gebhart/patrepeval huggingface dataset:
Expression of a pepT homologue from Bacillus subtilis (1996)

We isolated pepT from Bacillus subtilis, a gene with homology to various tripeptidases from different bacterial sources, pepT is preceded by genes encoding a two component regulatory system. Its expression is activated during stationary phase. In minimal medium this activation is boosted in the presence of phosphate. The response regulator is preceded by putative promoter consensus sequences recognized by the stationary phase specific sigma factors σH,σF, and σG. This is in accordance with the initiation of expression at the beginning of stationary phase. Inactivation of pepT causes no obvious phenotype.
Assessment of Caspase Activities in Intact Apoptotic Thymocytes Using Cell-Permeable Fluorogenic Caspase Substrates (2000)

To detect caspase activities in intact apoptotic cells at the single cell level, cell-permeable fluorogenic caspase substrates were synthesized incorporating the optimal peptide recognition motifs for caspases 1, 3/7, 6, 8, and 9. Caspase activities were then assessed at various times after in vitro treatment of mouse thymocytes with dexamethasone or anti-Fas antibody. Dexamethasone induced the following order of appearance of caspase activities as judged by flow cytometry: LEHDase, WEHDase, VEIDase, IETDase, and DEVDase. Since the relative order of caspases 3 (DEVDase) and 6 (VEIDase) in the cascade has been controversial, this caspase activation order was reexamined using confocal microscopy. The VEIDase activity appeared before DEVDase in every apoptotic cell treated with dexamethasone. In contrast, anti-Fas stimulation altered this sequence: IETDase was the first measurable caspase activity and DEVDase preceded VEIDase. In an attempt to determine the intracellular target of the potent antiapoptotic agent carbobenzoxy-valyl-alanyl-aspartyl(beta-methyl ester)-fluoromethyl ketone (Z-VAD[OMe]-FMK), we examined its ability to inhibit previously activated intracellular caspases. However, no significant reductions of these activities were observed. These fluorogenic caspase substrates allow direct observation of the caspase cascade in intact apoptotic cells, showing that the order of downstream caspase activation is dependent on the apoptotic stimulus.
Multiple small doses of levodopa plus entacapone produce continuous dopaminergic stimulation and reduce dyskinesia induction in MPTP‐treated drug‐naïve primates (2004)

Long-acting dopamine agonist drugs induce a lower incidence of dyskinesia in MPTP-treated primates and patients with Parkinson's disease compared to pulsatile treatment with levodopa, supporting the concept of continuous dopaminergic stimulation as a means of dyskinesia avoidance. We examined the effects of L-dopa administered with or without the COMT inhibitor entacapone on dyskinesia induction in previously untreated MPTP-treated common marmosets. Administration of L-dopa (12.5 mg/kg p.o.) plus carbidopa twice daily produced fluctuating improvement in motor behavior coupled with dyskinesia. Coadministration with entacapone produced similar patterns of motor improvement and dyskinesia that were not different from that produced by L-dopa alone. Treatment with L-dopa (6.25 mg/kg p.o.) plus carbidopa four times daily reversed motor disability and induced dyskinesia in a manner that was not different from the twice-daily treatment regimens. However, coadministration with entacapone produced more continuous improvement in locomotor activity with less dyskinesia than animals treated with L-dopa four times daily alone. These data support the notion that pulsatile stimulation contributes to the development of dyskinesia and suggests that more frequent dosing of L-dopa plus entacapone may be a useful treatment strategy for patients in the early stages of Parkinson's disease.
Langmuir Film Polymerization To Form a Soluble Poly(phenylenevinylene) (PPV) Precursor Polymer (1998)

ADVERTISEMENT RETURN TO ISSUEPREVCommunication to the...Communication to the EditorNEXTLangmuir Film Polymerization To Form a Soluble Poly(phenylenevinylene) (PPV) Precursor PolymerJ. H. Batten and R. S. DuranView Author Information The Butler Polymer Research Laboratories, University of Florida, Gainesville, Florida 32611 Cite this: Macromolecules 1998, 31, 9, 3148–3150Publication Date (Web):April 8, 1998Publication History Received29 October 1997Revised9 March 1998Published online8 April 1998Published inissue 1 May 1998https://pubs.acs.org/doi/10.1021/ma971597ehttps://doi.org/10.1021/ma971597erapid-communicationACS PublicationsCopyright © 1998 American Chemical SocietyRequest reuse permissionsArticle Views125Altmetric-Citations4LEARN 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-AlertscloseSupporting Info (1)»Supporting Information Supporting Information SUBJECTS:Monolayers,Polymer films,Polymerization,Polymers,Thin films Get e-Alerts
Single-strand nicks induce homologous recombination with less toxicity than double-strand breaks using an AAV vector template (2010)

