gebhart/patrepeval huggingface dataset:
Advances in dynamic modeling of colorectal cancer signaling-network regions, a path toward targeted therapies (2014)

// Lorenzo Tortolina 2,* , David J. Duffy 3,* , Massimo Maffei 1,* , Nicoletta Castagnino 1,* , Aimée M. Carmody 3,* , Walter Kolch 3 , Boris N. Kholodenko 3 , Cristina De Ambrosi 2 , Annalisa Barla 2 , Elia M. Biganzoli 4 , Alessio Nencioni 1,5 , Franco Patrone 1,5 , Alberto Ballestrero 1,5 , Gabriele Zoppoli 1,5 , Alessandro Verri 2 and Silvio Parodi 1 1 Department of Internal Medicine and Medical Specializations (DIMI), University of Genoa, Italy 2 Department of Informatics, Bioengineering, Robotics and Systems Engineering (DIBRIS), University of Genoa, Italy 3 Systems Biology Ireland, Conway Institute, University College Dublin, Belfield, Dublin, Ireland 4 Unit of Medical Statistics, Biometry and Bioinformatics “Giulio A. Maccacaro”, Department of Clinical Sciences and Community Health, University of Milan, Italy 5 Istituto a Carattere di Ricerca Clinic - Scientifico (IRCCS), Azienda Ospedaliera Universitaria San Martino, Istituto Nazionale Tumori (IST), Genoa, Italy * These authors contributed equally to this work Correspondence: Silvio Parodi, email: // Keywords : Colorectal cancer, Target therapies, Signaling-network, Dynamic modeling, Onco-protein inhibitors Received : December 17, 2014 Accepted : December 28, 2014 Published : December 31, 2014 Abstract The interconnected network of pathways downstream of the TGFβ, WNT and EGF-families of receptor ligands play an important role in colorectal cancer pathogenesis. We studied and implemented dynamic simulations of multiple downstream pathways and described the section of the signaling network considered as a Molecular Interaction Map (MIM). Our simulations used Ordinary Differential Equations (ODEs), which involved 447 reactants and their interactions. Starting from an initial “physiologic condition”, the model can be adapted to simulate individual pathologic cancer conditions implementing alterations/mutations in relevant onco-proteins. We verified some salient model predictions using the mutated colorectal cancer lines HCT116 and HT29. We measured the amount of MYC and CCND1 mRNAs and AKT and ERK phosphorylated proteins, in response to individual or combination onco-protein inhibitor treatments. Experimental and simulation results were well correlated. Recent independently published results were also predicted by our model. Even in the presence of an approximate and incomplete signaling network information, a predictive dynamic modeling seems already possible. An important long term road seems to be open and can be pursued further, by incremental steps, toward even larger and better parameterized MIMs. Personalized treatment strategies with rational associations of signaling-proteins inhibitors, could become a realistic goal.
Purification and genetic characterization of gassericin E, a novel co-culture inducible bacteriocin from Lactobacillus gasseri EV1461 isolated from the vagina of a healthy woman (2016)

The origin of the strain (vagina of healthy woman) and its ability to produce bacteriocins with inhibitory activity against vaginal pathogens may be an advantage for using L. gasseri EV1461 as a probiotic strain to fight and/or prevent bacterial infections as bacterial vaginosis (BV), since it could be better adapted to live and compete into the vaginal environment.
Élevage de porcs sur litière et sur caillebotis : influences du mode de logement et d’alimentation sur les besoins en eau (2010)

National audience
Catalytic Oxidation of Volatile Organic Compounds in Industrial Off-Gases (2002)

