gebhart/patrepeval huggingface dataset:
Assays for Transcriptional Activity Based on the Luciferase Reporter Gene (2003)

Reporter genes provide easy and efficient methods for the indirect measurement of relative rates of transcription. Utilizing common DNA cloning methods, a putative regulatory region can be coupled to the coding sequence of a reporter gene such that expression of the reporter protein product varies according to the regulatory potential of the DNA tested. The assays for reporter enzymes have the advantage of high sensitivity with low background, and, although an indirect measure, the amount of protein product is usually directly proportional to the level of transcriptional activation. Alternatives to reporter gene assays such as the direct measurement of the level of specific mRNAs for the endogenous gene can be influenced by RNA stability changes as well as transcription rates in response to stimulation. Assays for mRNA are also more labor intensive and difficult to quantify.
SPATULA, a gene that controls development of carpel margin tissues inArabidopsis, encodes a bHLH protein (2001)

Studies involving mutants of the gene SPATULA indicate that it promotes the growth of carpel margins and of pollen tract tissues derived from them. We show that it encodes a new member of the basic-helix-loop-helix family of transcription factors. SPATULA is expressed in marginal and pollen tract tissues throughout their development confirming its role in regulating their growth. It is also expressed in many other tissues where it may act redundantly to control growth, including the peripheral zone of the shoot apical meristem, and specific tissues within leaves, petals, stamens and roots. Expression in the stomium, funiculus and valve dehiscence zone indicates an additional role in abscission. SPATULA expression does not require the function of the other carpel development genes CRABS CLAW and AGAMOUS, although its expression is repressed in first whorl organs by the A function gene APETALA2. Further, we have shown that disruptions to gynoecial pattern formation seen in ettin mutants can largely be attributed to ectopic SPATULA action. ETTIN's role seems to be to negatively regulate SPATULA expression in abaxial regions of the developing gynoecium. SPATULA is the first basic-helix-loop-helix gene in plants known to play a role in floral organogenesis.
Visualization of IFNβ production by plasmacytoid versus conventional dendritic cells under specific stimulation conditions in vivo (2008)

Type I interferons, a protein family of multiple IFNalphas and a single IFNbeta, initially identified on the basis of their antiviral activities have recently been attributed important roles in bacterial and parasitic infections. To assess the cellular sources of IFNbeta, the IFN produced first in most situations, we created an IFNbeta reporter-knockin mouse, in which yellow fluorescent protein (YFP) is expressed from a bicistronic mRNA linked by an internal ribosomal entry site to the endogenous IFNbeta mRNA. This YFP expression allows spatiotemporal tracking of the initiation of the type I IFN response on a single-cell level. In vitro bone marrow-derived macrophages (BMMPhis) and bone marrow-derived dendritic cells (BMDCs) show IFNbeta production from distinct cell subpopulations in response to defined pathogen compounds. A subpopulation of GMCSF-derived BMDCs produced IFNbeta after poly(I:C), 3'5'-cytidylylguanosine (CpG), or LPS treatment, whereas Flt3-L-cultured plasmacytoid DCs (pDCs) responded mainly to CpG. After poly(I:C) injection in vivo, IFNbeta-producing cells localize to the splenic marginal zone and the lymph node subcapsular sinus. Infection with murine cytomegalovirus (MCMV) induces IFNbeta/YFP expression exclusively in few activated pDCs at the T cell/B cell interface of the splenic white pulp. This IFNbeta/YFP reporter mouse represents a reliable tool for the visualization and characterization of IFNbeta-producing cells in vitro and in vivo.
Clinical value of radiolabeled monoclonal antibodies in the management of carcinoma patients. (1994)

A significant number of monoclonal antibodies, suitable for in vivo management of carcinoma patients, have been recently developed and evaluated in clinical trials. They can be used successfully either for imaging or for radioimmunotherapy, although their clinical application shows advantages and limitations. With the advent of genetic engineering, it has become feasible to design molecules (i.e. chimeric and humanized antibodies, single-chain) to circumvent drawbacks or enhance a certain property. Several radionuclides can actually be used to be linked to monoclonal antibodies, including radiometallic isotopes which need bifunctional chelators. Coupling these radiometals to proteins will greatly increase diagnostic and therapeutic possibilities. The ability of radiolabeled monoclonal antibodies to localize tumors, markedly contributed to the development of a new intraoperative approach termed "Radioimmunoguided Surgery". This system, being used to better define tumor margin resection as well as occult tumor sites, is of importance in postoperative decision-making. Optimization of this technique is actually under evaluation at our Institution, especially in combination with Biological Response Modifiers.
Novel Multiubiquitin Chain Linkages Catalyzed by the Conjugating Enzymes E2EPF and RAD6 Are Recognized by 26 S Proteasome Subunit 5 (1996)

