gebhart/patrepeval huggingface dataset:
Factors Contributing to the Loss of Ethanologenicity of Escherichia coli B Recombinants pL0I297 and KO11 (1996)

To be economic and to be compatible with modern continuous bioconversion systems, it is imperative that the process organism exhibit an extremely high degree of stability. In the case of ethanol production from lignocellulosic biomass, functional stability of the potential process biocatalyst can be assessed in terms of the capacity to sustain high-performance fermentation during the continuous fermentation of biomass-derived sugars. This investigation employed glucose-or xylose-limited chemos tat culture to examine the functional stability of two patented, genetically engineered E. coli—namely E. coli B (ATCC 11303) carrying the Zymomonas genes for pyruvate decarboxylase and alcohol dehydrogenase II on a multicopy plasmid pLOI297 and a chromosomal pet integrant of strain 11303, designated as strain K011. Both recombinants carry markers for antibiotic resistance and have been reported to exhibit genetic stability in the absence of antibiotic selection. Chemostats were fed with Luria broth (LB) (with 25 gil sugar) at a dilution rate of 0.14 and 0.07 /h when the feed medium was glucose-LB and xylose-LB, respectively. The pH was controlled at 6.3. With glucose, both recombinants exhibited a rapid loss of ethanologenicity even when selection pressure was imposed by the inclusion of antibiotics in the feed medium. With strain KOll, increasing the concentration of chloramphenicol from 40 to 300 mg/L, resulted in a retardation in the rate of loss of ethanologenicity, but it did not prevent it. Under xylose limitation, the plasmid-bearing recombinant appeared to be stabilized by antibiotics, but this did not reflect genetic stability, since the slower-growing revertant was washed out at a dilution rate of 0.07/h. With both recombinants, interpretation of functional stability with xylose was complicated by the inherent ethanologenicity associated with the host culture. Based on an average cost for large bulk quantities of antibiotics at $55/kg and an amendment level of 40 g/ m3, the estimated economic impact regarding the potential requirement for operational stabilization by antibiotics in a plant operating in batch mode varied from a maximum of 29¢/ gal of E95 ethanol for antibiotic amendment of all fermentation media to a minimum of O.45¢/ gal where antibiotics were used exclusively for the preparation of the inocula for every fourth batch fermentation cycle. The high degree of instability observed in these continuous fermentations does not auger well for the proposed potential industrial utility of these patented, genetically engineered constructs for the production of fuel ethanol from biomass and wastes.
Bidirectional Transmembrane Signaling by Cytoplasmic Domain Separation in Integrins (2003)

Although critical for development, immunity, wound healing, and metastasis, integrins represent one of the few classes of plasma membrane receptors for which the basic signaling mechanism remains a mystery. We investigated cytoplasmic conformational changes in the integrin LFA-1 (alphaLbeta2) in living cells by measuring fluorescence resonance energy transfer between cyan fluorescent protein-fused and yellow fluorescent protein-fused alphaL and beta2 cytoplasmic domains. In the resting state these domains were close to each other, but underwent significant spatial separation upon either intracellular activation of integrin adhesiveness (inside-out signaling) or ligand binding (outside-in signaling). Thus, bidirectional integrin signaling is accomplished by coupling extracellular conformational changes to an unclasping and separation of the alpha and beta cytoplasmic domains, a distinctive mechanism for transmitting information across the plasma membrane.
Post‐transcriptional silencing of a neomycin phosphotransferase II transgene correlates with the accumulation of unproductive RNAs and with increased cytosine methylation of 3′ flanking regions (1997)

The transgenic tobacco plant GVCHS(320)‐1 harbours several T‐DNAs with the neomycin phosphotransferase II ( nptll )‐encoding chimeric gene under control of the cauliflower mosaic virus 35S promoter (CaMV 35S). These T‐DNAs are distributed over two loci, named A and B. The primary transformant GVCHS(320)‐1 had substantially reduced steady‐state nptll transcript levels due to the activity of a post‐transcriptional silencing mechanism. Silencing of the nptll ‐encoding transgenes in the progeny of GVCHS(320)‐1 requires the presence of the A locus that consists of two physically separated T‐DNAs. Although the B locus contains three T‐DNAs in the same orientation, it gives rise to high steady‐state nptll mRNA levels and NPTII protein levels even in homozygous condition. The B locus only becomes silenced in trans in the presence of a silencing locus. The data suggest that silencing of the nptll transgenes is reinforced by ageing. It is also suggested that silencing is correlated with a reduced NPTII protein/ nptll mRNA ratio, which may be interpreted as the accumulation of unproductive nptll RNA molecules in silenced plants. The data further demonstrate that the silenced state is correlated with extensive C‐methylation of diagnostic sites in the 3′ three‐quarters of the coding sequence and in the 3′ region up to 1400 bp downstream of the polyadenylation signal.
Experimental validation of predicted temperature rises in tissue-mimicking materials (1993)