Processes and apparatuses for catalytic oxidation of VOCs in industrial off-gases are described, including steady state and unsteady state processes, a combined adsorption-catalytic process and an advanced method of ozone induced oxidation for low concentrated exhausts. On the basis of research and development works a series of catalytic incinerators, operating in steady state and unsteady state mode, of various capacity were designed, constructed and tested in the purification of ventilation air and off-gases from VOCs. The principles of operation of different types of catalytic incinerators and possible areas of application are discussed. For VOC concentrations 150-1000 mg/m3 unsteady state catalytic incinerators of KART type should be used, for concentrations 1000-3000 mg/m3 steady state KROT apparatuses are recommended, and for concentrations over 3000 mg/m3 up to 7000 mg/m3 installations TKM-250. It is shown that for the purification of low concentrated gases with the content of organic vapors below 150 mg/m3 adsorptioncatalytic method or catalytic oxidation with ozone in the installation OKA-3000 are most effective. Main kinetic dependencies of the ozone induced oxidation of toluene and acetone over copper oxide catalyst are given and discussed. It is shown that the efficiency of this method of VOCs removal is based on low operation temperature 313-343 K, by contrast to conventional catalytic incineration by air requiring preliminary heating of the gases to 523-573 K. A special consideration is given to adsorptive damping as an efficient method for leveling the VOCs concentrations in the real industrial exhausts directed to the catalytic treatment. The use of adsorptive dampers filled with carbon allows elimination of large deviations of pollutant concentrations in the gas entering the catalyst bed, thus increasing the VOCs removal efficiency from average values. For calculations of adsorptive dampers, an equation describing the profiles of VOC concentrations in gas phase along the length of the adsorbate bed in the damper was derived.
Immune Monitoring in Recipients of a Combined Solid Organ and Facilitating Cell-Enriched Stem Cell Transplant: Durable Chimerism Predicts Outcome (2012)

Background: We have recently reported that low intensity conditioning in conjunction with facilitating cell (FC)-enriched hematopoietic stem cell transplantation (HSCT) can safely achieve high level, durable donor chimerism in unrelated and related mismatched kidney transplant recipients without acute or chronic GVHD. This is associated with stable renal function and successful IS withdrawal. We herein present data regarding the multilineage chimerism and donor-specific tolerance in our first 10 pts with ≥ 12 months F/U. Methods: HLA mismatched living donor renal Tx recipients received low intensity conditioning (fludarabine, cyclophosphamide, 200cGy TBI days -4 to -1), a living donor kidney Tx on day 0, followed by infusion of cryopreserved FC enriched HSCT on Day +1. Multilineage chimerism was assessed prospectively by STR Analysis. In addition, functional studies (MLR and CML) were performed. Results: All pts experienced an expected nadir period affecting leukocytes (ANC < 500, range 2-14 days) and platelets (< 50K, range 0-20 days). 9 of 10 pts demonstrated peripheral blood macrochimerism post-Tx, ranging from 6% to 100% at 1 month. The one pt who failed to engraft was highly sensitized (Class I PRA > 40%). No pt developed acute/chronic GVHD or “engraftment syndrome.” Mixed chimerism was lost in two pts at 3 and 6 months post-Tx. Durable multilineage (T, B, monocyte) “full donor” (>95%) chimerism was achieved in 6 pts and allowed for complete IS withdrawal. All pts demonstrated in vitro donor-specific hyporesponsiveness (DSH) by MLR +/- CML as early as 3 months post-Tx regardless of chimerism status. However, DSH present at 6 or 9 months post-Tx in pts absent/who lost peripheral blood chimerism was not predictive of further successful IS weaning, as 2 of 3 pts had subclinical rejection on their one year protocol biopsy. Full donor chimerism without GVHD correlated with the absence of in vitro proliferative responses of the 100% donor chimeric recipient PBMC against archived pre-Tx recipient stimulators Conclusions: The presence of durable, high level multilineage chimerism in combined kidney + FCRx recipients is a robust biomarker of tolerance. DSH in the first post-TX year alone does not predict successful IS withdrawal.
Designing high performance KrF and ArF single layer resists with methacrylate polymers. (1993)

The quest for a high performance positive chemically amplified (CA) resist is a significant challenge. I n this paper we will discuss two approaches to chemically amplified positive resists involving the use of a new and versatile class of acid-labile methacrylate polymers. Methacrylate terpolymers originally designed as chemically amplified positive resists for printed circuit board technology were found to have excellent optical transmission at 193nm. These materials serve as the basis for a high resolution single layer resist for ArF; imaging. In addition, these terpolymers form stable, one-phase mixtures with a variety of phenolic resins and strongly inhibit the dissolution of phenolics in aqueous base. The new dissolution inhibitors based on MMA-TBMA-MAA terpolymers have unusual and useful properties, including excellent optical transmission at 248nm, high glass transition temperatures, and dissolution inhibition/promotion power which can be tailored to accommodate the dissolution properties of a wide variety of phenolic resins.
Sequence variants of elaC homolog 2 (Escherichia coli)(ELAC2) gene and susceptibility to prostate cancer in the Health Professionals Follow-Up Study (2008)

