZn1-xS. In the method, anhydrous CdCl2, or ZnCl2, S, and KBH4 powders react at room temperature in various organic solvents, and the effect of the solvent on the quality of the nanoparticle product is investigated. Among the solvents used, tetrahydrofuran is shown to produce the highest quality single-phase nanoparticles. The nanoparticles are characterized by X-ray diffraction, transmission electron microscopy, UV−vis absorption, and photoluminescence. The particle size ranges from 4 to 8 nm. In the CdxZn1-xS, the lattice structure gradually changes from cubic to hexagonal with increasing percentage of Zn in the ternary compound CdxZn1-xS. The nanoparticles exhibit broad emission peaks that shift to shorter wavelength with increasing percentage of Zn in the ternary compound CdxZn1-xS. The control of the composition of CdxZn1-xS nanoparticles may lead to the development of ideal materials for short wavelength diode laser applications.
Determination of acetabular coverage of the femoral head with use of a single anteroposterior radiograph. A new computerized technique. (1993)

We developed a method for the estimation of three-dimensional acetabular coverage of the femoral head with use of only an anteroposterior radiograph of the hip. This technique also allows recalculation of the corrected value for coverage at neutral pelvic tilt. Provided that the acetabulum and femoral head are spherical and congruent, the results are as accurate as those obtained with computerized tomographic reconstruction, the dose of radiation is much lower, and much less time is required for calculation. The hips of 286 normal subjects showed increases with age in both anterior and posterior coverage and backward tilt of the pelvis, along with a decrease in the anterior-posterior ratio of coverage. The proportion of anterior acetabular coverage in female subjects was smaller than that in male subjects. There was more backward tilt of the pelvis and the anterior-posterior ratio of coverage was smaller when the subjects were standing than when they were supine.
Survival, Integration, and Differentiation of Cardiomyocyte Grafts (1999)

Grafted fetal and neonatal cardiomyocytes form new, mature myocardium with the capacity to couple with injured host myocardium. Optimal repair, however, may require reducing the isolation of the graft by the intervening scar tissue.
Human Monoclonal Antibody Fragments Binding to Insulin-like Growth Factors I and II with Picomolar Affinity (2011)

The type 1 insulin-like growth factor receptor (IGF1R) and its ligands (IGF-I and IGF-II) have been implicated in a variety of physiologic processes and in diseases such as cancer. In addition to IGF1R, IGF-II also activates the insulin receptor (IR) isoform A, and therefore, antibodies against IGF-II can inhibit cell proliferation mediated by the signaling through both IGF1R and IR triggered by IGF-II. We identified a new human monoclonal antibody (mAb), m708.2, which is bound to IGF-I and IGF-II but not to insulin. m708.2 potently inhibited signal transduction mediated by the interaction of IGF-I or IGF-II with the IGF1R and IGF-II with the IR. It also inhibited the growth of the breast cancer cell line MCF-7. An affinity-matured derivative of m708.2, m708.5, bound to IGF-I with equilibrium dissociation constant, K(D) = 200 pmol/L and to IGF-II with K(D) = 60 pmol/L. m708.5 inhibited signal transduction mediated by IGF-I and IGF-II and cancer cell growth more potently than m708.2. These results suggest that m708.5 could have potential as a candidate therapeutic for cancers driven by the IGF-I and IGF-II interactions with IGF1R and IR.
Electroosmosis: A Reliable Fluid Propulsion System for Flow Injection Analysis (1994)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTElectroosmosis: A Reliable Fluid Propulsion System for Flow Injection AnalysisPurnendu K. Dasgupta and Shaorong. LiuCite this: Anal. Chem. 1994, 66, 11, 1792–1798Publication Date (Print):June 1, 1994Publication History Published online1 May 2002Published inissue 1 June 1994https://doi.org/10.1021/ac00083a004RIGHTS & PERMISSIONSArticle Views796Altmetric-Citations106LEARN 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 InReddit PDF (2 MB) Get e-Alerts Get e-Alerts
Mining Genomes: Correlating Tandem Mass Spectra of Modified and Unmodified Peptides to Sequences in Nucleotide Databases (1995)