Increasingly, it is recognised that diagnostic ultrasound is capable of causing temperature rises sufficient to damage tissue. Predictions of this heating are often based on simplified models of both the in vivo conditions and the relevant physical effects. Few measurements have been made to verify these predictions, however, particularly for the tightly focused beams often employed in diagnosis. Furthermore, non-linear effects in both the acoustic field and the surrounding medium have largely been ignored in calculations. To provide an alternative way to estimate the heating, NPL has developed a measurement system to determine directly the temperature rise in tissue-mimicking materials. If necessary, the measurement results can be processed to model the effects of blood perfusion. The temperature is measured using thin-film thermocouples which have essentially no interaction with the ultrasound or thermal fields. Measurements were made on transducers operating in the frequency range 2-10 MHz and with focal beam-widths from 1 to 3 mm. The measurements agree with theoretical predictions that use either the measured beam-profile or a simplified (Gaussian) model. The results are also compared with the standard soft-tissue models developed by the National Council on Radiation Protection and Measurements (NCRP) and jointly between the American Institute of Ultrasound in Medicine and the National Electrical Manufacturers Association (AIUM/NEMA). On average, the predictions of the NCRP formula are 15% higher than the measurements, confirming its validity as a worst-case model. The predictions based on the AIUM/NEMA formula, however, are typically 30% lower than the measured values.
Physical and Genetic Mapping of the Human X Chromosome Centromere: Repression of Recombination (1998)

Classical genetic studies in Drosophila and yeast have shown that chromosome centromeres have a cis-acting ability to repress meiotic exchange in adjacent DNA. To determine whether a similar phenomenon exists at human centromeres, we measured the rate of meiotic recombination across the centromere of the human X chromosome. We have constructed a long-range physical map of centromeric alpha-satellite DNA (DXZ1) by pulsed-field gel analysis, as well as detailed meiotic maps of the pericentromeric region of the X chromosome in the CEPH family panel. By comparing these two maps, we determined that, in the proximal region of the X chromosome, a genetic distance of 0.57 cM exists between markers that span the centromere and are separated by at least the average 3600 kb physical distance mapped across the DXZ1 array. Therefore, the rate of meiotic exchange across the X chromosome centromere is <1 cM/6300 kb (and perhaps as low as 1 cM/17,000 kb on the basis of other physical mapping data), at least eightfold lower than the average rate of female recombination on the X chromosome and one of the lowest rates of exchange yet observed in the human genome.
Isolation and Characterization of Human Monoclonal Antibodies from Individuals Infected with West Nile Virus (2006)

Monoclonal antibodies (MAbs) neutralizing West Nile Virus (WNV) have been shown to protect against infection in animal models and have been identified as a correlate of protection in WNV vaccine studies. In the present study, antibody repertoires from three convalescent WNV-infected patients were cloned into an scFv phage library, and 138 human MAbs binding to WNV were identified. One hundred twenty-one MAbs specifically bound to the viral envelope (E) protein and four MAbs to the premembrane (prM) protein. Enzyme-linked immunosorbent assay-based competitive-binding assays with representative E protein-specific MAbs demonstrated that 24/51 (47%) bound to domain II while only 4/51 (8%) targeted domain III. In vitro neutralizing activity was demonstrated for 12 MAbs, and two of these, CR4374 and CR4353, protected mice from lethal WNV challenge at 50% protective doses of 12.9 and 357 mug/kg of body weight, respectively. Our data analyzing three infected individuals suggest that the human anti-WNV repertoire after natural infection is dominated by nonneutralizing or weakly neutralizing MAbs binding to domain II of the E protein, while domain III-binding MAbs able to potently neutralize WNV in vitro and in vivo are rare.
The evolution of percutaneous spinal endoscopy and discectomy: state of the art. (2000)

