gebhart/patrepeval huggingface dataset:
Identification of positively and negatively selected driver gene mutations associated with colorectal cancer with microsatellite instability (2018)

Background: Recent studies have shown that cancers arise due to the positive selection of driver somatic events in tumor DNA, with negative selection playing only a minor role. However, these investigations were concerned with alterations at non-repetitive sequences and did not take into account mutations in repetitive sequences that have very high pathophysiological relevance in the tumors displaying Microsatellite Instability (MSI) due to mismatch repair deficiency investigated in the present study. Methods: We performed whole exome sequencing of 47 MSI CRC and confirmed results in an independent cohort of 53 MSI CRC. We used probabilistic model of mutational events within microsatellites, while adapting preexisting models to analyze non-repetitive DNA sequences. Negatively selected coding alterations in MSI CRC were investigated for their functional and clinical impact in CRC cell lines and in a third cohort of 164 MSI CRC patients. Results: Both positive and negative selection of somatic mutations in DNA repeats was observed, leading us to identify the expected driver genes associated with the MSI-driven tumorigenic process. Several Coding negatively selected, MSI-related mutational events (n = 5) were demonstrated to have deleterious effects on tumor cells. In the tumors in which deleterious MSI mutations are observed despite the negative selection, they were associated with worse survival in MSI CRC patients (hazard ratio [HR], 3; 95% confidence interval, 1.1-7.9; p = 0.03), suggesting their anticancer impact should be offset by other as yet unknown oncogenic processes that contribute to poor prognosis. Conclusions: The present results shed new light on the main driver somatic mutations acting in MSI-driven tumorigenesis, suggesting that genomic instability in MSI CRC plays a dual role in achieving tumor cell transformation. Legal entity responsible for the study: INSERM. Funding: This work was supported by grants from the ‘Institut National du Cancer’ (INCa, PRTK MICROSPLICOTHER, SIRIC, and HTE CoLi, to AD), the Fondation ARC (to AC) and the Canceropole Ile de France (to AC). AD group has the label ‘La Ligue Contre le Cancer’. This work is part of the Cartes d’Identité des Tumeurs (CIT) research program, funded and developed by the Ligue Nationale Contre le Cancer. Disclosure: All authors have declared no conflicts of interest.
The relative contribution of electrostatic interactions to stabilization of collagen fibrils (1990)

Abstract Electrostatic energies of interaction between type I collagen molecules were calculated, using models developed by Timasheff and Hill. These energies, along with a contribution from hydrophobic forces, were then incorporated into an equation due to Flory that described phase equilibria of rod‐like polymers. The Flory formalism in turn permitted a calculation of the overall free energy of fibril formation (Δ F f ), and an assessment of the relative contribution of electrostatic and hydrophobic forces to Δ F f . Lastly, Δ F f Lastly, Δ F f was used in a nucleation‐growth model relating halftimes of fibril formation ( t 1/2 ) to ionic strength ( I ) and temperature. Because the theory provided no basis for setting absolute levels of the energetic contributions, five parameters in the model had to be derived from experimental data. Based on the fit of theory to experimental results both for intact and pepsinized collagen, it was found that very low electrostatic energies (about −1 kcal/mole per collagen molecule) were sufficient to explain experimental t 1/2 vs I relationships. This energy is equivalent to 1 close charge‐pair interaction per molecule and appears to be lower than the energy assignable to hydrophobic interactions.
Faster-than-Nyquist and beyond: how to improve spectral efficiency by accepting interference (2011)

We investigate the application of time and frequency packing techniques, an extension of the classical faster-than-Nyquist signaling, to long-haul optical links. These techniques provide a significant spectral efficiency increase and represent a viable alternative to overcome the theoretical and technological issues related to the use of high-order modulation formats. Adopting these techniques, we successfully demonstrate through simulations the transmission of 1 Tbps over 200 GHz bandwidth in a realistic (nonlinear) long-haul optical link.
A Framework for the Development and Interpretation of Different Sepsis Definitions and Clinical Criteria (2016)