Gene targeting by homologous recombination (HR) can be induced by double-strand breaks (DSBs), however these breaks can be toxic and potentially mutagenic. We investigated the I-AniI homing endonuclease engineered to produce only nicks, and found that nicks induce HR with both plasmid and adeno-associated virus (AAV) vector templates. The rates of nick-induced HR were lower than with DSBs (24-fold lower for plasmid transfection and 4- to 6-fold lower for AAV vector infection), but they still represented a significant increase over background (240- and 30-fold, respectively). We observed severe toxicity with the I-AniI 'cleavase', but no evidence of toxicity with the I-AniI 'nickase.' Additionally, the frequency of nickase-induced mutations at the I-AniI site was at least 150-fold lower than that induced by the cleavase. These results, and the observation that the surrounding sequence context of a target site affects nick-induced HR but not DSB-induced HR, strongly argue that nicks induce HR through a different mechanism than DSBs, allowing for gene correction without the toxicity and mutagenic activity of DSBs.
Growth mechanism of 6H-SiC in step-controlled epitaxy (1993)

Growth of SiC on off-oriented 6H-SiC{0001} substrates was performed between 1100 and 1500 °C. Homoepitaxial growth of 6H-SiC was achieved at temperatures as low as 1200 °C, utilizing step-flow growth. Twinned crystalline 3C-SiC was grown at 1100 °C; this result can be ascribed to suppressed surface migration of adsorbed Si species at the lower temperature, and to the occurrence of two-dimensional nucleation on terraces. The C/Si ratio significantly effected the surface morphology and growth rate. The growth rate was limited by the supply of Si species, where the growth rate activation energy was very small (3.0 kcal/mol), and little difference in the growth rates on Si and C faces was observed. The quantitative analysis revealed that growth of 6H-SiC in step-controlled epitaxy is controlled by the diffusion of reactants in a stagnant layer.
Association of circulating TNF-α and IL-6 with ageing and parkinsonism (1999)

Ageing and pathogenetic insult may be confounded, age being a progression, not a risk, factor.
Micro UAV Path Planning for Reconnaissance in Wind (2007)

The problem addressed in this paper is the control of a micro unmanned aerial vehicle (MAV) for the purpose of obtaining video footage of a set of known ground targets with preferred azimuthal viewing angles, using fixed onboard cameras. Control is exercised only through the selection of waypoints, without modification of the MAV's pre-existing autopilot and waypoint following capability. Specifically, we investigate problems and potential solutions of performing this task in the presence of a known constant wind. Simulations are provided in the presence of randomly perturbed wind, based on the Air Force Research Laboratory equipment and the high fidelity simulator MultiU <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">A</sub> V2.
Is All Bone the Same? Distinctive Distributions and Properties of Non-Collagenous Matrix Proteins in Lamellar Vs. Woven Bone Imply the Existence of Different Underlying Osteogenic Mechanisms (1998)

