gebhart/patrepeval huggingface dataset:
Transflip mutations produce deletions in pancreatic cancer (2015)

Pancreatic ductal adenocarcinoma (PDAC) is driven by the inactivation of the tumor suppressor genes (TSGs), CDKN2A (P16) and SMAD4 (DPC4), commonly by homozygous deletions (HDs). Using a combination of high density single-nucleotide polymorphism (SNP) microarray and whole genome sequencing (WGS), we fine-mapped novel breakpoints surrounding deletions of CDKN2A and SMAD4 and characterized them by their underlying structural variants (SVs). Only one third of CDKN2A and SMAD4 deletions (6 of 18) were simple interstitial deletions, rather, the majority of deletions were caused by complex rearrangements, specifically, a translocation on one side of the TSG in combination with an inversion on the other side. We designate these as "TransFlip" mutations. Characteristics of TransFlip mutations are: (1) a propensity to target the TSGs CDKN2A and SMAD4 (P < 0.005), (2) not present in the germline of the examined samples, (3) non-recurrent breakpoints, (4) relatively small (47 bp to 3.4 kb) inversions, (5) inversions can be either telomeric or centromeric to the TSG, and (6) non-reciprocal, and non-recurrent translocations. TransFlip mutations are novel complex genomic rearrangements with unique breakpoint signatures in pancreatic cancer. We hypothesize that they are a common but poorly understood mechanism of TSG inactivation in human cancer. © 2015 Wiley Periodicals, Inc.
Characterization of Complement Factor H Binding toYersinia enterocoliticaSerotype O:3 (2008)

A number of bacteria bind factor H (FH), the negative regulator of the alternative complement pathway, to avoid complement-mediated killing. Here we show that a gram-negative enteric pathogen, Yersinia enterocolitica serotype O:3, uses two virulence-related outer membrane (OM) proteins to bind FH. With Y. enterocolitica O:3 mutant strains displaying different combinations of surface factors relevant to complement resistance, we demonstrated that the major receptor for FH is the OM protein YadA. Another OM protein, Ail, also contributes to FH binding provided that it is not blocked by distal parts of the lipopolysaccharide (i.e., the O antigen and the outer core hexasaccharide). Importantly, we demonstrated that surface-bound FH was functional; both YadA- and Ail-bound FH displayed cofactor activity for factor I-mediated cleavage of C3b. With truncated recombinant FH constructs, we located the binding site of Ail specifically to short consensus repeats 6 and 7 of FH, while YadA showed a novel type of FH-binding pattern and appears to bind FH throughout the entire FH molecule. We thus conclude that Y. enterocolitica, via YadA and Ail, recruits functionally active FH to its surface. FH binding appears to be an important mechanism of the complement resistance of this pathogen.
Supplementary Figures 1-4 from Loss of E-Cadherin Promotes Ovarian Cancer Metastasis via α<sub>5</sub>-Integrin, which Is a Therapeutic Target (2023)

Supplementary Figures 1-4 from Loss of E-Cadherin Promotes Ovarian Cancer Metastasis via α&lt;sub&gt;5&lt;/sub&gt;-Integrin, which Is a Therapeutic Target
High Clarity, Thermally Stable and Mechanically Robust Titania Nanocomposites: Probing the Role of Binding Agent (2013)

Highly transparent nanocomposites were produced by in situ generation of titania network into an aromatic polyamide through a sol–gel process. These nanocomposites were fabricated using two different strategies, system-I involved the interaction of hydroxyl groups present on the backbone of the matrix with tetraisopropylorthotitanate (TPOT), while in system-II, 3-isocyanatopropyltriethoxysilane (ICTS) was exploited for extensive bonding between titania and hydroxyl groups of aromatic polyamide derived from the condensation of different diamines and terephthaloyl chloride. Thin nanocomposite films were analyzed for their structural, optical, mechanical, thermal, and morphological analyses. FTIR data confirmed the formation of nanocomposites and interaction among the phases. Tensile properties of these materials were improved with increasing titania content relative to pure polyamide. FESEM micrographs clearly showed homogeneous distribution of titania at nanolevel in the matrix. Thermal decomposition and glass transition temperatures of nanocomposites were found in the ranges 450–550 °C and 285–328 °C, respectively, depicting high thermal stability and interactions between the two phases.
ChemInform Abstract: Interconversion of CO2 and Formic Acid by Bio‐Inspired Ir Complexes with Pendent Bases (2014)