Although sepsis was described more than 2,000 years ago, and clinicians still struggle to define it, there is no "gold standard," and multiple competing approaches and terms exist. Challenges include the ever-changing knowledge base that informs our understanding of sepsis, competing views on which aspects of any potential definition are most important, and the tendency of most potential criteria to be distributed in at-risk populations in such a way as to hinder separation into discrete sets of patients. We propose that the development and evaluation of any definition or diagnostic criteria should follow four steps: 1) define the epistemologic underpinning, 2) agree on all relevant terms used to frame the exercise, 3) state the intended purpose for any proposed set of criteria, and 4) adopt a scientific approach to inform on their usefulness with regard to the intended purpose. Usefulness can be measured across six domains: 1) reliability (stability of criteria during retesting, between raters, over time, and across settings), 2) content validity (similar to face validity), 3) construct validity (whether criteria measure what they purport to measure), 4) criterion validity (how new criteria fare compared to standards), 5) measurement burden (cost, safety, and complexity), and 6) timeliness (whether criteria are available concurrent with care decisions). The relative importance of these domains of usefulness depends on the intended purpose, of which there are four broad categories: 1) clinical care, 2) research, 3) surveillance, and 4) quality improvement and audit. This proposed methodologic framework is intended to aid understanding of the strengths and weaknesses of different approaches, provide a mechanism for explaining differences in epidemiologic estimates generated by different approaches, and guide the development of future definitions and diagnostic criteria.
Activation-induced cytidine deaminase acts as a mutator in BCR-ABL1–transformed acute lymphoblastic leukemia cells (2007)

The Philadelphia chromosome (Ph) encoding the oncogenic BCR-ABL1 kinase defines a subset of acute lymphoblastic leukemia (ALL) with a particularly unfavorable prognosis. ALL cells are derived from B cell precursors in most cases and typically carry rearranged immunoglobulin heavy chain (IGH) variable (V) region genes devoid of somatic mutations. Somatic hypermutation is restricted to mature germinal center B cells and depends on activation-induced cytidine deaminase (AID). Studying AID expression in 108 cases of ALL, we detected AID mRNA in 24 of 28 Ph(+) ALLs as compared with 6 of 80 Ph(-) ALLs. Forced expression of BCR-ABL1 in Ph(-) ALL cells and inhibition of the BCR-ABL1 kinase showed that aberrant expression of AID depends on BCR-ABL1 kinase activity. Consistent with aberrant AID expression in Ph(+) ALL, IGH V region genes and BCL6 were mutated in many Ph(+) but unmutated in most Ph(-) cases. In addition, AID introduced DNA single-strand breaks within the tumor suppressor gene CDKN2B in Ph(+) ALL cells, which was sensitive to BCR-ABL1 kinase inhibition and silencing of AID expression by RNA interference. These findings identify AID as a BCR-ABL1-induced mutator in Ph(+) ALL cells, which may be relevant with respect to the particularly unfavorable prognosis of this leukemia subset.
Buried Tunnel Junction VCSEL with High Contrast Grating Top Reflector (2019)

Summary form only given. Emerging applications of optical sensing in consumer products, such as facial recognition based on structured light and time of flight proximity sensing, create high volume demand for low-cost illumination sources in the infrared wavelength range. Vertical Cavity Surface Emitting Lasers (VCSELs), manufactured into arrays of tens to thousands of elements, show superior beam quality compared to LEDs and edge emitter lasers and sufficient power for most applications. In this paper we present a high contrast grating enabled VCSEL with a buried tunnel junction emitting in the 980 nm wavelength range. The presented architecture with lithographically defined current aperture promises potential for highly uniform and dense VCSEL arrays. In our work we describe an epitaxial regrowth process for VCSELs incorporating a GaAs tunnel junction. Prototype single emitter devices with aperture sizes from 6-12 μm where fabricated. Devices with 6-8 μm apertures achieved submilliamp thresholds, while devices with 12 μm apertures demonstrated 1.4 mW peak power and a thermal resistance of 1.21 K/mW.
Imaging beyond the diffraction limit via dark states (2008)