The purpose of this review is to summarize recent functional and structural findings regarding non-collagenous matrix proteins in bone and teeth, to compare gene locations for bone and tooth matrix proteins with loci for hereditary skeletal diseases, and to present several provocative hypotheses which integrate this new information into a physiological context. Hypothesis I proposes that the molecular composition of rapidly deposited and mineralized woven bone, as well as the responsiveness of cells synthesizing woven bone to stimuli, is different from that for more slowly synthesized lamellar bone, implying the existence of distinctive osteogenic mechanisms. This review of recent research strongly supports this proposal. Briefly, the protein composition of woven bone matrix is enriched in acidic phosphoproteins BAG-75 and BSP, which are not expressed in lamellar bone, which is itself enriched in osteocalcin. De novo deposition and mineralization of woven bone occurs faster than in lamellar bone by means of a matrix-vesicle-assisted mechanism. Deposition of woven bone occurs at sites experiencing biomechanical strains higher than those experienced by lamellar bone. In addition, woven bone in metaphyseal regions is more susceptible to osteoclastic resorption after space flight, ovariectomy, and loss of weightbearing than is lamellar bone. Finally, osteoprogenitor cells responsive to parathyroid hormone reside in the metaphyseal region of long bones. Taken together, these findings suggest that Hypothesis I represents a useful paradigm for future studies. Specific functions mediated by most individual bone and tooth matrix proteins remain uncertain. A review of current literature suggests that the functionality of skeletal matrix proteins is expressed through specific binding sites composed of particular species-conserved structural motifs (Hypothesis 2). Examples include the previously recognized Asp-Ser-Ser motif of dentin phosphophoryns and the gamma-carboxyglutamic acid motif of matrix GLA protein and osteocalcin. A new polyacidic amino acid motif composed of consecutive Asp and Glu residues (n > 7) was defined in extracellular matrix components osteopontin, bone sialoprotein, and bone acidic glycoprotein-75 on the basis of strong functional analogies with similar polyacidic stretches in divalent metal storage proteins of the endoplasmic reticulum and sarcoplasmic reticulum. These structural motifs represent prime targets for future structure-function studies in vivo and in vitro.
Metformin Use Is Associated with Better Survival of Diabetic Patients with Pancreatic Cancer (2012)

Our finding that metformin use was associated with improved outcome of patients with diabetes and pancreatic cancer should be confirmed in independent studies. Future research should prospectively evaluate metformin as a supplemental therapy in this population.
Novel Ligands that Function as Selective Estrogens or Antiestrogens for Estrogen Receptor-α or Estrogen Receptor-β* (1999)

We report on the identification of novel, nonsteroidal ligands that show pronounced subtype-selective differences in ligand binding and transcriptional potency or efficacy for the two estrogen receptor (ER) subtypes, ER alpha and ER beta. An aryl-substituted pyrazole is an ER alpha potency-selective agonist, showing higher binding affinity for ER alpha and 120-fold higher potency in stimulation of ER alpha vs. ER beta in transactivation assays in cells. A tetrahydrochrysene (THC) has a 4-fold preferential binding affinity for ER beta; it is an agonist on ER alpha, but a complete antagonist on ER beta. Intriguingly, the antagonist activity of THC is associated with the R,R-enantiomer (R,R-THC). The S,S-enantiomer (S,S-THC) is an agonist on both ER alpha and ER beta but has a 20-fold lower affinity for ER beta than R,R-THC. This difference in binding affinity accounts for the full ER beta antagonist activity of the THC racemate (a 1:1 mixture of R,R-THC and S,S-THC). These compounds should be useful in probing the conformational changes in these two ERs that are evoked by agonists and antagonists, and in evaluating the distinct roles that ER beta and ER alpha may play in the diverse target tissues in which estrogens act.
Light-induced reactions of α-N-alkylanilino-ketones: formation of di-indolylmethanes (1972)

Irradiation of α-N-alkylanilino-ketones, PhN(CH2R1)·CHR2·COMe (R1 and/or R2= H, Me, or Ph), in methanol, propan-2-ol, or benzene caused fission of the α-carbon–nitrogen bond to give a secondary amine (PhNH · CH2R1), a ketone (R2CH2·COMe), an α-[p-(alkylamino) phenyl] ketone formed by para-rearrangement, and a substituted 2-methylindole formed by ortho-rearrangement with subsequent cyclodehydration. N-Alkylanilinoacetones, PhN·CH2R·CH2·COMe, also yielded a di-indol-3-ylmethane derived from the 2-methylindole. Di-indolylmethanes were also formed when anilino-ketones PhN(CH2R1)·CHR2·COMe were irradiated together with 1,2-dimethylindole. The mode of formation of di-indolylmethanes was studied and 1 -phenylazetidinols are suggested as labile intermediates. Other anilino-ketones PhNR1·CH2·COR2(R1= H, Me, or But; R2= Me, Et, But, or Ph) were also irradiated.
A Cryptanalysis of the Original Domingo-Ferrer's Algebraic Privacy Homomophism. (2003)