The correlation of uninterpreted tandem mass spectra of modified and unmodified peptides, produced under low-energy (10-50 eV) collision conditions, with nucleotide sequences is demonstrated. In this method nucleotide databases are translated in six reading frames, and the resulting amino acid sequences are searched "on the fly" to identify and fit linear sequences to the fragmentation patterns observed in the tandem mass spectra of peptides. A cross-correlation function is then used to provide a measurement of similarity between the mass-to-charge ratios for the fragment ions predicted by amino acid sequences translated from the nucleotide database and the fragment ions observed in the tandem mass spectrum. In general, a difference greater than 0.1 between the normalized cross-correlation functions for the first- and second-ranked search results indicates a successful match between sequence and spectrum. Measurements of the deviation from maximum similarity employing the spectral reconstruction method are made. The search method employing nucleotide databases is also demonstrated on the spectra of phosphorylated peptides. Specific sites of modification are identified even though no specific information relevant to sites of modification is contained in the character-based sequence information of nucleotide databases.
Suppression of arthritic bone destruction by adenovirus-mediated csk gene transfer to synoviocytes and osteoclasts (1999)

Rheumatoid arthritis (RA) is characterized by a chronic inflammation of the synovial joints resulting from hyperplasia of synovial fibroblasts and infiltration of lymphocytes, macrophages, and plasma cells, all of which manifest signs of activation. Recent studies have revealed the essential role of osteoclasts in joint destruction in RA. Src family tyrosine kinases are implicated in various intracellular signaling pathways, including mitogenic response to growth factors in fibroblasts, activation of lymphocytes, and osteoclastic bone resorption. Therefore, inhibiting Src activity can be a good therapeutic strategy to prevent joint inflammation and destruction in RA. We constructed an adenovirus vector carrying the csk gene, which negatively regulates Src family tyrosine kinases. Csk overexpression in cultured rheumatoid synoviocytes remarkably suppressed Src kinase activity and reduced their proliferation rate and IL-6 production. Bone-resorbing activity of osteoclasts was strongly inhibited by Csk overexpression. Furthermore, local injection of the virus into rat ankle joints with adjuvant arthritis not only ameliorated inflammation but suppressed bone destruction. In conclusion, adenovirus-mediated direct transfer of the csk gene is useful in repressing bone destruction and inflammatory reactions, suggesting the involvement of Src family tyrosine kinases in arthritic joint breakdown and demonstrating the feasibility of intervention in the kinases for gene therapy in RA. off
Evaluation of seven experimental phages for inclusion in the international phage set for the epidemiological typing of Listeria monocytogenes (1997)

The purpose of our study was to evaluate the inclusion of seven experimental phages into the international phage set for subtyping Listeria monocytogenes. The seven additional phages included the broad-host-range virulent Myoviridae phage A511 (M. J. Loessner, Appl. Environ. Microbiol. 57:1912-1918, 1991), three temperate phages from the Danish subsystem for typing serotype 1/2 strains (12682, 6223, and 5775) (P. Gerner-Smidt, V.T. Rosdahl, and W. Frederiksen, APMIS 101:160-167, 1993), and three temperate phages isolated by this laboratory in France (9425, 1313, and 197). A panel of 395 Listeria monocytogenes isolates (including 180 that were non-phage typeable by the international set) were used in the study for a comparison of the lytic spectra of the various bacteriophages. These results showed that the inclusion of five of the experimental phages contributed greatly to the overall typeability and discriminatory power of the system, especially for strains within serogroup 1/2.
Analysis of volatile organic compounds released from human lung cancer cells and from the urine of tumor-bearing mice (2012)

Both sample types produce distinct biomarker profiles, and VOCs have potential to distinguish between true- and false-positive screens for lung cancer.
Immunoassays for des-Arg9-Bradykinin (1993)

