gebhart/patrepeval huggingface dataset:
Effect of TGF-β2 on Proliferative Scar Fibroblast Cell Kinetics (1999)

Keloids, hypertrophic scars, and burn hypertrophic scars are all forms of proliferative scarring characterized by overabundant matrix formation. Recently these dermal proliferative disorders have been linked clinically to the cytokine transforming growth factor beta (TGF-beta), and in vitro tests have shown it to be responsible for the activation of fibroblasts and their production and deposition of collagen. Using an established in vivo animal model of proliferative scarring, the effects of this cytokine, specifically the isoform TGF-beta2, on these scars were examined. Proliferative scar specimens were implanted into athymic, asplenic nude rats and isolated in sandwich island flaps based on the superficial inferior epigastric pedicle. After establishment of the transferred flap, the scars were injected with varying doses of TGF-beta2 or vehicle for 5 consecutive days and then again on days 10, 15, and 20. The specimens were measured weekly during the period of dosing, and a biopsy was acquired on days 30 and 60. Fibroblasts from the explanted biopsies and the original scars were grown in cell culture, and cell proliferation studies were performed and the results compared. There was a dose response to TGF-beta2, with 200 ng showing the greatest effect. From the original scar specimens, keloid scars demonstrated the greatest cell proliferation kinetics--significantly faster than nonburn and burn hypertrophic scars. After treatment with TGF-beta2, both keloids and burn hypertrophic scars showed an increase in their cell proliferation kinetics compared with vehicle alone. This was not demonstrated with the nonburn hypertrophic scars. Elevated levels of TGF-beta2 are a major contributing factor to the process of proliferative scars, but because nonburn hypertrophic scars do not result in an equally increased response to this cytokine, a truly causative role for this cytokine cannot be promulgated. Rather, it is the combination of the proliferative scar fibroblasts' abnormal response to TGF-beta2 stimulation and elevated levels of this cytokine that controls more accurately the process of keloid and burn hypertrophic scar formation.
Structure and magnetic properties of MnII[N(CN)2]2(pyrazine). An antiferromagnet with an interpenetrating 3-D network structure (1998)

Mn[N(CN)2]2(pyz) (pyz = pyrazine) orders antiferromagnetically at low temperature and possesses intralayer µ-NCNCN and interlayer µ-pyz ligands that form a pseudo-ReO3 interpenetrating network structure.
DNA Transposons: Nature and Applications in Genomics (2010)

Repeated DNA makes up a large fraction of a typical mammalian genome, and some repetitive elements are able to move within the genome (transposons and retrotransposons). DNA transposons move from one genomic location to another by a cut-and-paste mechanism. They are powerful forces of genetic change and have played a significant role in the evolution of many genomes. As genetic tools, DNA transposons can be used to introduce a piece of foreign DNA into a genome. Indeed, they have been used for transgenesis and insertional mutagenesis in different organisms, since these elements are not generally dependent on host factors to mediate their mobility. Thus, DNA transposons are useful tools to analyze the regulatory genome, study embryonic development, identify genes and pathways implicated in disease or pathogenesis of pathogens, and even contribute to gene therapy. In this review, we will describe the nature of these elements and discuss recent advances in this field of research, as well as our evolving knowledge of the DNA transposons most widely used in these studies.
Reduction of nitrite to nitric oxide during ischemia protects against myocardial ischemia–reperfusion damage (2004)

Nitric oxide (NO.) is thought to protect against the damaging effects of myocardial ischemia-reperfusion injury, whereas xanthine oxidoreductase (XOR) normally causes damage through the generation of reactive oxygen species. In the heart, inorganic nitrite (NO(2)(-)) has the potential to act as an endogenous store of NO., liberated specifically during ischemia. Using a detection method that we developed, we report that under ischemic conditions both rat and human homogenized myocardium and the isolated perfused rat heart (Langendorff preparation) generate NO. from NO(2)(-) in a reaction that depends on XOR activity. Functional studies of rat hearts in the Langendorff apparatus showed that nitrite (10 and 100 microM) reduced infarct size from 47.3 +/- 2.8% (mean percent of control +/- SEM) to 17.9 +/- 4.2% and 17.4 +/- 1.0%, respectively (P < 0.001), and was associated with comparable improvements in recovery of left ventricular function. This protective effect was completely blocked by the NO. scavenger 2-(4-carboxyphenyl)-4,4,5,5-tetramethylimidazole-1-oxyl 3-oxide (carboxy-PTIO). In summary, the generation of NO. from NO(2)(-), by XOR, protects the myocardium from ischemia-reperfusion injury. Hence, if XOR is presented with NO(2)(-) as an alternative substrate, the resultant effects of its activity may be protective, by means of its production of NO. , rather than damaging.
Tiki, at the head of a new superfamily of enzymes (2013)