Abstract Review: 62 refs.
Sustained Antibacterial Activity from Triclosan-Loaded Nanostructured Mesoporous Silicon (2010)

In this work, nanostructured particles of porous silicon are demonstrated to act as an effective carrier for the sustained delivery of antibacterial agents with an enhanced inhibitory activity. Methods are described for the incorporation of significant amounts of the established antibacterial compound triclosan (Irgasan) into mesoporous silicon of varying porosities. Such materials were characterized by a combination of scanning electron microscopy (SEM), energy dispersive X-ray analysis (EDX), X-ray diffraction (XRD), thermal gravimetric analysis (TGA), and antimicrobial assays. Assessment of antibacterial activity was carried out versus the bacterium Staphylococcus aureus as a function of time with concomitant assessment of triclosan release; significant, sustained inhibition of bacterial growth is demonstrated in the triclosan-containing porous Si for time intervals greater than 100 days. Significantly, enhanced dissolution (relative to room temperature equilibrium solubility) of the triclosan was observed for the initial 15 days of drug release, inferring some amorphization or nanostructuring by the porous Si matrix.
Neural Network-Based Event Detection For Surveillance Applications (1998)

Publication in the conference proceedings of EUSIPCO, Rhodes, Greece, 1998
Impaired Postural Vasoconstriction: A Contributory Cause of Oedema in Patients with Chronic Venous Insufficiency (1988)

Dependent oedema is a common feature in patients suffering from venous insufficiency. Postural vasoconstriction which prevents oedema has been shown to be impaired in several conditions complicated by dependent oedema. We therefore investigated the postural vasoconstrictor response, foot swelling rate and capillary density in eight patients with venous insufficiency and seven normal controls. Foot skin blood flow was measured on the pulp of the big toe using laser–Doppler flowmetry with the foot at heart level (H) and placed approximately 1 metre below the heart (D). Postural fall in flow was calculated as (H – D) × 100/H. Foot swelling rate was measured simultaneously using a strain gauge Plethysmograph. Postural vasoconstriction was impaired in venous insufficiency at 62 ± 12% compared to 88 ± 4% in controls ( P &lt; 0.02). Capillary density in the forefoot was assessed using television microscopy and was significantly reduced in the venous insufficiency group at 26.83 ± 2.74 per mm 2 compared to 36.96 ± 1.09 per mm 2 ( P &lt; 0.01). These findings suggest impaired postural vasoconstriction may contribute to the formation of oedema characteristic of venous insufficiency. The apparent reduction in capillary density may be implicated in the pathogenesis of venous ulceration to which such patients are prone.
Non-ligated Nickel Chloride-Catalyzed Cross-Coupling of Aromatic Grignard Reagents with Aryl Halides (1990)

The reaction between aryl Grignard reagents and aryl halides in the presence of non-ligated nickel(II) chloride affords the cross-coupling products in high yields (60-98%).
Studies on the Chinese crude drug "forsythiae fructus." VII. A new caffeoyl glycoside from forsythia viridissima. (1984)

In addition to a known caffeoyl glycoside of 3, 4-dihydroxyphenethyl alcohol, acteoside (1), a new caffeoyl glycoside of β, 3, 4-trihydroxyphenethyl alcohol, designated as β-hydroxyacteoside (2), was isolated from the fruits of Forsythia viridissima LINDLEY (Oleaceae). The structure of 2 was established as β, 3, 4-trihydroxyphenethyl-O-α-L-rhamnopyranosyl-(1→3)-4-O-caffeoyl-β-D-glucopyranoside on the basis of analysis of the carbon-13 nuclear magnetic resonance spectrum and chemical evidence.
Mechanisms Counteracting the Growth of Large Grains in Industrial ZnS Grown by Chemical Vapor Deposition (2013)

Polycrystalline ZnS produced by chemical vapor deposition (CVD) is analyzed using X-ray diffraction (XRD) and scanning electron microscopy (SEM) including electron backscatter diffraction (EBSD) to gain insight into the growth mechanism. Epitaxial growth of ZnS (111) layers is indicated in cubic CVD-ZnS. Mechanisms counteracting the growth of large, homogeneously oriented grains are proposed. This includes the summation of faults at low-angle grain boundaries during the deposition of new layers as well as the formation of new growth directions perpendicular to the sides of large grains. Wurtzite could be identified as a product of instable deposition conditions at the beginning and end of the deposition process.
Saliency-Cognizant Error Concealment in Loss-Corrupted Streaming Video (2012)

