gebhart/patrepeval huggingface dataset:
Archvie of SID Heterologous Proteins Production in Escherichia coli: An Investigation on the Effect of Codon Usage and Expression Host Optimization (2011)

Objective: The production of heterologous proteins in Escherichia coli is strongly affected by codon bias. This phenomenon occurs when the codon usage of mRNA coding for the foreign protein differs from that of the bacterium. The ribosome pauses upon encountering a rare codon and may detach from mRNA, thereby the yield of recombinant protein production reduces. The aim of this study is to investigate the effect of these codon numbers reductions on the recombinant protein production. Materials and Methods: Since most amino acids are encoded by more than one codon, codons were changed in order to their usage in a special host such as E. coli without any transformation in amino acids sequence. Silent mutations in 5' codons of human basic fibroblast growth factor cDNA carried out by site-directed mutagenesis and the expression level of the recombinant protein is analyzed by means of sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) and Western blot. Results: Expression level in mutant and wild-type genes indicated a considerable difference. In contrast with the remarkable bands of wild-type gene in all the strains particularly in codon plus strain, there were no significant bands related to mutant gene in SDS-PAGE analysis. Conclusion: Because of the same conditions of mutant and wild-type genes during the translation and transcription, this significant difference may relate to mRNA efficiency for translation. Our results indicate that increased stability of 5' mRNA secondary structures in E. coli prevents efficient translation initiation. Furthermore, wild-type gene significant bands in codon plus strain support the hypothesis that the possible elimination of translational pauses that increase translation rate leads to over expression.
A rapid and cheap protocol for preparation of PCR templates in peanut (2009)

This paper describes a simple, low cost and reliable DNA template preparation protocol for polymerase chain reaction (PCR) using immature leaves from peanut seeds or leaves from field-grown plants. The technique may find wide utility in studies involving PCR-based molecular markers, rapid screening for transformants and gene cloning.
Ultrasensitive Detection of Enzymatic Activity with Nanowire Electrodes (2007)

Protein detection strategies that will have a positive impact on cancer diagnosis must be highly sensitive, very specific, and utilize time- and cost-effective methods. We report on the development of a method that fulfills these criteria by using a nanowire-based electrode platform that enables use of an electrochemical reporter system for protein detection. The prostate-specific antigen is detected with peptide-modified nanowires. An electrocatalytic reporter system is used to transduce the activity of the enzymes into a measurable electrochemical signal that accurately reports on physiologically relevant picomolar quantities of the analytes.
Mechanisms of constitutive activation of Janus kinase 2‐V617F revealed at the atomic level through molecular dynamics simulations (2009)

The current results indicated that this simulation-derived mechanism of JAK2 autoregulation is consistent with current available experimental evidence and may lead to a deeper understanding of JAK2 and other kinase systems that are regulated by pseudokinases.
Minimal Disseminated Disease in Childhood T-Cell Lymphoblastic Lymphoma: A Report From the Children's Oncology Group (2009)

PURPOSE Disease dissemination to the bone marrow is detected at diagnosis in approximately 15% of children with T-cell lymphoblastic lymphoma (T-LL). It is unclear whether the remaining patients have submicroscopic systemic disease and, if so, what is the clinical significance of this finding. PATIENTS AND METHODS Using a flow cytometric method that can detect one T-LL cell among 10,000 normal cells, we examined bone marrow and peripheral-blood samples collected from 99 children with T-LL at diagnosis, as well as blood samples collected from 42 patients during treatment. Results In 71 (71.7%) of the 99 marrow samples obtained at diagnosis, T-LL cells represented 0.01% to 31.6% (median, 0.22%) of mononuclear cells; 57 of the 71 T-LL-positive samples were from patients with stage II/III disease. Results of studies in bilateral marrow aspirates were highly concordant. Two-year event-free survival (EFS) was 68.1% +/- 11.1% (SE) for patients with > or = 1% T-LL cells in bone marrow versus 90.7% +/- 4.4% for those with lower levels of marrow involvement (P = .031); EFS for patients with > or = 5% lymphoblasts was 51.9% +/- 18.0% (P = .009). T-LL cells were as prevalent in blood as in marrow; monitoring residual T-LL cells in blood during remission induction therapy identified patients with slower disease clearance. CONCLUSION More than two thirds of children with T-LL have disseminated disease at diagnosis, a proportion much higher than previously demonstrated. Measurements of disease dissemination at diagnosis might provide useful prognostic information, which can be further refined by monitoring response to therapy through blood testing.
Elucidation of the DNA sequence preferences of daunomycin. (1988)