Two non-synonymous single-nucleotide polymorphisms (SNPs), Ser217Leu and Ala541Thr, in the elaC homolog 2 (Escherichia coli) (ELAC2) gene have been related to prostate cancer risk in previous studies, though with inconsistent results. The association of ELAC2 haplotypes with prostate cancer risk has not yet been explored. We assessed whether sequence variants in ELAC2 were associated with the risk of total or aggressive prostate cancer. In a nested case-control design within the Health Professionals Follow-Up Study, we identified 659 participants with prostate cancer diagnosed after they provided a blood specimen in 1993 and before January 2000. Controls were 656 age-matched men without prostate cancer who had had a prostate-specific antigen test after providing a blood specimen. We genotyped eight tagging SNPs in ELAC2 to test for the association between sequence variances in ELAC2 and prostate cancer. No individual SNP (including Ser217Leu) was associated with the risk of prostate cancer. Ala541Thr is a rare SNP in this population. One common haplotype (hap4) was statistically significantly associated with an increased risk of prostate cancer [odds ratio (OR) = 1.39, 95% confidence interval = 1.05-1.85]. Two common promoter SNPs and three common haplotypes were statistically significantly associated with aggressive prostate cancer (carriers versus non-carriers-snp2: OR = 1.43, snp3: OR = 0.69, hap1: OR = 1.47, hap2: OR = 0.72, hap4: OR = 1.51; global P-value for all common haplotypes = 0.11). Common SNPs and haplotypes of ELAC2 were associated with risk of aggressive prostate cancer.
Fiber Optic Chemical Sensor For Jet Fuel (1990)

Leaking underground storage tanks (UST's) are contaminating the ground water in many parts of the United States, thus causing a major environmental concern. The United States Environmental Protection Agency (EPA) has mandated that all UST's (both old and newly installed double walled tanks) be monitoredl. The majority of the UST's contain hydrocarbon fuels such as gasoline, jet fuel, kerosine and diesel.
Isolation and characterization of a 70-kDa metalloprotease (gelatinase) that is elevated in Rous sarcoma virus-transformed chicken embryo fibroblasts. (1991)

Chicken embryo fibroblasts (CEF) transformed by Rous sarcoma virus (RSVCEF) secrete a 70-kDa metallo-gelatinase at elevated levels over that of normal CEF. The 70-kDa enzyme has been purified from RSVCEF conditioned medium and represents 1-3% of the total protein in the RSVCEF conditioned medium. A 22-kDa protein, which appears to be the avian form of the tissue inhibitor of metalloproteases (TIMP), is co-isolated in association with the 70-kDa enzyme and can be separated from the enzyme by gel filtration carried out under denaturing conditions. The isolated 70-kDa species is in the zymogen form. It can be activated by treatment with the organomercurial, p-aminophenylmercuric acetate (APMA), yielding a 62-kDa active species derived by an apparent autoproteolytic cleavage from the 70-kDa proenzyme as determined by both substrate gel analysis and immunoblots using a monospecific antibody to the 70-kDa proenzyme. The proenzyme is poorly activated by trypsin and not activated by plasmin. The APMA-activated enzyme rapidly degrades denatured collagens but under identical conditions is unable to degrade native collagens, including basement membrane type IV collagen. Only at very high enzyme to substrate ratios (1:2) will native type IV collagen be hydrolyzed. Partial N-terminal amino acid sequencing of both the 70-kDa proenzyme and the 62-kDa active enzyme indicates that the avian enzyme is a member of the matrix metalloprotease family (MMP-2). When CEF cultures, infected with a temperature sensitive mutant of RSV, conditional for the expression of the transforming src oncogene, were incubated at the permissive and nonpermissive temperatures, differential levels of the 70-kDa enzyme were produced in direct proportion to the functioning of the src oncogene.
Practical algorithms for finding prime attributes and testing normal forms (1989)

