gebhart/patrepeval huggingface dataset:
Analysis of intracellular distribution and apoptosis involvement of the Ufd1l gene product by over‐expression studies (2003)

UFD1L is the human homologue of the yeast ubiquitin fusion degradation 1 (Ufd1) gene and maps on chromosome 22q11.2 in the typically deleted region (TDR) for DiGeorge/velocardiofacial syndromes (DGS/VCFS). In yeast, Ufd1 protein is involved in a degradation pathway for ubiquitin fused products (UFD pathway). Several studies have demonstrated that Ufd1 is a component of the Cdc48-Ufd1-Npl4 multiprotein complex which is active in the recognition of several polyubiquitin-tagged proteins and facilitates their presentation to the 26S proteasome for protein degradation or even more specific processing. The multiprotein complex Cdc48-Ufd-Npl4 is also active in mammalian cells. The biochemical role of UFD1L protein in human cells is unknown, even though the interaction between UFD1L and NPL4 proteins has been maintained. In order to clarify this issue, we examined the intracellular distribution of the protein in different mammalian cells and studied its involvement in the Fas and ceramide factors-mediated apoptotic pathways. We established that in mammalian cells, Ufd1l is localized around the nucleus and that it does not interfere with Fas-and ceramide-mediated apoptosis.
Indolizines and pyrrolo[1,2-c]pyrimidines decorated with a pyrimidine and a pyridine unit respectively (2015)

The three possible structural isomers of 4-(pyridyl)pyrimidine were employed for the synthesis of new pyrrolo[1,2-c]pyrimidines and new indolizines, by 1,3-dipolar cycloaddition reaction of their corresponding N-ylides generated in situ from their corresponding cycloimmonium bromides. In the case of 4-(3-pyridyl)pyrimidine and 4-(4-pyridyl)pyrimidine the quaternization reactions occur as expected at the pyridine nitrogen atom leading to pyridinium bromides and consequently to new indolizines via the corresponding pyridinium N-ylides. However, in the case of 4-(2-pyridyl)pyrimidine the steric hindrance directs the reaction to the pyrimidinium N-ylides and, subsequently, to the formation of the pyrrolo[1,2-c]pyrimidines. The new pyrrolo[1,2-c]pyrimidines and the new indolizines were structurally characterized through NMR spectroscopy. The X-ray structures of two of the starting materials, 4-(2-pyridyl)pyrimidine and 4-(4-pyridyl)pyrimidine, are also reported.
Ergodic theory and visualization. II. Harmonic mesochronic plots visualize (quasi)periodic sets (2008)

We present a new method of analysis of measure-preserving dynamical systems, based on frequency analysis and ergodic theory, which extends our earlier work [1]. Our method employs the novel concept of harmonic time average [2], and is realized as a computational algorithms for visualization of periodic and quasi-periodic sets or arbitrary periodicity in the phase space. Besides identifying all periodic sets, our method is useful in detecting chaotic phase space regions with a good precision. The range of method's applicability is illustrated using well-known Chirikov standard map, while its full potential is presented by studying higher-dimensional measure-preserving systems, in particular Froeschlé map and extended standard map.
Bayesian Networks based Hybrid Quantum-Classical Machine Learning Approach to Elucidate Gene Regulatory Pathways (2019)

We report a scalable hybrid quantum-classical machine learning framework to build Bayesian networks (BN) that captures the conditional dependence and causal relationships of random variables. The generation of a BN consists of finding a directed acyclic graph (DAG) and the associated joint probability distribution of the nodes consistent with a given dataset. This is a combinatorial problem of structural learning of the underlying graph, starting from a single node and building one arc at a time, that fits a given ensemble using maximum likelihood estimators (MLE). It is cast as an optimization problem that consists of a scoring step performed on a classical computer, penalties for acyclicity and number of parents allowed constraints, and a search step implemented using a quantum annealer. We have assumed uniform priors in deriving the Bayesian network that can be relaxed by formulating the problem as an estimation Dirichlet parameters. We demonstrate the utility of the framework by applying to the problem of elucidating the gene regulatory network for the MAPK/Raf pathway in human T-cells using proteomics data where the concentration of proteins, nodes of the BN, are interpreted as probabilities.
Influence of Temperature and Salt Addends on Vapor Equilibration of Headspace (1965)

SUMMARY The effects and interrelationships of time, temperature, and solute concentration on the vapor space equilibration of a dilute ester system is described. The results, which are of interest to those engaged in gas chromatographic headspace analysis or in sniff‐test methodology, show that dilute solutions behave in a predictable manner, even though the data do not fit the Clausius‐Clapeyron equation.
Impact of preoperative Controlling nutritional status (CONUT) score on perioperative morbidity and survival outcomes in patients with bladder cancer treated with radical cystectomy (2020)