Tiki proteins appear to antagonize Wnt signalling pathway by acting as Wnt proteases, thereby affecting Wnt solubility by its amino-terminal cleavage. Tiki1 protease activity was shown to be metal ion-dependent and was inhibited by chelating agents and thus was tentatively proposed to be a metalloprotease. Nevertheless, Tiki proteins exhibit no detectable sequence similarity to previously described metalloproteases, but instead have been reported as being homologues of TraB proteins (Pfam ID: PF01963), a widely distributed family of unknown function and structure. Here, we show that Tiki proteins are members of a new superfamily of domains contained not just in TraB proteins, but also in erythromycin esterase (Pfam ID: PF05139), DUF399 (domain of unknown function 399; Pfam ID: PF04187) and MARTX toxins that contribute to host invasion and pathogenesis by bacteria. We establish the core fold of this enzymatic domain and its catalytic residues.
Homozygous truncation of the fibrinogen Aα chain within the coiled coil causes congenital afibrinogenemia (2000)

The molecular basis of a novel congenital afibrinogenemia has been determined. The proposita, the only affected member in a consanguineous Norwegian family, suffers from a moderate to severe bleeding disorder due to the total absence of any detectable fibrinogen. Dot blots of solubilized platelets revealed a small amount of γ chain but no A or Bβ chains, whereas no chains were detected in plasma dot blots. DNA sequencing of the A chain gene revealed a homozygous C→T transversion 557 nucleotides from the transcription initiation site. This nucleotide change predicts the nonsense mutation A 149 Arg (CGA)→stop (TGA). Early truncation of the A chain appears to result in defective assembly or secretion of fibrinogen, probably due to the removal of the C-terminal disulfide ring residues that are critically required for the formation of a stable 3-chained half molecule.
Signals, switches, regulons and cascades : control of bacterial gene expression (2002)

Editor's preface 1. Microbial reaction to environment: bacterial stress responses revisited in the genomic-proteomic era F. C. Neidhardt 2. Gene variation and gene regulation in bacterial pathogenesis D. Hood and R. Moxon 3. DNA topology and regulation of bacterial gene expression C. J. Dorman DNA rearrangements and regulation of gene expression I. C. Blomfield 4. Structures of multisubunit DNA-dependent RNA polymerases R. D. Finn, E. V. Orlova, M. van Heel and M. Buck 5. The ECF sigma factors of Streptomyces coelicolor A3(2) M. S. B. Paget, H-J. Hong, M. Bibb and M. J. Buttner 6. Secrets of bacterial transcription initiation taught by the Escherichia coli FNR protein D. Browning, D. Lee, J. Green and S. Busby 7. What can be learned from the LacR family of Escherichia coli? B. Muller-Hill 8. Regulation of the L-arabinose operon in Escherichia coli R. Schleif 9. Transcription termination control in bacteria T. M. Henkin 10. Antisense RNAs in programmed cell death K. Gerdes 11. Control of signal transduction in the sporulation phosphorelay J. A. Hoch 12. A stranglehold on a transcriptional activator by its partner regulatory protein - the case of the NifL-NifA two-component regulatory system R. Dixon 13. Is anybody here? Cooperative bacterial gene regulation via peptide signals between Gram-positive bacteria D. A. Morrison 14. Quorum sensing in Gram-negative bacteria: global regulons controlled by cell-density-dependent chemical signalling N. A. Whitehead, A. K. P. Harris, P. Williams and G. P. C. Salmond Index.
Acute Toxicity Studies of Xerox Reprographic Toners (1994)