Splenocytes from a female, BALB/c mouse immunized with bradykinin conjugated to ovalbumin with toluene diisocyanate were fused with mouse myeloma cells, X63/Ag8.653, using polyethylene glycol. Seventy-nine hybridomas were identified by ELISA to be making kinin reactive antibodies. In preliminary specificity studies it was determined that all of these hybridomas were producing antibodies more reactive with des-Arg9-bradykinin than with bradykinin. ELISAs were developed with the five clones that displayed the highest affinities for des-Arg9-bradykinin. Radioimmunoassays were developed for 3 of these 5 clones as well as with 5 monoclonal antibodies previously described (Odya and Lee 1990). The most sensitive des-Arg9-bradykinin assay developed was a radioimmunoassay in which carboxypeptidase B-treated [Tyr5]-bradykinin was the labeled antigen, clone OLNBK-5 was the antibody, and dextran-coated charcoal was used to separate bound from free radioactivity. The concentration of des-Arg9-bradykinin that inhibited 50% of the radioactive peptide binding was 0.08 +/- 0.03 nM. The relative specificity of this assay (des-Arg9-bradykinin = 100%) was: 29% bradykinin and about 1% with each of the following: lysyl-bradykinin, methionyl-lysyl-bradykinin, des-Arg1-bradykinin and des-Phe8-Arg9-bradykinin.
TGF-β receptor kinase inhibitor enhances growth and integrity of embryonic stem cell–derived endothelial cells (2003)

Recent findings have shown that embryonic vascular progenitor cells are capable of differentiating into mural and endothelial cells. However, the molecular mechanisms that regulate their differentiation, proliferation, and endothelial sheet formation remain to be elucidated. Here, we show that members of the transforming growth factor (TGF)-beta superfamily play important roles during differentiation of vascular progenitor cells derived from mouse embryonic stem cells (ESCs) and from 8.5-days postcoitum embryos. TGF-beta and activin inhibited proliferation and sheet formation of endothelial cells. Interestingly, SB-431542, a synthetic molecule that inhibits the kinases of receptors for TGF-beta and activin, facilitated proliferation and sheet formation of ESC-derived endothelial cells. Moreover, SB-431542 up-regulated the expression of claudin-5, an endothelial specific component of tight junctions. These results suggest that endogenous TGF-beta/activin signals play important roles in regulating vascular growth and permeability.
Comparative Genomics of Foot-and-Mouth Disease Virus (2005)

Here we present complete genome sequences, including a comparative analysis, of 103 isolates of foot-and-mouth disease virus (FMDV) representing all seven serotypes and including the first complete sequences of the SAT1 and SAT3 genomes. The data reveal novel highly conserved genomic regions, indicating functional constraints for variability as well as novel viral genomic motifs with likely biological relevance. Previously undescribed invariant motifs were identified in the 5' and 3' untranslated regions (UTR), as was tolerance for insertions/deletions in the 5' UTR. Fifty-eight percent of the amino acids encoded by FMDV isolates are invariant, suggesting that these residues are critical for virus biology. Novel, conserved sequence motifs with likely functional significance were identified within proteins L(pro), 1B, 1D, and 3C. An analysis of the complete FMDV genomes indicated phylogenetic incongruities between different genomic regions which were suggestive of interserotypic recombination. Additionally, a novel SAT virus lineage containing nonstructural protein-encoding regions distinct from other SAT and Euroasiatic lineages was identified. Insights into viral RNA sequence conservation and variability and genetic diversity in nature will likely impact our understanding of FMDV infections, host range, and transmission.
Why Sex and Recombination? (1998)