We propose a cryptanalysis of the original Domingo-Ferrer’s algebraic privacy homomorphism. We show that the scheme over Zn can be broken by d + 1 known plaintexts in O(d3 log n) time when it has d times expansion through the encryption. Furthermore even when the public modulus n is kept secret, it can be broken by d + 2 known plaintexts in time at most O(d5 log(dn)).
Onion Routing for Anonymous and Private Internet Connections (1999)

Preserving privacy means not only hiding the content of messages, but also hiding who is talking to whom (traffic analysis). Much like a physical envelope, the simple application of cryptography within a packet-switched network hides the messages being sent, but can reveal who is talking to whom, and how often. Onion Routing is a general purpose infrastructure for private communication over a public network [8, 9, 4]. It provides anonymous connections that are strongly resistant to both eavesdropping and traffic analysis. The connections are bidirectional, near real-time, and can be used for both connection-based and connectionless traffic. Onion Routing interfaces with off the shelf software and systems through specialized proxies, making it easy to integrate into existing systems. Prototypes have been running since July 1997. As of this article's publication, the prototype network is processing more than 1 million Web connections per month from more than six thousand IP addresses in twenty countries and in all six main top level domains. [7]
Idiopathic pulmonary fibrosis: current understanding of the pathogenesis and the status of treatment (2004)

Idiopathic pulmonary fibrosis (IPF) is a progressive and lethal pulmonary fibrotic lung disease. The diagnostic histological changes are called usual interstitial pneumonia and are characterized by histological temporal heterogeneity, whereby normal lung tissue is interspersed with interstitial fibrosis, honeycomb cysts and fibroblast foci. Pulmonary functions show restricted volumes and capacities, preserved flows and evidence of decreased gas exchange. High-resolution computed axial tomography demonstrates evidence of fibrosis and lung remodelling such as honeycomb cysts and traction bronchiectasis. There is no known effective treatment for IPF, but lung transplantation improves survival.
Decreased PARP and procaspase-2 protein levels are associated with cellular drug resistance in childhood acute lymphoblastic leukemia (2005)

Drug resistance in childhood acute lymphoblastic leukemia (ALL) and acute myeloid leukemia (AML) is associated with impaired ability to induce apoptosis. To elucidate causes of apoptotic defects, we studied the protein expression of Apaf-1, procaspases-2, -3, -6, -7, -8, -10, and poly(adenosine diphosphate [ADP]-ribose) polymerase (PARP) in cells from children with acute lymphoblastic leukemia (ALL; n = 43) and acute myeloid leukemia (AML; n = 10). PARP expression was present in all B-lineage samples, but absent in 4 of 15 T-lineage ALL samples and 3 of 10 AML cases, which was not caused by genomic deletions. PARP expression was a median 7-fold lower in T-lineage ALL (P < .001) and 10-fold lower in AML (P < .001) compared with B-lineage ALL. PARP expression was 4-fold lower in prednisolone, vincristine and L-asparaginase (PVA)-resistant compared with PVA-sensitive ALL patients (P < .001). Procaspase-2 expression was 3-fold lower in T-lineage ALL (P = .022) and AML (P = .014) compared with B-lineage ALL. In addition, procaspase-2 expression was 2-fold lower in PVA-resistant compared to PVA-sensitive ALL patients (P = .042). No relation between apoptotic protease-activating factor 1 (Apaf-1), procaspases-3, -6, -7, -8, -10, and drug resistance was found. In conclusion, low baseline expression of PARP and procaspase-2 is related to cellular drug resistance in childhood acute lymphoblastic leukemia.
Coupling carbon nanotubes through DNA linker using a biological recognition complex (2006)

Abstract We present a simple and versatile method for linking single wall carbon nanotubes (SWNT) together through DNA by non‐covalent chemistry using streptavidin‐biotin recognition complex. Streptavidin coated SWNTs are reacted with biotin or bis‐biotin ended DNA double strands leading to SWNT‐DNA and SWNT‐DNA‐SWNT adducts in high yield. This method avoids strong acidic treatment of SWNTs prior to functionalization as usually required in covalent routes. Complementary characterizations by gel electrophoresis and AFM demonstrated the efficiency of the present binding method. In addition, SWNTs bound to DNA can be aligned on a substrate using the combing properties of DNA strands, bringing a new tool into the toolkit for self‐assembling SWNTs onto surfaces. (© 2006 WILEY‐VCH Verlag GmbH &amp; Co. KGaA, Weinheim)
The RWTH Aachen German-English Machine Translation System for WMT 2014 (2014)