Targeting of substrates for degradation by the ATP, ubiquitin-dependent pathway requires formation of multiubiquitin chains in which the 8.6-kDa polypeptide is linked by isopeptide bonds between carboxyl termini and Lys-48 residues of successive monomers. Binding of Lys-48-linked chains by subunit 5 of the 26 S proteasome regulatory complex commits the attached target protein to degradation with concomitant release of free ubiquitin monomers following disassembly of the chains. Point mutants of ubiquitin (Lys-->Arg) were used to map the linkage specificity for ubiquitin-conjugating enzymes previously demonstrated to form novel multiubiquitin chains not attached through Lys-48. Recombinant human E2EPF catalyzed multiubiquitin chain formation exclusively through Lys-11 of ubiquitin while recombinant yeast RAD6 formed chains linked only through Lys-6. Multiubiquitin chains linked through Lys-6, Lys-11, or Lys-48 each bound to subunit 5 of partially purified human 26 S proteasome with comparable affinities. Since chains bearing different linkages are expected to pack into distinct structures, competition between Lys-11 and Lys-48 chains for binding to subunit 5 demonstrates that the latter possesses determinants for recognizing alternatively linked chains and precludes the existence of subunit 5 isoforms recognizing distinct structures. In addition, competition studies provided an estimate of Kd < or = 18 nM for the intrinsic binding of Lys-48-linked chains of linkage number n > 4. This result suggests that the principal mechanistic advantage of multiubiquitin chain formation is to enhance the affinity of the associated substrate for the 26 S complex relative to that of unconjugated target protein. Complementation studies with E1/E2-depleted rabbit reticulocyte extract demonstrated RAD6 supported isopeptide ligase-dependent degradation only through Lys-48-linked chains, while E2EPF retained the ability to target a model radiolabeled substrate through Lys-11-linked chains. Therefore, the linkage specificity exhibited by these E2 isozymes depends on their catalytic context with respect to isopeptide ligase.
Antigenicity of inactivated swine influenza virus concentrated by centrifugation. (1976)

Swine influenza virus grown in fertile chicken eggs was inactivated with a 1:4000 dilution of formalin for three days. Centrifugation at 47,000 g for 1-3 hours concentrated the viral particles. Reconstitution to 1/10 the original volume for use as a vaccine resulted in a product having an HA titer of 1:64 to 1:512. Two doses of 4 ml given three weeks apart resulted in a serologic response in three of six gilts of breeding age. Experimental challenge of two vaccinated and two control gilts to swine influenze virus showed that vaccinated gilts did not react by production of a marked HI antibody response when compared to unvaccinated gilts.
Efficient scheduling of conditional behaviors for high-level synthesis (2002)

As hardware designs get increasingly complex and time-to-market constraints get tighter there is strong motivation for high-level synthesis (HLS). HLS must efficiently handle both dataflow-dominated and controlflow-dominated designs as well as designs of a mixed nature. In the past efficient tools for the former type have been developed but so far HLS of conditional behaviors lags behind. To bridge this gap an efficient scheduling heuristic for conditional behaviors is presented. Our heuristic and the techniques it utilizes are based on a unifying design representation appropriate for both types of behavioral descriptions, enabling the proposed heuristic to exploit under the same framework several well-established techniques (chaining, multicycling) as well as conditional resource sharing and speculative execution which are essential in efficiently scheduling conditional behaviors. Preliminary experiments confirm the effectiveness of our approach and prompted the development of the CODESIS HLS tool for further experimentation.
High-throughput discovery of rare insertions and deletions in large cohorts (2010)

Pooled-DNA sequencing strategies enable fast, accurate, and cost-effect detection of rare variants, but current approaches are not able to accurately identify short insertions and deletions (indels), despite their pivotal role in genetic disease. Furthermore, the sensitivity and specificity of these methods depend on arbitrary, user-selected significance thresholds, whose optimal values change from experiment to experiment. Here, we present a combined experimental and computational strategy that combines a synthetically engineered DNA library inserted in each run and a new computational approach named SPLINTER that detects and quantifies short indels and substitutions in large pools. SPLINTER integrates information from the synthetic library to select the optimal significance thresholds for every experiment. We show that SPLINTER detects indels (up to 4 bp) and substitutions in large pools with high sensitivity and specificity, accurately quantifies variant frequency (r = 0.999), and compares favorably with existing algorithms for the analysis of pooled sequencing data. We applied our approach to analyze a cohort of 1152 individuals, identifying 48 variants and validating 14 of 14 (100%) predictions by individual genotyping. Thus, our strategy provides a novel and sensitive method that will speed the discovery of novel disease-causing rare variants.
Systemic administration of lidocaine reduces morphine requirements and postoperative pain of patients undergoing thoracic surgery after propofol–remifentanil-based anaesthesia (2009)