Typical reprographic toners consist of a thermoplastic polymer or polymers as the major component, a colorant or colorants (carbon black or color pigments), and small quantities of additives such as charge control and/or lubricating/release agents. Another type of toner contains iron oxides and polymers) as the major components. As a complement to the recently published Xerox chronic inhalation studies of toners, we are reporting the acute toxicity studies of some typical Xerox toners. The studies include acute oral toxicity in rats, acute dermal toxicity in rabbits, acute inhalation toxicity in rats, eye irritation in rabbits, skin irritation in rabbits, skin sensitization in guinea pigs, and the repeated-insult patch test in humans. These studies represent our acute toxicity testing using different protocols with various toners carried out during the period 1969–1984. In addition, we recently carried out acute dermal toxicity testing at 5 g/kg with two representative toners, for the purpose of classification of waste toners in the State of California. The test results consistently indicate that all toners were practically nontoxic: oral LD 50 from &lt;5 to &lt;35 g/kg; dermal LD 50 from &lt;2 to &lt;5 g/kg; and inhalation LC 50 (4 h) from &lt;0.17 to &lt;10.2 g/m 3 . They were nonirritating to the eye and nonirritating/ nonsensitizing to the skin.
Pseudorabies virus avirulent strains fail to express a major glycoprotein (1985)

The unique short (Us) region of the pseudorabies virus (PRV) genome, which displays high transcriptional activity during the late phase of infection and has been found to code for glycoproteins, is partially deleted in the genomes of three vaccine strains (A57, Norden, and NIA-4). This deletion is located in the SalI subfragment 7A of BamHI fragment 7. To identify possible viral gene products involved in PRV virulence, we investigated the transcriptional and translational pattern of the deleted part of the Us region. Northern blots demonstrated that one major RNA species (3.8 kilobases) transcribed from fragment 7A was missing in the vaccine strains, whereas other transcripts were altered. Radioimmunoprecipitation of in vivo-labeled PRV glycoproteins and of in vitro-translated polypeptides with hyperimmune serum and monoclonal antibodies indicated a lack of glycoprotein gI. Hybrid-selection experiments with subcloned DNA fragments confirmed the absence of gI and of a 40,000-molecular-weight polypeptide. We suggest that both viral proteins are involved in the expression of PRV virulence.
Notes- Phosphorus Pentaoxide as a Reagent in Peptide Synthesis (1961)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTNotes- Phosphorus Pentaoxide as a Reagent in Peptide SynthesisBernard Erlanger and Nicholas KokowskyCite this: J. Org. Chem. 1961, 26, 7, 2534–2536Publication Date (Print):July 1, 1961Publication History Published online4 March 2003Published inissue 1 July 1961https://pubs.acs.org/doi/10.1021/jo01351a605https://doi.org/10.1021/jo01351a605research-articleACS PublicationsRequest reuse permissionsArticle Views84Altmetric-Citations16LEARN 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
Relative attributes (2011)

Human-nameable visual “attributes” can benefit various recognition tasks. However, existing techniques restrict these properties to categorical labels (for example, a person is `smiling' or not, a scene is `dry' or not), and thus fail to capture more general semantic relationships. We propose to model relative attributes. Given training data stating how object/scene categories relate according to different attributes, we learn a ranking function per attribute. The learned ranking functions predict the relative strength of each property in novel images. We then build a generative model over the joint space of attribute ranking outputs, and propose a novel form of zero-shot learning in which the supervisor relates the unseen object category to previously seen objects via attributes (for example, `bears are furrier than giraffes'). We further show how the proposed relative attributes enable richer textual descriptions for new images, which in practice are more precise for human interpretation. We demonstrate the approach on datasets of faces and natural scenes, and show its clear advantages over traditional binary attribute prediction for these new tasks.
Low temperature InP layer transfer (1999)

High quality single crystalline 3 in Inp thin layers were transferred onto oxidised Si substrates at 150°C by wafer bonding and layer splitting from InP wafers which were co-implanted by B and H ions with the H implantation performed at 90°C.
Characterization and presumptive identification of Helicobacter pylori isolates from rhesus monkeys (1994)