This paper describes the statistical machine translation (SMT) systems developed at RWTH Aachen University for the GermanEnglish translation task of the ACL 2014 Eighth Workshop on Statistical Machine Translation (WMT 2014). Both hierarchical and phrase-based SMT systems are applied employing hierarchical phrase reordering and word class language models. For the phrase-based system, we run discriminative phrase training. In addition, we describe our preprocessing pipeline for GermanEnglish.
An RNA aptamer that interferes with the DNA binding of the HSF transcription activator (2006)

Heat shock factor (HSF) is a conserved and highly potent transcription activator. It is involved in a wide variety of important biological processes including the stress response and specific steps in normal development. Reagents that interfere with HSF function would be useful for both basic studies and practical applications. We selected an RNA aptamer that binds to HSF with high specificity. Deletion analysis defined the minimal binding motif of this aptamer to be two stems and one stem-loop joined by a three-way junction. This RNA aptamer interferes with normal interaction of HSF with its DNA element, which is a key regulatory step for HSF function. The DNA-binding domain plus a flanking linker region on the HSF (DL) is essential for the RNA binding. Additionally, this aptamer inhibits HSF-induced transcription in vitro in the complex milieu of a whole cell extract. In contrast to the previously characterized NF-kappaB aptamer, the HSF aptamer does not simply mimic DNA binding, but rather binds to HSF in a manner distinct from DNA binding to HSF.
Autonomous functions of structural domains on human tissue-type plasminogen activator. (1986)

Transfected mouse Ltk- cells were employed for transient expression of recombinant human tissue-type plasminogen activator (t-PA; EC 3.4.21.31) or of recombinant-t-PA deletion proteins, encoded by SV40-pBR322-derived t-PA cDNA plasmids. The t-PA cDNA deletion mutants have two features in common, i.e., cDNA programming the signal peptide and the coding region for the light chain. Consequently, recombinant t-PA mutant proteins are efficiently secreted and display plasminogen activator activity. The gene encoding the amino-terminal heavy chain [an array of structural domains homologous to other plasma proteins (finger, epidermal growth factor, and kringle domains)] was mutated using restriction endonucleases to delete one or more structural domains. The stimulatory effect of fibrinogen fragments on the plasminogen activator activity of t-PA was demonstrated to be mediated by the kringle K2 domain and to a lesser extent by the finger/epidermal growth factor region but not by the kringle K1 domain. These data correlate well with the fibrin-binding properties of the recombinant t-PA deletion proteins, indicating that the stimulation of the activity by fibrinogen fragments is based on aligning the substrate plasminogen and t-PA on the fibrin matrix. Our results support the evolutionary concept of exon shuffling, arranging structural domains that constitute autonomous functions of the protein.
An efficient MPEG video encryption algorithm (2002)

Multimedia data security is important for multimedia commerce. Previous cryptography studies have focused on text data. The encryption algorithms developed to secure text data may not be suitable to multimedia applications because of large data sizes and real time constraints. For multimedia applications, light weight encryption algorithms are attractive. We present an efficient MPEG video encryption algorithm. This algorithm uses a secret key randomly changing the sign bits of encoded differential values of DC coefficients of I pictures and the sign bits of encoded differential values of motion vectors of B and P pictures. The encryption effects are achieved by the IDCT during MPEG video decompression processing. This algorithm adds very small overhead to MPEG codec. A software implementation is fast enough to meet the real time requirement of MPEG video applications. Experimental results show that this algorithm achieves satisfying results. We believe that it can be used to secure video-on-demand, video conferencing and video email applications.
Phase I Evaluation of ISIS 3521, an Antisense Oligodeoxynucleotide to Protein Kinase C-Alpha, in Patients With Advanced Cancer (1999)

No dose-limiting toxicity of ISIS 3521 was identified, and clinical activity was observed. A short elimination half-life was identified, which suggests that alternate schedules with prolonged administration may be necessary for further clinical development.