Systemic administration of lidocaine could reduce morphine requirements, postoperative pain and intraoperative propofol C(e) of patients undergoing thoracic surgery after propofol-remifentanil-based anaesthesia.
Colorectal and extracolonic cancer variations in MLH1/MSH2 hereditary nonpolyposis colorectal cancer kindreds and the general population (1998)

PURPOSE: This clinical case review aimed to identify phenotypic variations in colorectal and extracolonic cancer expression between hereditary nonpolyposis colorectal cancer (HNPCC) families with MLH1 and MSH2 germline mutations and the general population. METHODS: Colorectal cancer onset and site distribution were compared among 67 members of MLH1 kindreds, 45 members of MSH2 kindreds, and 1,189 patients from the general population. Synchronous and metachronous cancer rates, tumor stage, extracolonic cancer incidence, and survival were also compared. RESULTS: Mean ages of colorectal cancer onset were 44, 46, and 69 years for MLH1, MSH2, and the general population, respectively (P<0.001). More proximal and fewer distal colon cancers were noted in HNPCC than the general population (P<0.001, P=0.04). Site distribution showed disparity of rectal cancers (8 percent MLH1 vs. 28 percent MSH2; P=0.01) based on genotypes. Overall, synchronous colorectal cancer rates were 7.4, 6.7, and 2.4 percent for MLH1, MSH2, and the general population, respectively (P=0.016). Annual metachronous colorectal cancer rates were 2.1, 1.7, and 0.33 percent for MLH1, MSH2, and the general population, respectively (P=0.041). Colorectal cancer stage presentation was lower in HNPCC than the general population (P=0.0028). Extracolonic cancers were noted in 33 percent of MSH2 patients, compared with 12 percent of MLH1 patients and 7.3 percent of the general population with colorectal cancers (P<0.001). Combined MLH1 and MSH2 ten-year survival was 68.7 percent compared with 47.8 percent for the general population (P=0.009 stage stratified, hazard ratio 0.57). CONCLUSION: The presence of rectal cancer should not preclude the diagnosis of HNPCC, because the incidence of rectal cancer in MSH2 was comparable with that in the general population. Phenotypic variations, including the preponderance of extracolonic cancers in MSH2 patients, did not result in survival differences between genotypic subgroups. These phenotypic features of HNPCC genotypes may have clinical significance in the design of specific screening, surveillance, and follow-up for affected individuals.
Dextromethorphan protects against cerebral injury following transient focal ischemia in rabbits. (1988)

We investigated dextromethorphan, both a dextrorotatory opioid derivative and a clinically tested N-methyl-D-aspartate (NMDA) receptor antagonist, in a rabbit model of transient focal cerebral ischemia. Fourteen rabbits were randomly assigned to treatment with a 20 mg/kg i.v. loading dose followed by a 10 mg/kg/hr infusion of 0.4% dextromethorphan in normal saline or with an equivalent volume of normal saline alone. One hour after treatment, the rabbits underwent a 1-hour occlusion of the left internal carotid and anterior cerebral arteries followed by 4 hours of reperfusion. The seven dextromethorphan-treated rabbits showed a significant decrease in the area of neocortical severe ischemic neuronal damage (10.5%) compared with the seven normal saline-treated controls (49.6%, p less than 0.001). The dextromethorphan-treated rabbits also demonstrated significantly smaller areas of cortical edema (10.2%) on magnetic resonance imaging than the controls (38.6%, p less than 0.01). Analysis of somatosensory evoked potentials revealed recovery of the ipsilateral amplitude to contralateral values within 5 minutes of reperfusion in the dextromethorphan-treated rabbits but not in the controls (p less than 0.01). In our rabbit model of transient focal cerebral ischemia, dextromethorphan appears to protect the brain against ischemic neuronal damage and edema, as well as to promote neurophysiologic recovery. This clinically available drug should be further investigated as having potential therapeutic value in the treatment of stroke.
Atmospheric pressure ionization mass spectrometry with laser-produced ions (1986)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTAtmospheric pressure ionization mass spectrometry with laser-produced ionsLeonidas. Kolaitis and David M. LubmanCite this: Anal. Chem. 1986, 58, 9, 1993–2001Publication Date (Print):August 1, 1986Publication History Published online1 May 2002Published inissue 1 August 1986https://doi.org/10.1021/ac00122a017Request reuse permissionsArticle Views144Altmetric-Citations20LEARN 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 (1 MB) Get e-Alertsclose Get e-Alerts
Studies on glycolipids. Part VIII. Isolation and Identification of Anti-tumor-Promoting Principles from the Fresh-Water Cyanobacterium Phormidium tenue. (1993)