The 2.8 mm operating channel scope produced clear visualization of annular tears, disc fragments, foraminal osteophytes, and the epidural space. Monitoring of the microinstruments in the disc space and spinal canal was readily accomplished. The quality of the imaging provided by discography improved the definition of the disc pathology. Adjuvant use of lasers, radiofrequency, chymopapain, and intradiscal steroids and the newer slotted tube system, have contributed to the advances in minimally invasive technique for endoscopic discectomy.
Functional Polymers from Novel Carboxyl-Terminated Trithiocarbonates as Highly Efficient RAFT Agents (2002)

ADVERTISEMENT RETURN TO ISSUEPREVCommunication to the...Communication to the EditorNEXTFunctional Polymers from Novel Carboxyl-Terminated Trithiocarbonates as Highly Efficient RAFT AgentsJohn T. Lai, Debby Filla, and Ronald SheaView Author Information Noveon, Inc., 9911 Brecksville Rd, Brecksville, Ohio 44141 Cite this: Macromolecules 2002, 35, 18, 6754–6756Publication Date (Web):August 2, 2002Publication History Received8 March 2002Revised12 July 2002Published online2 August 2002Published inissue 1 August 2002https://pubs.acs.org/doi/10.1021/ma020362mhttps://doi.org/10.1021/ma020362mrapid-communicationACS PublicationsCopyright © 2002 American Chemical SocietyRequest reuse permissionsArticle Views26091Altmetric-Citations1327LEARN 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 SUBJECTS:Monomers,Organic compounds,Polymers,Radical polymerization,RAFT polymerization Get e-Alerts
Electronic Media Content (1991)

PRAY TV: TELEVANGELISM IN AMERICA by Steven Bruce (New York: Routledge, Chapman & Hall, 1990–$16.95, paper, ISBN 0-415-03098-6, 272 pp.) RELIGIOUS TELEVISION: CONTROVERSIES AND CONCLUSIONS edited by Robert Abelman and Stewart M. Hoover (Norwood, NJ: Ablex, 1990—price not given, ISBN 0-89391-643-9, 366 pp.) THE GAME BEHIND THE GAME: HIGH STAKES, HIGH PRESSURE IN TELEVISION SPORTS by Terry O'Neil (New York: Harper & Row [now HarperCollins], 1989—$17.95, ISBN 0-06-016019-5, 291 pp.) GAMES AND SETS: THE CHANGING FACE OF SPORT ON TELEVISION by Steven Barnett (London: British Film Institute/Bloomington: Indiana University Press, 1990—$35.00/13.95, ISBN 0-85170-267-8 hard, 0-85170-268-6 paper, 214 pp.) SPLIT IMAGE: AFRICAN AMERICANS IN THE MASS MEDIA edited by Jannette L. Dates and William Barlow (Howard University Press, 2900 Van Ness St. NW, Washington, DC 20008—$29.95/14.95, ISBN 0-88258-035-3 hard, 0-88258-063-9 paper, 492 pp.) TELEVISION AND WOMEN'S CULTURE: THE POLITICS OF THE POPULAR edited by Mary Ellen Brown (Newbury Park, CA: Sage, 1990—$45.00/18.95, ISBN 0-8039-8228-3 hard, and 0-8039-8229-1 paper, 244 pp.) SOCIAL AND CULTURAL ASPECTS OF VCR USE edited by Julia R. Dobrow (Hillsdale, NJ: Lawrence Erlbaum, 1990—$29.95, ISBN 0-8058-0499-4, 219 pp.) ADVENTURES ON PRIME TIME: THE TELEVISION PROGRAMS OF STEPHEN J. CANNELL by Robert J. Thompson (New York: Praeger, 1990—$37.95, ISBN 0-275-93330-X, 143 pp.)
Priming Interleukin 8 Production (1999)

Although LPS and PAF activated p38, only LPS induced IL-8 production; PAF acted as a priming agent. It seems that p38 activation is necessary but not sufficient for IL-8 production by human mononuclear cells. Identifying and evaluating the activation state of inflammatory signal transduction pathways might lead to methods for controlling and preventing neutrophil-induced tissue injury without interfering with the normal host immune response.
Psoriatic Skin (1965)