Introduction: Despite several improvements in surgical technique,radical cystectomy (RC) remains an highly morbid operation and evenin contemporary series the combined surgical, medical and diseasemorbidity results in a low 5-years overall survival (OS). Furthermore,the age of patients undergoing RC has increased and the ability topredict perioperative morbidity is crucial in the preoperative workupof RC. Immune-nutritional status have gained special attention inoncological patients and might play an important role in humancancer development and progression. The controlling nutritionalstatus (CONUT), a score based on the serum albumin concentration,lymphocyte count and total cholesterol concentration, is a compre-hensive index that could provide an immune response status and long-term nutritional effect of the host. Recently, its prognostic value hasbeen reported in many types of malignancies but it’s never tested inbladder cancer (BC). The aim of the study is to evaluate the role ofpreoperative CONUT score in the assessment of both oncologicaloutcomes and perioperative morbidity in patients underwent RC fornon-metastatic BC.&#13;\nMaterials and methods: We retrospectively evaluated data from 347patients who underwent RC for BC at five european high-volumecenters between January 2002 and December 2018. Patients weredivided into two groups according to the optimal cut-off value of CONUT score. Relationships of CONUT score with clinicopathologicalcharacteristics, perioperative complications (according to the Calvien-Dindo system), 30-days readmission, 90-days mortality, cancer-specific mortality (CSM), overall mortality (OM) and progression-freesurvival (PFS) were analyzed.&#13;\nResults: Cut-off value to discriminate between high and low CONUTscore was determined calculating the ROC curve: the area under thecurve was 0.72 with an optimal cut-off of 3 points. A high preoperativeCONUT score was.significantly correlated with older age, worse ASA score, advanced pTstage, high grade and node-positive disease, positive surgical margins(PSM), higher median length of stay and 30-days readmission (allp &amp;lt; 0.05). At multivariable binomial logistic regression analysisadjusted for age, sex, BMI, ASA score, pT, pN and type of urinarydiversion, high CONUT was an independent predictor of perioperativemajorcomplications (grade 3–5) (OR 2.9; 95%CI 1.6–5.4; p &amp;lt; 0.001) and30-days readmission(OR 2.5; 95%CI 1.3–4.9; p = 0.001). At multi-variable Cox’s regression analysis adjusted for age, sex, BMI, ASA score,presence of adjuvant therapy, pT, pN, LVI, PSM and concomitant cis,high CONUT was an independent predictor of CSM(HR 3.6; 95%CI 2.4–5.5; p &amp;lt; 0.001), OM(HR 2.5; 95%CI 1.7–3.4; p &amp;lt; 0.001) and worse PFS(HR 2.7; 95%CI 1.9–3.9; p &amp;lt; 0.001).&#13;\nConclusions: Preoperative CONUT score can be used as a simple andinexpensive biomarker to predict perioperative morbidityand survivaloutcomes in patients with BC after radical cystectomy.
Pore diffusional limitations in the liquid-phase methanol synthesis process (1987)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTPore diffusional limitations in the liquid-phase methanol synthesis processVetkav Parameswaran and Sunggyu LeeCite this: Energy Fuels 1987, 1, 2, 217–222Publication Date (Print):March 1, 1987Publication History Published online1 May 2002Published inissue 1 March 1987https://pubs.acs.org/doi/10.1021/ef00002a013https://doi.org/10.1021/ef00002a013research-articleACS PublicationsRequest reuse permissionsArticle Views258Altmetric-Citations14LEARN 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
Red Orange and Bitter Orange IntegroPectin: Structure and Main Functional Compounds (2022)

DRIFT, HPLC-MS and SPME-GC/MS analyses used to unveil the structure and the main functional compounds of red (blood) orange (Citrus sinensis) and bitter orange (Citrus aurantium) IntegroPectin show evidence that these new citrus pectins are comprised of pectin rich in RG-I hairy regions functionalized with citrus biophenols, chiefly flavonoids, and volatile molecules, mostly terpenes. Remarkably, IntegroPectin from the peel of fresh bitter oranges is the first high methoxyl citrus pectin isolated so far via hydrodynamic cavitation, whereas red orange IntegroPectin is a low methoxyl pectin. C. aurantium IntegroPectin has a uniquely high concentration of adsorbed flavonoids, especially flavanone glycosides hesperidin, naringin and eriocitrin.
Introducing prob-a-sag - a probabilistic method for voltage sag management (2005)