The sequence specificity of daunomycin was assessed using competition equilibrium dialysis, DNAse I footprinting and an E. coli RNA polymerase transcription inhibition assay; similar studies were performed on adriamycin and a new bis-intercalating daunomycin dimer. The results clearly demonstrate that the highest affinity sites are CA for daunomycin and adriamycin, and CACA for the bis-daunomycin. Other modest affinity (GC, CG, CT, TC, CC, AC) and poor affinity binding sites (AA, AT, TA) were also observed. Our results are in agreement with (a) the observed 5'-pyrimidine-purine-3' sequence preference of intercalating drugs, (b) the reported role played by OH(9) of daunomycin in the stabilization of the drug/DNA intercalation complex, and (c) the thermodynamics of nearest neighbour base-pair unstacking at the intercalation site. The CA specificity of daunomycin and adriamycin suggests that their biological activity may arise from association with the CA containing sequences which are thought to be associated with genetic regulatory elements in eukaryotes. The implications for future anthracycline drug design are presented in this context.
Training feedforward networks with the Marquardt algorithm (1994)

The Marquardt algorithm for nonlinear least squares is presented and is incorporated into the backpropagation algorithm for training feedforward neural networks. The algorithm is tested on several function approximation problems, and is compared with a conjugate gradient algorithm and a variable learning rate algorithm. It is found that the Marquardt algorithm is much more efficient than either of the other techniques when the network contains no more than a few hundred weights.
Fatty acid inhibition of angiotensin II-stimulated inositol phosphates in smooth muscle cells (1993)

Inositol phosphate (InsP) responses to angiotensin II (ANG II) stimulation were measured in cultured rat vascular smooth muscle cells (VSMC) incubated with and without fatty acids (FA). VSMC were washed after 24 h of FA incubation to achieve cellular incorporation of FA yet eliminate ambient FA. Incubation with eicosapentaenoic acid (EPA)-supplemented medium resulted in concentration-dependent incorporation of EPA and depletion of arachidonic acid in VSMC membranes. Incubation with EPA, but not other FA, resulted in inhibition of ANG II-stimulated InsP formation (29% inhibition with 100 microM EPA). In contrast, InsP formation in response to guanine nucleotide-binding protein stimulation was not affected by EPA. ANG II receptor binding to membranes prepared from EPA-loaded VSMC was 18% lower than binding in membranes from sham-loaded cells. In other studies, VSMC were exposed acutely to FA to avoid cellular incorporation. Exposure to all FA resulted in concentration-dependent reductions in ANG II binding and ANG II-stimulated InsP formation; binding affinity was reduced without changes in receptor density. We conclude that ANG II-stimulated InsP formation is modestly and selectively inhibited by EPA incorporation and more profoundly inhibited by acute exposure to many FA via interference with ANG II receptor binding.
A Prospective Multicenter Clinical and Endoscopic Follow-Up Study of Patients with Gastroesophageal Reflux Disease (2005)

With respect to its clinical as well as its endoscopic manifestations, gastroesophageal reflux disease does not appear to be very stable over time. However, in most cases this is due to regression rather than progression of the disease.
Ubiquitin cross-reactive protein gene expression is increased in decidualized endometrial stromal cells at the initiation of pregnancy (1999)

Ubiquitin cross-reactive protein (UCRP; also known as ISG15) is an interferon-upregulated protein implicated in the response to viral infection. An equivalent protein has been demonstrated within the bovine uterus in early pregnancy in response to conceptus-derived interferon-tau. We have previously shown the upregulation of UCRP within decidualized stromal cells of the human and non-human primate endometria. We now show that an increase in UCRP gene expression within the decidualized stromal cell accompanies these increased protein concentrations. Using Northern blotting techniques we demonstrate basal concentrations of URCP mRNA within the non-pregnant endometrium and an increase in signal within some decidual specimens of first trimester decidua. This signal may represent increased URCP transcription within the sub-population of stromal cells that undergo decidualization, since this cell type exhibits an increase in UCRP message as detected by in-situ hybridization.
Two Avirulent, Lentogenic Strains of Newcastle Disease Virus Are Cytotoxic for Some Human Pancreatic Tumor Lines In Vitro (2012)

On average, 1,555 times more NDV-B1 was needed to kill normal cells than most pancreatic tumor cells and 558 times more NDV-U to kill the two most sensitive pancreatic cancer lines. These innately-targeted lentogenic viruses may have meaningful potential in treating pancreatic cancer.
A conserved repetitive DNA element located in the centromeres of cereal chromosomes (1996)