REVIEW Most higher organisms reproduce sexually, despite the automatic reproductive advantage experienced by asexual variants. This implies the operation of selective forces that confer an advantage to sexuality and genetic recombination, at either the population or individual level. The effect of sex and recombination in breaking down negative correlations between favorable variants at different genetic loci, which increases the efficiency of natural selection, is likely to be a major factor favoring their evolution and maintenance. Various processes that can cause such an effect have been studied theoretically. It has, however, so far proved hard to discriminate among them empirically.
TFEB has DNA-binding and oligomerization properties of a unique helix-loop-helix/leucine-zipper family. (1991)

The DNA-binding factor TFEB contains adjacent helix-loop-helix (HLH) and leucine zipper (LZ) domains flanked by an upstream basic region. This arrangement of interactive motifs has recently been observed in several other transcription factors and in the Myc family of oncogenes. TFEB was isolated by virtue of its binding to the major late promoter of adenovirus. DNA binding by a soluble protein was achieved by deleting a hydrophobic amino-terminal domain and permitted the structural analysis of the oligomerization and DNA-binding properties of TFEB. TFEB specifically bound DNA as both a homodimer and a heterodimer with another b-HLH-LZ protein TFE3. The LZ domain was essential for homo- or hetero-oligomerization and high-affinity DNA binding. In the absence of DNA a tetramer-sized form of TFEB was observed that dissociates to bind added DNA as a dimer. Binding by TFEB and TFE3 to related, but different, naturally occurring DNA target sequences was observed with distinct binding preferences. Analysis of basic domain residues in this family of proteins revealed a pattern of sequence conservation predictive of an interacting alpha-helical face. Common oligomerization and DNA-binding features suggest the b-HLH-LZ domain structure to define a distinct family of DNA-binding factors.
ChemInform Abstract: Structural Chemistry of Sc(III): An Overview (1999)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Recombination of Univalent Subunits Derived from Rabbit Antibody (1961)

SUMMARY Univalent 3.5 S fragments of rabbit antibody have been re- combined in good yield by oxidation to give 5 S protein that again has the capacity to form specific precipitates. The fragments were prepared by successive treatments of specifically purified antiovalbumin or antibovine gamma globulin with pepsin and 0.01 M mercaptoethylamine at 37”. The sedimentation co- efficient after reoxidation was almost identical to that observed before reduction, suggesting that the reconstituted antibody is bivalent. Upon reduction of the recombined material, break- down to -3.5 S occurs once again. The amino acid composition of the 5 S protein formed by peptic digestion is consistent with previous evidence indicating that this fragment consists es- sentially of Porter’s fractions I and II. 1. 2. 3. 4. 5. 6. 7. 8. 9. 10. 11. 12. 13. 14. 15. 16. 17. 18. 19. 20. REFERENCES PORTER, R. R., Nature, 182, 670 (1958).
Invited Review Article: Pump-probe microscopy (2016)

Multiphoton microscopy has rapidly gained popularity in biomedical imaging and materials science because of its ability to provide three-dimensional images at high spatial and temporal resolution even in optically scattering environments. Currently the majority of commercial and home-built devices are based on two-photon fluorescence and harmonic generation contrast. These two contrast mechanisms are relatively easy to measure but can access only a limited range of endogenous targets. Recent developments in fast laser pulse generation, pulse shaping, and detection technology have made accessible a wide range of optical contrasts that utilize multiple pulses of different colors. Molecular excitation with multiple pulses offers a large number of adjustable parameters. For example, in two-pulse pump-probe microscopy, one can vary the wavelength of each excitation pulse, the detection wavelength, the timing between the excitation pulses, and the detection gating window after excitation. Such a large parameter space can provide much greater molecular specificity than existing single-color techniques and allow for structural and functional imaging without the need for exogenous dyes and labels, which might interfere with the system under study. In this review, we provide a tutorial overview, covering principles of pump-probe microscopy and experimental setup, challenges associated with signal detection and data processing, and an overview of applications.
Neisseria gonorrhoeae — Rising Infection Rates, Dwindling Treatment Options (2018)

As antibiotic resistance grows, patients with gonorrhea infection may require extended hospital stays and additional follow-up visits, which could impose a serious burden on health care systems and social productivity internationally.