Get PDF Email Share Share with Facebook Tweet This Post on reddit Share with LinkedIn Add to CiteULike Add to Mendeley Add to BibSonomy Get Citation Copy Citation Text G. R. Welch, H. Li, V. Sautenkov, M. M. Kash, A. V. Sokolov, Y. V. Rostovtsev, M. S. Zubairy, and M. O. Scully, "Imaging beyond the diffraction limit via dark states," in Frontiers in Optics 2008/Laser Science XXIV/Plasmonics and Metamaterials/Optical Fabrication and Testing, OSA Technical Digest (CD) (Optica Publishing Group, 2008), paper FThO4. Export Citation BibTex Endnote (RIS) HTML Plain Text Citation alert Save article
Molecular Engineering of Algal H2 Production (2002)

Hydrogen production by green algae has significant advantages over other photobiological systems: ATP production is not required, high theoretical efficiencies are possible, and water is used directly as the source of reductant without the need to produce biomass or to store intermediary carbon metabolites. However, algal H2 photoproduction is sensitive to O2, a coproduct of photosynthesis, and this sensitivity is a major factor currently limiting the use of algal systems for H2 production. We are investigating ways to surmount this problem, by focusing on the amino acid sequence and structure of the reversible [Fe]-hydrogenase (the enzyme that releases H2 gas). Previous studies (McTavish et al., 1995; Ghirardi et al., 1997; Seibert et al., 2001; Flynn et al., 1999; 2002) indicate that mutagenesis can be used to decrease the O2 sensitivity of the hydrogenase and thus eventually lead to a system that produces H2 under aerobic conditions. Last year, we cloned and sequenced the hydA1 [Fe]-hydrogenase gene in Chlamydomonas reinhardtii. We also cloned and partially sequenced a second, unexpected hydrogenase gene, hydA2. This year, we completed the sequencing of hydA2, confirmed that it is expressed at the
Clinical Utility of Targeted Next-Generation Sequencing in the Evaluation of Low-Grade Lymphoproliferative Disorders (2020)

Overall, implementation of this targeted lymphoid NGS panel as part of regular hematopathology practice was found to be a beneficial adjunct in the evaluation of low-grade LPDs.
Intrinsic white-light emission from zinc oxide nanorods heterojunctions on large-area substrates (2011)

Zinc oxide (ZnO) and especially in the nanostructure form is currently being intensively investigated world wide for the possibility of developing different new photonic devices. We will here present our recent findings on the controlled low temperature chemical growth of ZnO nanorods (NRs) on different large area substrates. Many different heterojunctions of ZnO NRs and p-substrates including those of crystalline e.g. p-GaN, p-SiC or amorphous nature e.g. p-polymer coated plastic and p-polymer coated paper will be shown. Moreover, the effect of the p-electrode of these heterojunctions on tuning the emitted wavelength and changing the light quality will be discussed. An example using ZnO NR/p-GaN will be shown and the electrical and electro-optical characteristics will be analyzed. For these heterojunctions the effect of post growth annealing and its effect on the electroluminescence (EL) spectrum will be shown. Finally, intrinsic white light emitting diodes based on ZnO NRs on foldable and disposable amorphous substrates (plastic and paper) will also be presented.
Status report on the radio frequency accelerating system of the APS at Argonne (2003)

Argonne National Laboratory is designing a 7-GeV Advanced Photon Source (APS). The RF systems of the APS include 10-MHz and 120-MHz systems for the Positron Accumulator Ring (PAR), a multicell 352-MHz system for the booster synchrotron, and a system of mode-damped, single-cell 352-MHz cavities for the storage ring. The authors describe the design of the PAR cavities, the configuration of the booster system, test results of the junction circulator developed for the cavities, and results of higher-order mode damping as applied to the storage ring cavities.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Infrared spectroscopy of matrix-isolated propadienone (1987)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTInfrared spectroscopy of matrix-isolated propadienoneOrville L. Chapman, Michael D. Miller, and Steven M. PitzenbergerCite this: J. Am. Chem. Soc. 1987, 109, 22, 6867–6868Publication Date (Print):October 1, 1987Publication History Published online1 May 2002Published inissue 1 October 1987https://pubs.acs.org/doi/10.1021/ja00256a060https://doi.org/10.1021/ja00256a060research-articleACS PublicationsRequest reuse permissionsArticle Views236Altmetric-Citations26LEARN 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
Síntese de hidróxidos duplos lamelares para aplicação na condensação aldólica de furfural e acetona (2021)