Bioassay-directed fractionation of the extract of the cyanobacterium P. tenue led to the isolation of the three classes of glycolipids, viz., monogalactosyl diacylglycerol (MGDG), digalactosyl diacylglycerol (DGDG), and sulfoquinovosyl diacylglycerol (SQDG) as anti-tumor-promoters. In comparing the anti-tumor-promoting effect of the three classes of glycolipids with various acyl residues, MGDG and DGDG inhibited tumor promotion more intensely than SQDG. With respect to MGDG and DGDG, the inhibitory activity of each glycolipid possessing a single pair of acyl residues was also investigated after HPLC separation. Among the 17 tested MGDGs (1a--h) and DGDGs (2a--i), three of the DGDGs (2a, b, e) showed more potent inhibitory activity toward tumor promotion than the others.
Stereochemical control on yeast reduction of .alpha.-keto esters. Reduction by immobilized bakers' yeast in hexane (1988)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTStereochemical control on yeast reduction of .alpha.-keto esters. Reduction by immobilized bakers' yeast in hexaneKaoru Nakamura, Kiyoko Inoue, Kazutoshi Ushio, Shinzaburo Oka, and Atsuyoshi OhnoCite this: J. Org. Chem. 1988, 53, 11, 2589–2593Publication Date (Print):May 1, 1988Publication History Published online1 May 2002Published inissue 1 May 1988https://pubs.acs.org/doi/10.1021/jo00246a035https://doi.org/10.1021/jo00246a035research-articleACS PublicationsRequest reuse permissionsArticle Views1331Altmetric-Citations113LEARN 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
Diffuse large cell lymphoma (2001)

A review of new or emerging ideas concerning diffuse large B-cell lymphomas is presented, with particular emphasis on histologic classification, genetic prognostic factors, first-line and salvage treatments, and specific locations such as neurologic, cutaneous, or gastrointestinal sites. This lymphoma remains the most heterogeneous of all lymphomas for its clinical characteristics and outcome. This heterogeneity is probably secondary to the fact that a large proportion of lymphomas seems to occur from a transformation of an unknown indolent lymphoma.
Influenza and the Rates of Hospitalization for Respiratory Disease among Infants and Young Children (2000)

Infants and young children without chronic or serious medical conditions are at increased risk for hospitalization during influenza seasons. Routine influenza vaccination should be considered in these children.
<title>Micromirrors for direct writing systems and scanners</title> (1999)

Three different types of deformable mirror Spatial Light Modulators (SLMs) based on device concepts like Viscoelastic Control Layer (VCL), Cantilever Beam Mirror (CBM), and Moving Liquid Mirror (MLM) have been developed. All of them allow to create deformation profiles which act as phase gratings whose period is defined by the pitch of the pixel electrodes. The diffraction of the incident light is used to achieve spatial light modulation. The operation principles of the different types of SLMs are outlined in detail. All the mentioned SLMs can be manufactured on top of a high voltage CMOS circuitry. SLMs with up to 2 million pixels in analog operation mode have been realized up to now. The benefits of the different approaches with respect to fabrication aspects and respect to different applications will be addressed. For the angular deflection of light a new type of resonant microscanner mirror was developed. The device is based on a silicon micromechanical torsional actuator. The new approach for the configuration of the electrodes and the resulting driving principle allows to achieve large scanning angles (plus or minus 30 degree optically at atmospheric pressure) at low driving voltages (20 V max.) and low power consumption (less than 1 (mu) W). The operation principle of the new device enables the realization of 2D scanners as well.
Kinetics of the acid hydrolysis of cellulose found in paper refuse (1971)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTKinetics of the acid hydrolysis of cellulose found in paper refuseRobert D. Fagan, Hans E. Grethlein, Alvin O. Converse, and Andrew PorteousCite this: Environ. Sci. Technol. 1971, 5, 6, 545–547Publication Date (Print):June 1, 1971Publication History Published online1 May 2002Published inissue 1 June 1971https://pubs.acs.org/doi/10.1021/es60053a006https://doi.org/10.1021/es60053a006research-articleACS PublicationsRequest reuse permissionsArticle Views724Altmetric-Citations77LEARN 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