Comprehensive voltage sag management in a power distribution system includes the technical and economic impact of sags, annual frequency of sags, as well as the effect of possible mitigative means. A probabilistic approach is required for performing the task in complicated industrial processes. Prob-a-sag is a novel method combining all these features. Two-dimensional arrays are used for expressing the quantities and carrying out the analysis or optimization. Equipment sag sensitivity is expressed as tripping probability, which enables the probabilistic sensitivity assessment of a large process. The method is very flexible; increasing the array resolution improves the result precision. If sag quantities other than depth and duration are preferred, we may increase the number of array dimensions accordingly. Prob-a-sag is compatible with any spreadsheet application, or may be implemented in sophisticated network analysis software.
Biomarkers of Disease and Treatment in Murine and Cynomolgus Models of Chronic Asthma (2012)

These results significantly advance our understanding of the biomarkers present in various tissue compartments in animal models of asthma, including those induced early during asthma and modulated with therapeutic intervention, and show that BAL cells (or their surrogate, induced sputum cells) are a viable choice for biomarker examination.
Antibody responses induced by Trichobilharzia regenti antigens in murine and human hosts exhibiting cercarial dermatitis (2008)

Cercariae of bird schistosomes (genus Trichobilharzia) are able to penetrate the skin of mammals (noncompatible hosts), including humans, and cause a Th2-associated inflammatory cutaneous reaction termed cercarial dermatitis. The present study measured the antibody reactivity and antigen specificity of sera obtained after experimental infection of mice and natural infection of humans. Sera from mice re-infected with T. regenti showed a bias towards the development of antigen-specific IgM and IgG1 antibodies and elevated levels of total serum IgE, indicative of a Th2 polarized immune response. We also demonstrate that cercariae are a source of antigens triggering IL-4 release from basophils collected from healthy human volunteers. Analysis of sera from patients with a history of cercarial dermatitis revealed elevated levels of cercarial-specific IgG, particularly for samples collected from adults (> 14 years old) compared with children (8-14 years old), although elevated levels of antigen-specific IgE were not detected. In terms of antigen recognition, IgG and IgE antibodies in the sera of both mice and humans preferentially bound an antigen of 34 kDa. The 34 kDa molecule was present in both homogenate of cercariae, as well as cercarial excretory/secretory products, and we speculate it may represent a major immunogen initiating the Th2-immune response associated with cercarial dermatitis.
Abstract 4118: Rapid, non-subjective characterization of disease in preclinical cancer research using desorption electrospray ionization mass spectrometry (2018)

Abstract Cancer tissue smears are routinely used in rapid intraoperative pathology workflows using quick staining methods to characterize cancer in surgical margin assessments or tumor pathology. Mass spectrometry (MS) is a sensitive analytic platform that can detect the presence of cancer from the pattern of cancer-specific molecules present in the mass spectrum of the tissue under examination. In particular, mass spectrometry analysis with desorption electrospray ionization (DESI-MS) is shown to have utility in research models for cancer characterization or even for grading different subclasses of disease based on tumor-specific small molecule lipid or metabolites. DESI does not require extensive tissue preparation, and the data collection and analysis can be done within a few seconds. In this work, we evaluate the combination of rapid DESI-MS detection with rapid tissue smear preparation for research use in preclinical xenograft models of breast cancer and pediatric medulloblastoma requiring only seconds of sampling, and an overall preparation and analysis time of less than one minute. Principal component analysis (PCA) was performed to evaluate the concordance between DESI-MS profiles of breast cancer from tissue slices and smears prepared on various surfaces. PCA suggested no statistical discrimination between DESI-MS profiles of tissue sections and tissue smears prepared on glass, polytetrafluoroethylene (PTFE), and porous PTFE. However, the abundances of cancer biomarker ions varied between sections and smears, with DESI-MS analysis of tissue sections yielding higher ion abundances of cancer biomarkers compared with smears. The coefficient of variance (CV) analysis suggests DESI-MS profiles from tissue smears are as reproducible as the ones from tissue sections. The limit of detection with smear samples from single pixel analysis is comparable to tissue sections that average the signal from a tissue area of 0.01 mm2. The smears prepared on the PTFE surface possessed a higher degree of homogeneity compared with the smears prepared on the glass surface. This allowed single MS scans (~1 s) from random positions across the surface of the smear to be used in rapid cancer typing with good reproducibility, providing useful pathologic information at speeds suitable for research use. Likewise, DESI-MS enabled the rapid classification of subgroups of medulloblastoma in these preclinical models. Citation Format: Michael Woolman, Alessandra Tata, Isabelle Ferry, Claudia Kuzan-Fischer, Megan Wu, Sunit Das, Michael D. Taylor, James T. Rutka, Howard J. Ginsberg, Arash Zarrine-Afsar. Rapid, non-subjective characterization of disease in preclinical cancer research using desorption electrospray ionization mass spectrometry [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 4118.
Identification of a novel recessive RELN mutation using a homozygous balanced reciprocal translocation (2007)