Autor(es): Marcos Paulo Monteiro Mariano – Bolsa: CNPq/PIBIC Orientador(es): Cláudio José de Araújo Mota Daniella Rodrigues Fernandes Área Temática: Química Orgânica Resumo: A adição de aldol é uma s
NOS2A and the modulating effect of cigarette smoking in Parkinson's disease (2006)

Our findings support NOS2A as a genetic risk factor in PD, potentially by influencing AAO and by modifying the inverse association between PD and smoking.
An Overview of Live Attenuated Recombinant Pseudorabies Viruses for Use as Novel Vaccines (2014)

Pseudorabies virus (PRV) is a double-stranded, DNA-based swine virus with a genome approximating 150 kb in size. PRV has many nonessential genes which can be replaced with genes encoding heterologous antigens but without deleterious effects on virus propagation. Recombinant PRVs expressing both native and foreign antigens are able to stimulate immune responses. In this paper, we review the current status of live attenuated recombinant PRVs and live PRV-based vector vaccines with potential for controlling viral infections in animals.
VEGFC/FLT4-induced cell-cycle arrest mediates sprouting and differentiation of venous and lymphatic endothelial cells (2021)

The formation of new vessels requires a tight synchronization between proliferation, differentiation, and sprouting. However, how these processes are differentially activated, often by neighboring endothelial cells (ECs), remains unclear. Here, we identify cell cycle progression as a regulator of EC sprouting and differentiation. Using transgenic zebrafish illuminating cell cycle stages, we show that venous and lymphatic precursors sprout from the cardinal vein exclusively in G1 and reveal that cell-cycle arrest is induced in these ECs by overexpression of p53 and the cyclin-dependent kinase (CDK) inhibitors p27 and p21. We further demonstrate that, in vivo, forcing G1 cell-cycle arrest results in enhanced vascular sprouting. Mechanistically, we identify the mitogenic VEGFC/VEGFR3/ERK axis as a direct inducer of cell-cycle arrest in ECs and characterize the cascade of events that render "sprouting-competent" ECs. Overall, our results uncover a mechanism whereby mitogen-controlled cell-cycle arrest boosts sprouting, raising important questions about the use of cell cycle inhibitors in pathological angiogenesis and lymphangiogenesis.
Cloning of  Vascular Adhesion Protein 1 Reveals a Novel Multifunctional Adhesion Molecule (1998)

Vascular adhesion protein 1 (VAP-1) is a human endothelial sialoglycoprotein whose cell surface expression is induced under inflammatory conditions. It has been shown previously to participate in lymphocyte recirculation by mediating the binding of lymphocytes to peripheral lymph node vascular endothelial cells in an L-selectin-independent fashion. We report here that the VAP-1 cDNA encodes a type II transmembrane protein of 84.6 kD with a single transmembrane domain located at the NH2-terminal end of the molecule and six potential N-glycosylation sites in the extracellular domain. In vivo, the protein exists predominantly as a homodimer of 170-180 kD. Ax endothelial cells transfected with a VAP-1 cDNA express VAP-1 on their cell surface and bind lymphocytes, and the binding can be partially inhibited with anti-VAP-1 mAbs. VAP-1 has no similarity to any currently known adhesion molecules, but has significant identity to the copper-containing amine oxidase family and has a monoamine oxidase activity. We propose that VAP-1 is a novel type of adhesion molecule with dual function. With the appropriate glycosylation and in the correct inflammatory setting, its expression on the lumenal endothelial cell surface allows it to mediate lymphocyte adhesion and to function as an adhesion receptor involved in lymphocyte recirculation. Its primary function in other locations where it is expressed, such as smooth muscle, may depend on its inherent monoamine oxidase activity.
Bending moduli and stability of copolymer bilayers (1991)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTBending moduli and stability of copolymer bilayersArmand Ajdari and Ludwik LeiblerCite this: Macromolecules 1991, 24, 25, 6803–6805Publication Date (Print):December 1, 1991Publication History Published online1 May 2002Published inissue 1 December 1991https://pubs.acs.org/doi/10.1021/ma00025a043https://doi.org/10.1021/ma00025a043research-articleACS PublicationsRequest reuse permissionsArticle Views151Altmetric-Citations18LEARN 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
Induction of specific immunity at mucosal surfaces: prospects for vaccine development. (1995)