We characterized 38 Helicobacter isolates, including 22 from gastric biopsy samples obtained from 14 rhesus monkeys and single isolates from 16 monkeys in a different colony. Biochemical profiles of these isolates were nearly identical to that of Helicobacter pylori ATCC 43504. Restriction fragment length polymorphism (RFLP) analysis indicated that each infected monkey harbored one to four strains. The 17 RFLP types found among these 22 isolates differed from all seven RFLPs found among the other 16 isolates. Thus, monkeys within a given colony are more likely to be infected by Helicobacter isolates with the same or a similar RFLP than are monkeys from different colonies. A 16S rRNA gene was amplified by PCR and cloned from the Helicobacter isolate from rhesus monkey 85D08. Ribotyping with this probe demonstrated less diversity among isolates from rhesus monkeys than was reported among isolates of H. pylori from humans, as did RFLP analysis of a PCR fragment of the ureA-ureB gene cluster. The DNA sequence of the cloned 16S rRNA gene was determined and compared with sequences reported for H. pylori and other Helicobacter species. Our analysis of 127 nucleotides (corresponding with residues 1240 to 1366 of the Escherichia coli 16S rRNA gene) indicated that the Helicobacter isolate from monkey 85D08 was 99.2 to 100% homologous to isolates of H. pylori from humans but only 83.5 to 96.9% homologous with other Helicobacter species in this region of the 16S rRNA gene. These data provide strong support for the presumptive identification of these isolates as H. pylori.
Shallow trench isolation for advanced ULSI CMOS technologies (2002)

This paper reviews the requirements and challenges in designing a Shallow Trench Isolation (STI) process flow for 0.1 /spl mu/m CMOS technologies. Various processing techniques are described for the steps in the STI flow viz. trench definition, corner rounding, gapfill, planarization and well implants. The current capability and scaling requirements for each process step, discussed in the paper, are as follows: (a) Trenches have sidewall angle >/spl sim/80/spl deg/ to maintain trench depth and isolation at narrow space. The trench bottom is rounded to minimize stress. (b) Pad oxide undercut, prior to liner oxidation in halogen ambient or at high temperature, provides adequate corner rounding to suppress edge leakage, with minimum loss of active area. (c) HDP and TEOS-O/sub 3/ CVD oxides can fill 0.16 /spl mu/m wide trenches free of voids. Lower trench aspect ratios (thinner nitride and liner oxide, and shallower trenches), and process improvements allow scaling to smaller dimensions. Gapfill process, liner oxide, and thermal cycles are tailored to prevent stress-induced defects, trench sidewall and corner damage. (d) CMP step height uniformity is improved by using dummy active areas, nitride overlayer or patterned etchback. (e) Optimization of retrograde well and channel stop implants minimizes sensitivity of N/sup +/-P/sup +/ isolation to overlay tolerance and improves latch-up performance.
Fecal Transplant for Recurrent Clostridium difficile Infection (2013)

Clostridium difficile infection (CDI) results in clinical manifestations ranging from mild diarrhea to life-threatening pseudomembranous colitis. Infection is most often initiated by antimicrobial therapy which causes an imbalance in normal colonic microflora. The pathogenesis of C. difficile is predominantly controlled by the production of its two cytotoxins, A and B, which damage the intestinal mucosa. In recent years a nationwide increase in the rate of CDI has been noted as well as an increase in mortality, reduced initial response to antimicrobials, extended resolution time, and increased rates of recurrence. Traditional treatment includes administration of antimicrobials. Fecal microbiota transplant (FMT) is an alternative therapy for CDI that is effective and promising in multiple CDI relapse patients. This paper will provide an overview of CDI epidemiology, pathogenesis, diagnosis, and treatment, and explore the case of a 53-year-old woman suffering from her sixth episode of CDI.
Taxol and vinorelbine: a new active combination for disseminated malignant melanoma (1996)

We evaluated the activity and toxicity of two sequences of taxol combined with vinorelbine in disseminated malignant melanoma, metastatic beyond regional lymph nodes. Fifteen previously untreated patients, nine males and six females (median age 56 years), were enlisted between May 1994 and February 1995. Eight patients received vinorelbine 30 mg/m2 (maximum dose 50 mg) first, follow 24 h later by taxol 120 mg/m2 (maximum dose 240 mg) infused over 3 h (the V/T sequence). Seven patients received the reverse (T/V) sequence. In 79 administered courses there were no anaphylactic episodes, the main toxicity being alopecia (WHO grade 3). Significant neutropenia, emesis or neuropathy was not observed in either schedule (WHO grades 0 or 1). Three major responses, all with the V/T sequences, were seen; one complete (CR) in nodal and cutaneous sites lasting 13 months and two partial (PR), omental, ascites in one and hepatic, splenic and nodal in the other, lasting 7 and 6 months, respectively. Clinically meaningful tumor regressions, not qualifying strictly for the criteria of major response, were observed in two additional patients in the T/V sequence. Taxol combined with vinorelbine is active against disseminated malignant melanoma. The importance of sequencing the two drugs remains to be determined with accrual of more patients into the study.
Phase III non-inferiority study of cabazitaxel (C) 20 mg/m2 (C20) versus 25 mg/m2 (C25) in patients (pts) with metastatic castration-resistant prostate cancer (mCRPC) previously treated with docetaxel (D). (2016)