All cutaneous neural elements in clinically normal-looking skin from psoriatics are altered compared with those in skin from healthy persons, whose genetical makeup does not include a family history of psoriasis. Accelerated turnover of neural elements goes hand-in-hand with invasion of the epidermis by axons, Schwann cells, and perineurial cells. These are shed together with keratin. In plaques this process is intensified, the majority of adventitial cells being distorted Schwann or perineurial cells. Fewer cells and axons penetrate the hyperplastic epidermis, but immigrant cells damage epidermal cells in their pathway. Some of the dermal and epidermal cells in both clinically normal and plaque skin are strongly periodic acid-Schiff (PAS) positive. Despite alterations of innervation, no changes in cutaneous sensibility were found in either clinically normal skin or plaques of psoriatics.
Electroreduction of Oxygen in Polymer Electrolyte Fuel Cells by Activated Carbon Coated Cobalt Nanocrystallites Produced by Electric Arc Discharge (1997)

Carbon-coated fcc cobalt nanocrystallites produced by the carbon arc method have practically no activity as catalysts for O2 reduction in H2/O2 polymer electrolyte fuel cells. This material, containing 17.0 wt % Co, was activated by a pyrolysis step at 1000 °C in Ar containing acetonitrile vapor. When it was used at the cathode of a single fuel cell element, it provided an initial current of 0.10 A/cm2 mg of Co at 0.5 V and 50 °C. This current decreased by 40% after 300 h. Only a fraction of the carbon-coated metal in the initial material was activated by the pyrolysis treatment. XPS and TEM characterizations were performed on the catalyst at various stages of its preparation.
Storage of messenger RNA in eukaryotes: Envelopment with protein, translational barrier at 5′ side, or conformational masking by 3′ side? (1994)

Messenger RNA can be stored in the cytoplasm of higher Eukaryotes in the form of masked messenger ribonucleoprotein particles (masked mRNPs, or informosomes). The typical example is the storage of mRNPs in germ cells (oocytes and spermatocytes). The masked mRNPs are inactive in translation, stable, i.e., protected against degradation, and unavailable for poly(A) tail processing, such as cytoplasmic polyadenylation and deadenylation. The major nonspecific mRNA-binding protein forming mRNPs and belonging to a special p50 family of basic, glycine-rich, phosphorylatable proteins seems to be necessary, but not sufficient for the masking. In some cases, mRNA-specific repressor proteins bound to the 5'-untranslated regions (5'-UTR) of mRNAs may be involved. Interactions of the 3'-untranslated regions (3'-UTR) with sequence-specific proteins seem to be of decisive importance for the masking of mRNPs. The hypothesis is proposed that the masking is achieved through a 3'-UTR-induced conformational rearrangement of mRNP; closing into a circle and condensation of mRNP are considered plausible.
Method development and validation for clinical cfDNA extraction from blood. (2015)

e22185 Background: Detection of cell-free DNA (cfDNA, 100-300 base pairs) in blood and body fluids is of growing interest for non-invasive diagnosis and monitoring of disease in cancer patients. This study was designed to create a robust, standardized process for clinical cfDNA isolation from blood. Methods: Pre-analytical and analytical components of cfDNA extraction suitable for clinical environments were evaluated, including specimen collection and stability, plasma preparation, cfDNA extraction and quantification, and reference range determination. Data was analyzed with IBM SPSS Statistics 22 package (95% CI). Results: Specimen Collection and Stability. Paired samples (n = 36) were collected in K3EDTA (BD) and BCT tubes (STRECK). STRECK tubes offered 24% higher cfDNA yields (p = 0.008, CI = -6.7 to -1.1) and sample stability up to 14 days without significant loss of cfDNA (n = 5, p = 0.853, CI = -1.6 to 1.8). Plasma Preparation. Standard double-spin (800 g x 10 min, 18000 g x 10 min) and single-spin (2500 g x 10 min) centrifugation protocols produced plasma cfDNA of similar quality and quantity (n = 5, p = 0.174, CI = -6.2 to 24.6). cfDNA Extraction. Two automated extraction platforms were evaluated - QIAGEN QIAsymphony SP and Roche MagNA Pure Compact. Both produced comparable cfDNA yields from 1 ml of plasma (n = 20, p = 0.21, CI = -62.4 to 14.7). QIAsymphony SP was implemented due to its ability to process up to 3 mL of plasma with linear yields (n = 10, p = 0.806, CI = -18.1 to 14.5) and within run and between run precision of 25% (n = 12) and 27% (n = 18), respectively. Reagent lot to lot variation was 14% (n = 8). cfDNA Quantification. Agilent 2200 TapeStation (TS) and 2100 Bioanalyzer (BA) were compared (n = 45). Unlike BA, TS does not run samples through a common channel, eliminating interference from carry-over. TS provided linear measurements for dilutions up to 1:320 and within run precision of 8% (n = 5). Reference Range. In healthy volunteers, the median plasma cfDNA concentration was 4 ng/ml with a maximum of 13 ng/mL (n = 30). Conclusions: We have developed a robust, semi-automated, scalable method that yields high quality cfDNA for clinical diagnostic and monitoring applications.
Isotope selection for permanent prostate implants? An evaluation of 103Pd versus 125I based on radiobiological effectiveness and dosimetry. (2000)