Error concealment in packet-loss-corrupted streaming video is inherently an under-determined problem, as there are insufficient number of well-defined criteria to recover the missing blocks perfectly. When a Region-of-Interest (ROI) based unequal error protection (UEP) scheme is deployed during video streaming -- i.e., more visually salient regions are strongly protected -- a %(e.g., using strong Forward Error Correction (FEC) codes) -- a lost block is likely to be of low saliency in the original frame. In this paper, we propose to add a low-saliency prior to the error concealment problem as a regularization term. It serves two purposes. First, in ROI-based UEP video streaming, low-saliency prior provides the right side information for the client to identify the correct replacement blocks for concealment. Second, in the event that a perfectly matched block cannot be unambiguously identified, the low-saliency prior reduces viewer's visual attention on the loss-stricken region, resulting in higher overall subjective quality. We study the effectiveness of a low-saliency prior in the context of a previously proposed RECAP[1] error concealment system. RECAP transmits a low-resolution (LR) version of an image alongside the original high-resolution (HR) version, so that if blocks in the HR version are lost, the correctly-received LR version can serve as a template for matching of suitable replacement blocks from a previously correctly-decoded HR frame. We add a low-saliency prior to the block identification process, so that only replacement candidate blocks with good match and low saliency can be selected. Further, we design and apply four saliency reduction operators iteratively in a loop, in order to reduce the saliency of candidate blocks. Experimental results show that: i) PSNR of the error-concealed frames can be increased dramatically (up to $3.2$dB over the original RECAP), showing the effectiveness of a low-saliency prior in the under-determined error concealment problem, and ii) subjective quality of the repaired video using our proposal, as confirmed by an extensive user study, is better than the original RECAP.
Qualitative simulation of genetic regulatory networks: method and application (2001)

Computer modeling and simulation are indispensable for understanding the functioning of an organism on a molecular level. We present an implemented method for the qualitative simulation of large and complex genetic regulatory networks. The method allows a broad range of regulatory interactions between genes to be represented and has been applied to the analysis of a real network of biological interest, the network controlling the inititation of sporulation in the bacterium B. subtilis.
Water-window soft X-ray high-harmonic generation up to the nitrogen K-edge driven by a kHz, 2.1 µm OPCPA source (2016)

Water-window soft X-ray harmonics up to ~450 eV are generated, with a kHz, multi-mJ mid-infrared optical parametric chirped-pulse amplifier (OPCPA) in a neon-filled gas cell. The photon flux at the nitrogen K-edge is ~1 × 106 photons/s/1% bandwidth.
Die Reaktion von Cyanurchlorid mit Dimethylformamid (1960)

Abstract Cyanurchlorid reagiert bei Raumtemperatur mit Dimethylformamid unter Bildung einer Additionsverbindung vom Vilsmeier‐Haak ‐Typ. Bei der weiteren Umsetzung mit Dimethylformamid entstehen aus dieser Additionsverbindung unter Eliminierung von 3 Mol CO 2 und Spaltung des Cyanurringes 3 Mol des bisher unbekannten 3‐Dimethylamino‐2‐azaprop‐2‐en‐1‐ylidendimethylammoniumchlorids, , das als Azaisologes des zuerst von W. T. Simpson dargestellten N‐Methyl‐[2]‐dimethylaminovinyl)‐formimin‐methojodids , aufzufassen ist. Die Konstitution dieses Salzes konnte durch Spaltungsreaktionen und unabhängige Synthesen, sowie durch UV‐ und IR‐Spektrum sichergestellt werden. Mit anderen Formylverbindungen sekundärer Amine reagiert Cyanurchlorid in analoger Weise. Die auf diesem Wege gewonnenen Aminoazapropenylidenammoniumsalze sind geeignete Zwischenprodukte, aus monosubstituierten Hydrazinen oder aus Amidinen durch Angliederung von Triazole bzw. Triazine aufzubauen; z.B. 2‐Phenyl‐1.3.5‐triazin aus Benzamidin.
Phenol Catalytic Hydrogenation over Palladium Nanoparticles Supported on Metal‐Organic Frameworks in the Aqueous Phase (2018)