5008 Background: The Phase III TROPIC study (NCT00417079) reported a significant improvement in overall survival (OS) for C plus prednisone (P) (25 mg/m2once every 3 weeks plus 10 mg orally once daily) versus mitoxantrone plus P (Hazard Ratio [HR] 0.70; P < 0.0001) in pts with mCRPC previously treated with D. This PROSELICA study (NCT01308580) was designed to determine the relative efficacy and safety profile of C20 plus P compared with C25 plus P. Methods: In this randomized, open-label, multinational phase III study, pts with mCRPC and ECOG performance status 0–2, who progressed after treatment with D, were stratified (ECOG, RECIST, region) and randomized 1:1 to C20 or C25. To show that C20 could preserve ≥ 50% of the efficacy benefit showed by C25 in TROPIC, the HR of C20 vs C25 for the primary endpoint OS could not exceed 1.214 under 1-sided 98.89% confidence level adjusted after interim analyses. Secondary endpoints included progression free survival (PFS), safety, PSA, pain and tumor responses and quality of life. Results: From April 2011 to December 2013, 1200 pts were randomized (C20 n = 598; C25 n = 602). Patient characteristics were similar for C20 and C25. Median number of C cycles was 6 for C20 and 7 for C25. The median survival of C20 and C25 did not differ significantly and the HR boundaries (99% confidence level) were within the non-inferiority margins assumptions, therefore meeting the study’s non-inferiority endpoint. PSA and RECIST response rates were higher in C25 (see Table). Grade 3–4 adverse events: 39.7% C20; 54.5% C25. Grade 4 laboratory neutropenia: 21.3% C20; 48.6% C25. Neutropenic sepsis/infection: 2.2% C20; 6.1% C25. Conclusions: In pts with mCRPC progressing after treatment with D, C20 demonstrates non-inferiority for OS compared with C25 and an improved overall safety profile. Clinical trial information: NCT01308580.Outcome (HR) C20 N = 598 C25 N = 602 C20 vs C25 Median OS, mos 13.4 (12.19 to 14.88) 14.5 (13.47 to 15.28) Upper Limit of 98.89% Confidence Interval (CI): 1.184 Median PFS, mos 2.9 (2.79 to 3.45) 3.5 (3.12 to 3.94) HR (95% CI): 1.099 (0.974 to 1.24) PSA response, % 29.5 (25.6 to 33.3) 42.9 (38.8 to 47.1) P < 0.0001 ORR, n/N 50/271 18.5% 60/256 23.4%
Antiviral activity in L1210 cells of liposome‐encapsulated (2′‐5′)oligo(adenylate) analogues (1985)

Evidence is available for a role of a (2'-5')(A)n-activated endoribonuclease (RNase L) in the antiviral activity of interferon for several RNA viruses. (2'-5')(A)n and their analogues might thus provide an interesting alternative to exogenous interferons or their inducers in antiviral chemotherapy. In addition, the evaluation of the activity of (2'-5)(A)n as mediators of interferon's biological activities or as cell growth regulators requires biochemical studies using agonists or antagonists of the system. Non-disruptive techniques for the introduction of (2'-5')(A)n and their analogues into cell lines or tissues are required for these studies since these highly charged compounds are cell impermeable. (2'-5')(A)n oligomers and analogues of increased stability towards phosphodiesterases were derived by chemical modification of their 2' end and encapsulated in protein-A-bearing liposomes. The specific delivery of liposome contents into L1210 mouse leukemic cells was achieved with the help of monoclonal antibodies directed against the appropriate class I major histocompatibility complex-encoded proteins expressed by these cells. This intracellular delivery led to transient inhibition of protein synthesis and an antiviral activity, both compatible with activation of RNase L. This activity was enhanced for the analogues designed to resist degradation, with respect to the natural product.