Several decision problems for relational schemas with functional dependencies are computationally hard. Such problems include determining whether an attribute is prime and testing if a schema is in normal form. Algorithms for these problems are needed in database design tools. The problems can be solved by trivial exponential algorithms. Although the size of the instance is usually given by the number of attributes and hence is fairly small, such exponential algorithms are not usable for all design tasks. We give algorithms for these problems whose running time is polynomial in the number of maximal sets not determining an attribute or, equivalently, the number of generators of the family of closed attribute sets. There is theoretical and practical evidence that this quantity is small for the schemas occurring in practice and exponential only for pathological schemas. The algorithms are simple to implement and fast in practice. They are in use in the relational database design tool Design-By-Example.
Extranodal Follicular Lymphoma - a Retrospective Review and Comparison with Localized Nodal Follicular Lymphoma. (2004)

Abstract Follicular lymphoma arising in an extranodal site is uncommon and its natural history and treatment is poorly characterized in the literature. We retrospectively reviewed a large cohort of patients with stage I and II follicular lymphoma and analyzed the outcomes of patients with extranodal (EN-FL) presentations to identify sites of involvement and treatment outcome, and compared these to patients with nodal follicular lymphoma. From 1967 to 1999, 668 cases of limited stage follicular lymphoma (stage I and II) were treated at the Princess Margaret Hospital. Of these, 157 cases (23.5%) presented in extra-nodal sites. The most common site of presentation was in the head and neck area (42%) followed by gastro-intestinal tract (14.6%) then skin (10.8%). The majority of patients had stage I disease (61.8%). Pathological type was follicular grade I: 22.9%, grade II: 33.1%, and grade III: 43.9%. Treatment consisted of involved field radiation therapy in 72%, combined modality therapy in 22.3% and chemotherapy alone in 3.8%. The treatment changed over time with increased use of combined modality treatment (CMT) [1967–77: 10.5%, vs. 1989–99: 33%] mainly due to the adoption of CMT for follicular grade III lymphoma. Overall complete response rate (CR) to primary treatment was 93%; the CR rate for radiation alone was 97.3%. The cumulative incidence of relapse (RR) was 44% at 10 years. The RR at 10 years was higher for patients age &gt;60 (62% vs. 49%; p =0.059) but did not vary according to stage, tumour bulk, gender or histologic grade. For extranodal lymphoma, the 10-year overall survival (OS) rate was 56% and the 10-year disease free survival (DFS) was 42% and was similar for major sites of presentation. Comparison of Stage I–II Nodal and Extra-nodal Follicular Lymphoma Nodal Follicular Lymphoma Extra-nodal Follicular Lymphoma 10 yr Overall Survival 61% 56% (p=0.97) 10 year Disease Free Survival 41% 42% (p=0.27) 10 yr Relapse Rate 50% 44% (p=0.11) In conclusion, a significant number of patients with localized FL present with extra-nodal disease, involving diverse sites. Patients with EN-FL were more likely to have follicular grade III histology. OS, DFS and RR were similar to nodal follicular lymphoma. These results suggest that the clinical management of stage I and II extra-nodal follicular lymphoma should be the same as for nodal, and that a significant proportion of patients have prolonged DFS with radiation-based therapy.
Mutational analysis of the octapeptide sequence motif at the NS1-NS2A cleavage junction of dengue type 4 virus (1992)

We have previously shown that proper processing of dengue type 4 virus NS1 from the NS1-NS2A region of the viral polyprotein requires a hydrophobic N-terminal signal and the downstream NS2A. Results from deletion analysis indicate that a minimum length of eight amino acids at the C terminus of NS1 is required for cleavage at the NS1-NS2A junction. Comparison of this eight-amino-acid sequence with the corresponding sequences of other flaviviruses suggests a consensus cleavage sequence of Met/Leu-Val-Xaa-Ser-Xaa-Val-Xaa-Ala. Site-directed mutagenesis was performed to construct mutants of NS1-NS2A that contained a single amino acid substitution at different positions of the consensus cleavage sequence or at the immediate downstream position. Three to eight different substitutions were made at each position. A total of 50 NS1-NS2A mutants were analyzed for their cleavage efficiency relative to that of the wild-type dengue type 4 virus sequence. As predicted, nearly all substitutions at positions P1, P3, P5, P7, and P8, occupied by conserved amino acids, yielded low levels of cleavage, with the exception that Pro or Ala substituting for Ser (P5) was tolerated. Substitutions of an amino acid at the remaining positions occupied by nonconserved amino acids generally yielded high levels of cleavage. However, some substitutions at nonconserved positions were not tolerated. For example, substitution of Gly or Glu for Gln (P4) and substitution of Val or Glu for Lys (P6) each yielded a low level of cleavage. Overall, these data support the proposed cleavage sequence motif deduced by comparison of sequences among the flaviviruses. This study also showed that in addition to the eight-amino-acid sequence, the amino acid immediately following the NS1-NS2A cleavage site plays a role in cleavage.
Abstract 3552: Pharmacological Inhibition or Genetic Disruption of Protein Tyrosine Phosphatase 1B Attenuates both Myocardial and Endothelial Dysfunction in Mice with Heart Failure (2008)