Repetitive DNA sequences have been demonstrated to play an important role for centromere function of eukaryotic chromosomes, including those from fission yeast, Drosophila melanogaster, and humans. Here we report on the isolation of a repetitive DNA element located in the centromeric regions of cereal chromosomes. A 745-bp repetitive DNA clone pSau3A9, was isolated from sorghum (Sorghum bicolor). This DNA element is located in the centromeric regions of all sorghum chromosomes, as demonstrated by fluorescence in situ hybridization. Repetitive DNA sequences homologous to pSau3A9 also are present in the centromeric regions of chromosomes from other cereal species, including rice, maize, wheat, barley, rye, and oats. Probe pSau3A9 also hybridized to the centromeric region of B chromosomes from rye and maize. The repetitive nature and its conservation in distantly related plant species indicate that the pSau3A9 family may be associated with centromere function of cereal chromosomes. The absence of DNA sequences homologous to pSau3A9 in dicot species suggests a faster divergence of centromererelated sequences compared with the telomere-related sequences in plants.
Gedunin inhibits pancreatic cancer by altering sonic hedgehog signaling pathway (2016)

Overall, our data suggests that gedunin could serve as a potent anticancer agent against pancreatic cancers.
Molecular Pathways: ROS1 Fusion Proteins in Cancer (2013)

Genetic alterations that lead to constitutive activation of kinases are frequently observed in cancer. In many cases, the growth and survival of tumor cells rely upon an activated kinase such that inhibition of its activity is an effective anticancer therapy. ROS1 is a receptor tyrosine kinase that has recently been shown to undergo genetic rearrangements in a variety of human cancers, including glioblastoma, non-small cell lung cancer (NSCLC), cholangiocarcinoma, ovarian cancer, gastric adenocarcinoma, colorectal cancer, inflammatory myofibroblastic tumor, angiosarcoma, and epithelioid hemangioendothelioma. These rearrangements create fusion proteins in which the kinase domain of ROS1 becomes constitutively active and drives cellular proliferation. Targeting ROS1 fusion proteins with the small-molecule inhibitor crizotinib is showing promise as an effective therapy in patients with NSCLC whose tumors are positive for these genetic abnormalities. This review discusses the recent preclinical and clinical findings on ROS1 gene fusions in cancer.
Synthesis, Structure, and Deoxyribonucleic Acid Sequencing with a Universal Nucleoside: 1-(2'-Deoxy-.beta.-D-ribofuranosyl)-3-nitropyrrole (1995)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSynthesis, Structure, and Deoxyribonucleic Acid Sequencing with a Universal Nucleoside: 1-(2'-Deoxy-.beta.-D-ribofuranosyl)-3-nitropyrroleDonald E. Bergstrom, Peiming Zhang, Pascal H. Toma, Philip C. Andrews, and Ruthann NicholsCite this: J. Am. Chem. Soc. 1995, 117, 4, 1201–1209Publication Date (Print):February 1, 1995Publication History Published online1 May 2002Published inissue 1 February 1995https://doi.org/10.1021/ja00109a003RIGHTS & PERMISSIONSArticle Views238Altmetric-Citations52LEARN 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
Single-Molecule Observation of Protein Adsorption onto an Inorganic Surface (2010)

Understanding the interactions between silicon-based materials and proteins from the bloodstream is of key importance in a myriad of realms, such as the design of nanofluidic devices and functional biomaterials, biosensors, and biomedical molecular diagnosis. By using nanopores fabricated in 20 nm-thin silicon nitride membranes and highly sensitive electrical recordings, we show single-molecule observation of nonspecific protein adsorption onto an inorganic surface. A transmembrane potential was applied across a single nanopore-containing membrane immersed into an electrolyte-filled chamber. Through the current fluctuations measured across the nanopore, we detected long-lived captures of bovine serum albumin (BSA), a major multifunctional protein present in the circulatory system. Based upon single-molecule electrical signatures observed in this work, we judge that the bindings of BSA to the nitride surface occurred in two distinct orientations. With some adaptation and further experimentation, this approach, applied on a parallel array of synthetic nanopores, holds potential for use in methodical quantitative studies of protein adsorption onto inorganic surfaces.
Preliminary report of anti-hepatitis C virus activity of chloroquine and hydroxychloroquine in huh-5-2 cell line (2006)

Chloroquine and hydroxychloroquine screened for antiviral activity against Hepatitis C virus in Huh-5-2 cells. Chloroquine and hydroxychloroquine reduces the HCV RNA and promote the cell growth with respect to untreated control at concentration of 10.75 µM and 6.6 µM respectively.
Adenovirus-mediated expression of BMP-7 suppresses the development of liver fibrosis in rats (2006)

These data demonstrate that BMP-7, Smad 1/5/8 and Ids interact to antagonise hepatic fibrogenesis.
Margin Infused Relaxed Algorithm for Moses (2011)