Two siblings from a consanguineous Egyptian marriage showed an identical phenotype of cortical lissencephaly with cerebellar hypoplasia, severe epilepsy, and mental retardation. Examination of karyotype revealed 46, t(7;12)(q22;p13)mat (7;12)(q22;p13)pat in both affected children, suggesting a homozygous reciprocal balanced translocation. Each healthy parent was a carrier of the balanced translocation in the heterozygous state, suggesting homozygous disruption of a gene involved in brain development. There were early spontaneous abortions in this family, as would be expected from transmission of an unbalanced chromosome. A disruption of RELN at 7q22.1 with absence of encoded protein was identified. This is the first demonstration that such rare homozygous translocations can be used to identify recessive disease gene mutations.
Physical and biochemical characterisation of leucocyte membrane complexes containing GP1-anchored proteins (1997)

This thesis is a study of the biochemical constituents and physical properties of leukocyte membrane complexes. The complexes studied are rich in a subset of surface glycoproteins which are anchored to the membrane by a glycosylphosphatidylinositol (GPI) moiety. The proteins have no apparent contact with the intracellular environment yet they are able to transduce cellular activation signals. The approach taken in this project was to characterise the physical properties of CD14, Thy-1, and CD59 containing complexes with respect to their solubility in non-ionic detergents. The post-translational acquisition of these physical properties by membrane proteins was also studied and was found to be dependent on the presence of a GPI anchor. The relative amounts of membrane proteins contained within the complexes was established under different solubilising conditions. The association of intracellular signalling enzymes with GPI-anchored proteins has previously been described. This was confirmed for CD14 and the nature of association was investigated both biochemically and microscopically. The results demonstrate that src-family kinase molecules are present in low density complexes present in detergent lysates and that they are associated with GPI-anchored proteins. Kinases are removed from the complexes in a temperature dependent fashion but GPI- anchored proteins remain associated indicating different mechanisms of association with the complexes. Analysis of the lipid heterogeneity within the complexes was performed under different solubilising temperatures, the results of which led to the conclusion that the physical properties of the GPI-anchored proteins within the complexes reflected those of the lipids contained in the complexes. The distribution of GPI-anchored proteins on the cell surface was examined by confocal microscopy in capping experiments, as was their association with specific kinase enzymes and their catalytic products, in an attempt to demonstrate their physical and functional association in vivo. Finally plasmids encoding GPI-anchored and transmembrane forms of the green fluorescent protein were generated. The cellular distribution of the products of the two constructs were investigated in transiently transfected Cos-7 cells. Results demonstrate an altered cellular distribution of the products of the two newly generated plasmids when compared with the product of the native GFP plasmid indicating that these will provide to be useful tools in the study of GPI-anchored protein maturation and behaviour at the cell surface
Singlet and Triplet Excitation Management in a Bichromophoric Near-Infrared-Phosphorescent BODIPY-Benzoporphyrin Platinum Complex (2010)

Multichromophoric arrays provide one strategy for assembling molecules with intense absorptions across the visible spectrum but are generally focused on systems that efficiently produce and manipulate singlet excitations and therefore are burdened by the restrictions of (a) unidirectional energy transfer and (b) limited tunability of the lowest molecular excited state. In contrast, we present here a multichromophoric array based on four boron dipyrrins (BODIPY) bound to a platinum benzoporphyrin scaffold that exhibits intense panchromatic absorption and efficiently generates triplets. The spectral complementarity of the BODIPY and porphryin units allows the direct observation of fast bidirectional singlet and triplet energy transfer processes (k(ST)((1)BDP→(1)Por) = 7.8 × 10(11) s(-1), k(TT)((3)Por→(3)BDP) = 1.0 × 10(10) s(-1), k(TT)((3)BDP→(3)Por) = 1.6 × 10(10) s(-1)), leading to a long-lived equilibrated [(3)BDP][Por]⇌[BDP][(3)Por] state. This equilibrated state contains approximately isoenergetic porphyrin and BODIPY triplets and exhibits efficient near-infrared phosphorescence (λ(em) = 772 nm, Φ = 0.26). Taken together, these studies show that appropriately designed triplet-utilizing arrays may overcome fundamental limitations typically associated with core-shell chromophores by tunable redistribution of energy from the core back onto the antennae.
Determination of Carbon Monoxide in Air by Use of Red Mercuric Oxide (1947)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTDetermination of Carbon Monoxide in Air by Use of Red Mercuric OxideJ. D. McCullough, R. A. Crane, and A. O. BeckmanCite this: Anal. Chem. 1947, 19, 12, 999–1002Publication Date (Print):December 1, 1947Publication History Published online1 May 2002Published inissue 1 December 1947https://pubs.acs.org/doi/10.1021/ac60012a016https://doi.org/10.1021/ac60012a016research-articleACS PublicationsRequest reuse permissionsArticle Views60Altmetric-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