We have shown previously that acute, in vitro inhibition of protein tyrosine phosphatase 1B (PTP1B) improved endothelial function of peripheral resistance arteries in mice with chronic heart failure (CHF), as demonstrated by the restored flow-mediated, NO-dependent vasodila-tation (FMD). This is most likely due to increased tyrosine phosphorylation pathways involved in shear stress-induced activation of eNOS. The present study evaluates the impact of chronic pharmacological inhibition or genetic disruption of PTP1B, on cardiac and endothelial dysfunction in CHF mice. CHF was induced by coronary ligation, either in C57BL/6 mice, or in wild type (WT) or PTP1B-deficient (PTP1B−/−) BALB/c mice. CHF mice (either C57BL/6 or BALB/c WT) were untreated or treated with the PTP1B inhibitor AS279 (60 mg/kg/day) for 2 months. Mice were then anesthetized with isoflurane for echocardiographic evaluation of left ventricular (LV) function and remodeling. After euthanasia, small mesenteric artery segments were isolated and mounted in an arteriograph for the evaluation of FMD. Echocardiographic results are shown in the Table . In parallel, in vitro vascular studies showed that chronic AS279 restored FMD both in C57BL/6 (max FMD: control: 17±2, n=9; CHF untreated: -1±1, n=9; CHF + AS279: 14±2%, n=19; p<0.01 vs. CHF untreated) and BALB/c CHF mice (Control: 29±4, n=16; CHF untreated: 7±1, n=5; CHF + AS279: 24±6%, n=7; p<0.01 vs. CHF untreated). Compared to CHF WT, FMD was also increased in PTP1B−/− CHF mice (WT: 7±1, n=5, PTP1B−/−: 16±6%, n=6, p<0.05). Additionally, in vitro downregulation of PTP1B (by a 3 day incubation with shRNA) also increased FMD in arteries isolated from CHF mice (max FMD: untreated: 6±2; scrambled shRNA: 7±2; shRNA PTP1B: 27±2%, p<0.01). Thus, chronic pharmacological inhibition or genetic disruption of PTP1B both restores endothelial function and improves cardiac dysfunction and remodeling, suggesting that this enzyme may be a new target for the treatment of CHF. Echocardiographic results in mice with 2 months CHF
From the Decks to the Bridges: Optoelectronics in [2.2]Paracyclophane Chemistry (2010)

Abstract In this microreview, we highlight optical properties of [2.2]paracyclophanes (pCps). We demonstrate how the spectroscopic properties that stem from the strained and π‐stacked structure have resulted in pCps being incorporated in materials science and polymer synthesis. As a result of chromophore substitution, internal charge transfer (ICT) between the two rings of the cyclophane core produce frameworks with unique optical properties. Deck‐substituted molecules and polymers have beensynthesized that possess donor and acceptor groups that affect internal charge transfer (ICT). We also demonstrate that bridge‐substituted [2.2]paracylophanes, although not well studied in this context, display unexpected optical properties owing to nonconventional ICT. A highlight is a recent templated solid‐state synthesis that affords a pCp that exhibits dramatic red‐shifted fluorescence.
Derivatives of 1,2,3,4-Tetramethylcyclobutene. Stable Cations in Sulfuric Acid<sup>1</sup> (1963)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTDerivatives of 1,2,3,4-Tetramethylcyclobutene. Stable Cations in Sulfuric Acid1Charles F. Wilcox Jr. and David L. NealyCite this: J. Org. Chem. 1963, 28, 12, 3446–3450Publication Date (Print):December 1, 1963Publication History Published online1 May 2002Published inissue 1 December 1963https://pubs.acs.org/doi/10.1021/jo01047a041https://doi.org/10.1021/jo01047a041research-articleACS PublicationsRequest reuse permissionsArticle Views58Altmetric-Citations10LEARN 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