Abstract The front cover artwork for issue 12/2018 is provided by Xi'an Jiaotong University and Tsinghua University (China). The image illustrates the different reaction barriers that must be overcome in the phenol hydrogenation to either cyclohexanol or cyclohexanone. See the Full Paper itself at https://doi.org/10.1002/cctc.201800211 .
Endothelial-to-Mesenchymal Transition in Human Adipose Tissue Vasculature Alters the Particulate Secretome and Induces Endothelial Dysfunction (2019)

We demonstrated the presence of EndoMT in human AT in obesity. EndoMT in vitro resulted in production of EV that transferred some of the functional and metabolic features to recipient naïve EC. This result suggests that functional and molecular features of EC that underwent EndoMT in vivo can be disseminated in a paracrine or endocrine fashion and may induce endothelial dysfunction in distant vascular beds.
Regulation of human natural killing. II. Protective effect of interferon on NK cells from suppression by PGE2. (1982)

Activation of human natural killer (NK) cells in vitro with interferon (IFN) and poly I:C results in a partial loss of sensitivity of these cells to suppression by PGE2. The acquired resistance to suppression can be induced with the large granular lymphocytes (LGL) in the absence of monocytes. With K562, HSB, and CEM used as NK target cells, the IFN-induced resistance to suppression by PGE2 is observed with all three target cells. Furthermore, ADCC activity of IFN-activated cells against tumor (SB-TNP) and erythroid (CRC-TNP) target cells is also less susceptible to suppression by PGE2. The dual effect of IFN on NK cells is prompt; the augmentation of NK activity and the acquired resistance to suppression by PGE2 can be seen after 3 hr of treatment with IFN. Both of these characteristics seem to be quite stable for at least 24 hr. Spleen cells from mice (CBA, C3H, and BALB/c nude) treated in vivo with poly I:C also acquire partial resistance to suppression by PGE2. Our data therefore suggest that IFN-stimulated NK cells are protected from suppression by PGE2. Biologically, the IFN-induced protective effect may be beneficial to host resistance to neoplasia.
Screening of various plant extracts used in ayurvedic medicine for inhibitory effects on human immunodeficiency virus type 1 (HIV‐1) protease (1995)

Abstract To identify substances with anti‐human immunodeficiency virus (HIV) activity in traditional medicines, water and methanol extracts of crude drugs used in Indian traditional medicine (Ayurveda) were subjected to screening for their inhibitory effects on HIV type 1 protease (PR). The enzyme activity was determined by HPLC and of the 39 crude drugs tested, the extracts of the seeds of Areca catechu , the bark of Eugenia jambolana , the bark of Saraca indica and the stem bark of Terminalia arjuna inhibited the HIV‐1 PR activity by more than 70% at a concentration of 0.2 mg/mL. The most potent inhibition was shown by the A. catechu extract, from which some procyanidins were isolated. One of them, arecatannin B1 showed significant HIV‐1‐PR inhibitory activity.
Understood Complexity: Ibsen's 'An Enemy of the People'—On Complexity, Sense-Making, Understanding, and Exit/Voice/Loyalty (2009)

‘Understood complexity’ is a term of Albert Hirschman (1976) whose economicpolitical theory of ‘exit’ (‘vote with your feet’) versus ‘voice’ (feedback or use your influence for change) (1970), has often been used to (try to) understand whistleblowing (Alford, 2001; Maclagen, 1998). Real complexity is not linear and cannot be adequately studied an model of ‘A causes B’. Complexity entails ‘A causes B’ in a situation wherein ‘B causes A’. Bateson in his ‘ecology of the mind’ understood the circularity of the hermeneutic of complexity; while Weick did not in his theory of sense-making. I argue in this article, via an examination of a play of Ibsen, that circular thinking spiraling towards new insight(s) is much more a possibility of literature (studies) than of social science. Social complexity theory needs (at least partially) I believe to methodologically merge with literary studies.
Hysteretic current–voltage characteristics and resistance switching at a rectifying Ti∕Pr0.7Ca0.3MnO3 interface (2004)