Transperineal interstitial permanent prostate brachytherapy (TIPPB) has become an increasingly popular treatment for early-stage/favorable-risk adenocarcinoma of prostate. Within TIPPB, permanent implants often use either (103)Pd (T(1/2) = 17 days) or (125)I (T(1/2) = 60 days). This review compares the radiobiological and treatment planning effectiveness of (103)Pd and (125)I implants by using the linear-quadratic model with recently published data regarding: prostate tumor cell doubling times, T(pot), alpha and alpha/beta, ratio. The tumor potential doubling times (T(pot)) were determined based on recently published proliferation constants (K(p)). The initial slope of the cell radiation dose survival curve, alpha, the terminal slope beta and the alpha/beta ratio were taken from recent published clinical and cellular results. The total dose delivered from each isotope was the dose used clinically, that is, 120 Gy for (103)Pd and 145 Gy for (125)I. Dale's modified linear-quadratic equation was used to estimate the biological effective dose, the cell-surviving fraction, the effective treatment time, and the wasted radiation dose for different values of T(pot). Treatment plans for peripherally loaded implants were compared. The T(pot) reported for organ-confined prostate carcinomas varied from 16 to 67 days. At short T(pot) both isotopes were less effective, but (103)Pd had much less dependence on T(pot) than (125)I. However, at long T(pot) both isotopes produced similar effects. The minimum surviving fraction for exposure to (103)Pd decreased from 1.40 x 10(-4) to 1.31 x 10(-5) as the T(pot) increased from 16 to 67 days. By contrast for exposure to (125)I, the minimum surviving fraction decreased from 3.98 x 10(-3) to 1.98 x 10(-5) over the same range of T(pot). A comparison of treatment plans revealed that (103)Pd plans required more needles and seeds; however, this was a function of seed strength. Both isotopes had similar dose-volume histograms for prostate, urethra, and rectum. The theoretical prediction of effectiveness using the linear quadratic equation for the common clinically prescribed total radiation doses indicated that (103)Pd should be more effective than (125)I because it had less dependence on T(pot). The greatest benefit of (103)Pd was shown to be with tumors with a short T(pot). Although the regrowth delay would be longer with (125)I, the benefit was inconsequential compared with the very slow doubling times of localized prostate cancer. Treatment planning with either isotope revealed no significant differences. These findings may explain why clinically there seemed to be no clear difference in treatment outcome with either isotope. Based on these predictions, we recommend a clinical trial to compare the efficacy of the two isotopes.
RNF20 Links Histone H2B Ubiquitylation with Inflammation and Inflammation-Associated Cancer (2016)

Factors linking inflammation and cancer are of great interest. We now report that the chromatin-targeting E3 ubiquitin ligase RNF20/RNF40, driving histone H2B monoubiquitylation (H2Bub1), modulates inflammation and inflammation-associated cancer in mice and humans. Downregulation of RNF20 and H2Bub1 favors recruitment of p65-containing nuclear factor κB (NF-κB) dimers over repressive p50 homodimers and decreases the heterochromatin mark H3K9me3 on a subset of NF-κB target genes to augment their transcription. Concordantly, RNF20(+/-) mice are predisposed to acute and chronic colonic inflammation and inflammation-associated colorectal cancer, with excessive myeloid-derived suppressor cells (MDSCs) that may quench antitumoral T cell activity. Notably, colons of human ulcerative colitis patients, as well as colorectal tumors, reveal downregulation of RNF20/RNF40 and H2Bub1 in both epithelium and stroma, supporting the clinical relevance of our tissue culture and mouse model findings.