We have demonstrated the feasibility of studying antigen-specific immune responses in a variety of mucosal tissues in humans after vaccination and during infection. In this respect, we have documented the usefulness of both oral cholera and ETEC vaccines for assessing in functional terms specific subpopulations of B- and T-cell immunocytes during an immune response initiated and/or expressed in human mucosal tissues. Circulating specific IgA antibody-secreting cells in blood appear to reflect recent or ongoing antigen exposure of mucosal surfaces. This implies that the detection of such cells in blood, the most accessible lymphoid compartment in humans, represents the simplest way to assess the immunogenicity of mucosal vaccines and to supplement the diagnostic and monitoring of active mucosal infections. Our studies indicate that while the concept of an integrated mucosal immune network is clearly operational in humans (at least in regards to induction of secretory antibody responses), its generalization appears somewhat simplistic as illustrated by the compartmentalization of immune responses initiated in certain mucosal organs such as the small intestine and the tonsils. Finally, the potential of the cholera toxin B subunit as a carrier for delivery of chemically or genetically linked foreign epitopes for induction of disseminated mucosal immune responses raises hope for the development of broadly applicable vaccines to control mucosal infections.
Mimicking bioactive peptides. [8-Nβ-Guanidoacetyl-α,β-diaminopropionic acid]vasopressin (1989)

The title compound was prepared by solid phase methodology. It has 34.2 I.U./mg of pressor activity, 5.8 I.U./mg of uterotonic activity and by 3-4 orders of magnitude lower antidiuretic activity than DDAVP.
Stark shift and parity nonconservation for near-degenerate states of xenon (2014)

We identify a pair of near-degenerate states of opposite parity in atomic Xe, the $5{p}^{5}10s{\phantom{\rule{0.16em}{0ex}}}^{2}{[3/2]}_{2}^{o}$ at $E=94\phantom{\rule{0.16em}{0ex}}759.927$ cm${}^{\ensuremath{-}1}$ and $5{p}^{5}6f{\phantom{\rule{0.16em}{0ex}}}^{2}{[5/2]}_{2}$ at $E=94\phantom{\rule{0.16em}{0ex}}759.935$ cm${}^{\ensuremath{-}1}$, for which parity- and time-odd effects are expected to be enhanced by the small energy separation. We present theoretical calculations which indicate narrow widths for both states and we report a calculated value for the weak matrix element, arising from configuration mixing, of $|W|=2.1$ Hz for $^{132}\mathrm{Xe}$. In addition, we measured the Stark effect of the $5{p}^{5}6f$ ${}^{2}{[5/2]}_{2}$ and $5{p}^{5}6f{\phantom{\rule{0.16em}{0ex}}}^{2}{[3/2]}_{2}$ ($E=94\phantom{\rule{0.16em}{0ex}}737.121\phantom{\rule{0.222222em}{0ex}}{\mathrm{cm}}^{\ensuremath{-}1}$) states. The Stark shift of the $6f$ states is observed to be negative, revealing the presence of nearby $6g$ states at higher energies, which have not been observed before. The Stark-shift measurements imply an upper limit on the weak matrix element of $|W|&lt;5$ Hz for the near-degenerate states ($10s{\phantom{\rule{0.16em}{0ex}}}^{2}{[3/2]}_{2}^{o}$ and $6f{\phantom{\rule{0.16em}{0ex}}}^{2}{[5/2]}_{2}$), which is in agreement with the presented calculations.
Introduction of plants into the mediterranean-type climate area of Chile (1991)

The true mediterranean–climate zone of Chile can be divided phy siographically into four regions: the Cordillera de Los Andes in the east with numerous peaks over 5000 metres; the Cordillera de la Costa in the west with peaks that seldom rise over 1000 metres; between these two ranges lie a series of graben known as the 'Depresion Intermedia' or Central Valley. The fourth region is the littoral fringe, a narrow coastal strip of step–like marine terraces, sea cliffs, stacks, headlands, dunes and beaches bordering the Pacific Ocean.