We have characterized the vertical transport properties of epitaxial layered structures composed of Pr0.7Ca0.3MnO3(PCMO) sandwiched between SrRuO3(SRO) bottom electrode and several kinds of top electrodes such as SRO, Pt, Au, Ag, and Ti. Among the layered structures, Ti∕PCMO∕SRO is distinct due to a rectifying I–V characteristic with a large hysteresis. Corresponding to the hysteresis of the I–V characteristics, the contact resistance of the Ti∕PCMO interface reversibly switches between two stable states by applying pulsed voltage stress. We propose a model for the resistance switching at the Ti∕PCMO interface, in which the width and/or height of a Schottky-like barrier are altered by trapped charge carriers in the interface states.
The Study of the Guest Effect on the Nematic Phase Stabilization (1988)

Abstract The effect of azo-dye on some optical and thermodynamical properties of the liquid crystal 5CB are examined. The relation between molecular geometry of the guest, guest and host order parameters and nematic-isotropic transition temperature of the azo-dye/liquid crystal mixtures is determined. The experimental results are compared in some detail with calculations done on the basis of the molecular mean-field theory and predictions of the lattice models as well. It has been found that good agreement between experiment and theory can be obtained taking into account not only the molecular sizes of the solute and the guest-host interaction, but also the concentration dependence of the dye order parameter and the flexibility of the end-chain of the liquid crystal molecules. Key Words: guest—host systemsazo-dyesorder parameterphase transition temperature
Oxidation in the Benzene Series by Gaseous Oxygen. V. The Oxidation of Tertiary Hydrocarbons (1935)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTOxidation in the Benzene Series by Gaseous Oxygen. V. The Oxidation of Tertiary HydrocarbonsH. N. Stephens and Feliciano L. RodutaCite this: J. Am. Chem. Soc. 1935, 57, 12, 2380–2381Publication Date (Print):December 1, 1935Publication History Published online1 May 2002Published inissue 1 December 1935https://pubs.acs.org/doi/10.1021/ja01315a015https://doi.org/10.1021/ja01315a015research-articleACS PublicationsRequest reuse permissionsArticle Views92Altmetric-Citations12LEARN 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
Validating the Darken Relation for Diffusivities in Fluid Mixtures of Varying Densities by Use of MD Simulations (2006)

Abstract Molecular Dynamics (MD) simulations have been carried out to determine the self‐diffusivities, D i,self , of the pure hydrocarbons methane (C1), ethane (C2), propane (C3), and n‐hexane (nC6) at various fluid densities. The MD simulations are in reasonable agreement with published experimental data. The influence of fluid density on both D i,self and the Maxwell‐Stefan (M‐S) diffusivities, Đ ij , in binary C1‐C2, C1‐C3, C2‐C3, and C1‐nC6 mixtures was also investigated. The MD simulations show that the M‐S diffusivities in binary fluid mixtures can be estimated with good accuracy using the Darken relation.
Quantitative Real-Time PCR Assays for the Detection of Pathogenic Leptospira Species in Urine and Blood Samples in Canine Vaccine Clinical Studies: a Rapid Alternative to Classical Culture Methods (2021)

Leptospirosis is a vaccine-preventable bacterial zoonotic disease caused by pathogenic Leptospira species. The efficacy of <i>Leptospira</i> canine vaccines is assessed by challenging vaccinated and control dogs with virulent serovars of <i>Leptospira</i>, followed by detection of <i>Leptospira</i> in blood and urine. We assessed the consistency between results obtained for urine and blood samples from clinical studies with species-specific real-time quantitative PCR (qPCR) targeting the <i>lipL32</i> gene and those obtained with the reference culture method. The specificity of the qPCR assay was confirmed by negative results for nonpathogenic <i>Leptospira</i> and for several canine viruses, bacteria, and parasites. The results from the two methods were compared using McNemar's test, kappa coefficient (κ), and percentage of agreement analyses. The results for numbers of positive and negative dogs were similar, with no false-negative results with the qPCR assay. For both blood and urine, there was strong agreement between the culture method and qPCR results (κ = 0.68 [95% confidence interval (CI), 0.62 to 0.74] and κ = 0.65 [95% CI, 0.59 to 0.71], respectively). However, there was a statistically significant difference between blood samples (<i>P</i> < 0.001) and urine samples (<i>P</i> = 0.028). The negative percentage agreements were 97% and 84% and the positive percentage agreements were 68% and 83% for blood and urine samples, respectively. Although the cell culture method is the recommended gold standard, our results show that qPCR assay is a valid alternative method for the rapid and specific detection of pathogenic <i>Leptospira</i> spp. in urine and blood samples during vaccine efficacy studies, without loss of sensitivity.