Margin Infused Relaxed Algorithm for Moses We describe an open-source implementation of the Margin Infused Relaxed Algorithm (MIRA) for statistical machine translation (SMT). The implementation is part of the Moses toolkit and can be used as an alternative to standard minimum error rate training (MERT). A description of the implementation and its usage on core feature sets as well as large, sparse feature sets is given and we report experimental results comparing the performance of MIRA with MERT in terms of translation quality and stability.
Beginning Groovy and Grails (2008)

Web frameworks are playing a major role in the creation of today's most compelling web applications, because they automate many of the tedious tasks, allowing developers to instead focus on providing
INSIDE SOURCEFINDER: PREDICTING THE ACCEPTABILITY STATUS OF CANDIDATE READING-COMPREHENSION SOURCE DOCUMENTS (2006)

This paper describes the development, implementation, and evaluation of an automated system for predicting the acceptability status of candidate reading-comprehension stimuli extracted from a database of journal and magazine articles. The system uses a combination of classification and regression techniques to predict the probability that a given document will be deemed acceptable for use in completing a specified passage-creation assignment by at least one test developer. The text features that form the basis of the estimated models are automatically extracted by natural language processing techniques. Model performance is evaluated by comparing the proportion of acceptable documents located with the screening capability turned on to the proportion of acceptable documents located with the screening capability turned off. The evaluation suggests that the estimated models have succeeded in capturing useful information about the characteristics of texts that affect test developers' ratings of source acceptability and that they can help test developers find a greater number of high-quality sources in less time.
Overproduction and localization of components of the polyketide synthase of Streptomyces glaucescens involved in the production of the antibiotic tetracenomycin C (1991)

Three proteins, including the beta-keto acyl synthase and the acyl carrier protein, involved in the synthesis of the polyketide antibiotic tetracenomycin C by Streptomyces glaucescens GLA.0 were produced in Escherichia coli by using the T7 RNA polymerase-dependent pT7-7 expression vector. Changing the N-terminal codon usage of two of the genes greatly increased the level of protein produced without affecting mRNA levels, suggesting improvements in translational efficiency. Western immunoblot analysis of cytoplasmic and membrane fractions of S. glaucescens with antibodies raised to synthetic oligopeptides corresponding to the two presumed components of the beta-keto acyl synthase indicated that both proteins were membrane bound; one appears to be proteolytically cleaved before or during association with the membrane. The beta-keto acyl synthase could be detected in stationary-phase cultures but not in rapidly growing cultures, correlating with the time of appearance of tetracenomycin C in the medium.
Legislative Education Staffing in the States (1981)

Fifteen years ago a typical state legislator, when asked about the legislative role in elementary and secondary education, replied quizzically: Education is a local thing; we don't have anything to do with that; there's a formula. There was little recognition then, among legislators and among others, that state legislatures had the power not only to revise funding formulas, but to shape education policies. Today, by contrast, legislatures are up to their ears, or over their heads, in education. Most are in the thick of policymaking, while some even have wrested the initia-
Global Virulence Regulation in Staphylococcus aureus : Pinpointing the Roles of ClpP and ClpX in the sar/agr Regulatory Network (2005)

Staphylococcus aureus causes infections ranging from superficial wound infections to life-threatening systemic infections. Essential for S. aureus pathogenicity are a number of cell-wall-associated and secreted proteins that are controlled by a complex regulatory network involving the quorum-sensing agr locus and a large set of transcription factors belonging to the Sar family. Recently, we revealed a new layer of regulation by showing that mutants lacking the ClpXP protease produce reduced amounts of several extracellular virulence factors and that, independently of ClpP, ClpX is required for transcription of spa, encoding Protein A. Here we find that the independent effect of ClpX is not general for other cell wall proteins, as expression of fibronectin- and fibrinogen-binding proteins was increased in the absence of either ClpX or ClpP. To assess the roles of ClpX and ClpP within the sar/agr regulatory network, deletions in clpX and clpP were combined with mutations in these genes. Interestingly, the derepression of spa transcription normally observed in an agr-negative strain was abolished in cells devoid of ClpX, and apparently ClpX modulates both SarS-dependent and SarS-independent control of spa expression, perhaps through the Sar family member Rot. Examination of expression of a single secreted protein, the SspA serine protease, revealed that ClpXP, similar to agr, is required for growth phase-dependent transcriptional induction of sspa. Intriguingly, induction was restored by the concomitant inactivation of Rot. We hypothesize that RNAIII accumulating in the postexponential phase may target Rot for degradation by ClpXP, leading to derepression of sspA.