gebhart/patrepeval huggingface dataset:
The STRING database in 2017: quality-controlled protein–protein association networks, made broadly accessible (2016)

A system-wide understanding of cellular function requires knowledge of all functional interactions between the expressed proteins. The STRING database aims to collect and integrate this information, by consolidating known and predicted protein-protein association data for a large number of organisms. The associations in STRING include direct (physical) interactions, as well as indirect (functional) interactions, as long as both are specific and biologically meaningful. Apart from collecting and reassessing available experimental data on protein-protein interactions, and importing known pathways and protein complexes from curated databases, interaction predictions are derived from the following sources: (i) systematic co-expression analysis, (ii) detection of shared selective signals across genomes, (iii) automated text-mining of the scientific literature and (iv) computational transfer of interaction knowledge between organisms based on gene orthology. In the latest version 10.5 of STRING, the biggest changes are concerned with data dissemination: the web frontend has been completely redesigned to reduce dependency on outdated browser technologies, and the database can now also be queried from inside the popular Cytoscape software framework. Further improvements include automated background analysis of user inputs for functional enrichments, and streamlined download options. The STRING resource is available online, at http://string-db.org/.
Biological interpretation of morphological patterns in histopathological whole-slide images (2012)

We propose a framework for studying visual morphological patterns across histopathological whole-slide images (WSIs). Image representation is an important component of computer-aided decision support systems for histopathological cancer diagnosis. Such systems extract hundreds of quantitative image features from digitized tissue biopsy slides and produce models for prediction. The performance of these models depends on the identification of informative features for selection of appropriate regions-of-interest (ROIs) from heterogeneous WSIs and for development of models. However, identification of informative features is hindered by the semantic gap between human interpretation of visual morphological patterns and quantitative image features. We address this challenge by using data mining and information visualization tools to study spatial patterns formed by features extracted from sub-sections of WSIs. Using ovarian serous cystadenocarcinoma (OvCa) WSIs provided by the cancer genome atlas (TCGA), we show that (1) individual and (2) multivariate image features correspond to biologically relevant ROIs, and (3) supervised image feature selection can map histopathology domain knowledge to quantitative image features.
CMOS-integrated silicon 3d force sensor system for micro component coordinate measurement machines (2007)

This paper reports a CMOS-integrated three-axial force sensor system realized using a post-CMOS compatible low-temperature fabrication process which allows to process single IC dies as obtained from multi-project wafer (MPW) runs. The sensor system can be applied in coordinate measurement machines used for three-dimensional metrology of microcomponents. It is based on a flexible micromechanical cross structure suspended through thin silicon membrane hinges in a silicon frame. The cross is realized using double-sided deep reactive ion etching of IC chips comprising field effect transistor based piezoresistive stress sensor elements integrated with on-chip circuitry. The sensor elements are located on the membrane hinges and detect the deformations of the cross structure upon forces applied to a tactile element. The sensor system is able to monitor out-of-plane deflections of the cross structure with a resolution of 33 nm.
APPLICATIONS OF GOLD NANOPARTICLES IN THE EARLY DETECTION OF CANCER (2007)

Worldwide, oral cancer is the sixth most common cancer for both sexes. In Singapore, the 5-year survival rate of oral cancer is about 50%. The high mortality rate has been attributed to the difficulties in detecting the disease in an early treatable stage. Here, we present two application examples of gold nanoparticles in the early detection of oral cancer. In the first, gold nanoparticles were used as a reflective contrast agent for performing molecular imaging under confocal reflectance microscopy for the early diagnosis of epithelial carcinoma. While in the second, closely-packed gold nanoparticle, films were used as a bio-sensing surface for the chemical analysis of saliva via Surface Enhanced Raman Scattering. Preliminary results will be discussed.
Effect of acute sympathetic nervous system activation on flow-mediated dilation of brachial artery (2005)

We tested the hypothesis that flow-mediated dilation (FMD) of the brachial artery would be impaired by acute increases in sympathetic nervous system activity (SNA) in models where similar peak shear stress stimulus was achieved by varying the duration of forearm muscle ischemia. Eleven healthy young men were studied under four different conditions, each with its own control: lower body suction (LBS), cold pressor test (CPT), mental arithmetic task (MAT), and activation of muscle chemoreflex (MCR). The duration of ischemia before observation of FMD by ultrasound imaging was 5 min each for control, LBS, and CPT; 3 min for MAT; and 2-min for MCR. Peak shear rate was not different between control and any of the SNA conditions, although total shear in the first minute was reduced in MAT. MCR was the only condition in which brachial artery vasoconstriction was observed before forearm occlusion [4.38 (SD 0.53) vs. control 4.60 (SD 0.53) mm, P < 0.05]; however, diameter increased to the same absolute value as that of the control, so the percent FMD was greater for MCR [9.85 (SD 2.33) vs. control 5.29 (SD 1.50)%]. Blunting of the FMD response occurred only in the CPT model [1.51 (SD 1.20)%]. During SNA, the increase in plasma cortisol from baseline was significant only for MCR; the increase in plasma norepinephrine was significant for MCR, LBS, and CPT; and the increase in epinephrine was significant only for MCR. These results showed that the four models employed to achieve increases in SNA had different effects on baseline brachial artery diameter and that blunted FMD is not a general response to increased SNA.
Evaluation multicentrique et prospective de la mucosectomie et polypectomie endoscopique colorectale sous aspirine (étude OPERA) (2014)

Les récentes recommandations ESGE n'autorisent pas la poursuite de l'aspirine pour la réalisation d'une mucosectomie endoscopique (EMR). Les études de large effectifs, multicentriques et prospectives manquent dans le domaine. Le but de l'étude était d'évaluer le risque hémorragique des patients traités par EMR ou large polypectomie recto colique endoscopique en cas de prise au long cours et préventive d'aspirine.
Effect of computer-based alerts on the treatment and outcomes of hospitalized patients (1994)

<h3>Background:</h3> Hospital computing systems play an important part in the communication of clinical information to physicians. We sought to determine whether computer-based alerts for hospitalized patients can affect physicians' behavior and improve patients' outcomes. <h3>Methods:</h3> We performed a prospective time-series study to determine whether computerized alerts to physicians about rising creatinine levels in hospitalized patients receiving nephrotoxic or renally excreted medications led to more rapid adjustment or discontinuation of those medications, and to determine whether such alerts protected renal function. <h3>Results:</h3> Laboratory data were observed for 20 228 hospitalizations, with documentation of 1573 events (instances of rising creatinine levels during treatment with a nephrotoxic or renally excreted drug). During the intervention period, doses were adjusted or medications discontinued an average of 21.6 hours sooner after such an event (<i>P</i>&lt;.0001). For patients receiving nephrotoxic medications during the intervention period, the relative risk of serious renal impairment was 0.45 (95% confidence interval, 0.22 to 0.94) as compared with the control period, and the mean serum creatinine level was 14.1 μmol/L (0.16 mg/dL) lower on day 3 (<i>P</i>&lt;.01) and 25.6 μmol/L (0.29 mg/dL) lower on day 7 (<i>P</i>&lt;.05) after an event. Forty-four percent of physicians who responded to a questionnaire said that the alerts had been helpful in the care of their patients, whereas 28% found them annoying. Sixty-five percent wished to continue receiving alerts. <h3>Conclusions:</h3> Computer-based alerts regarding patients with rising creatinine levels affect physician behavior, prevent serious renal impairment, preserve renal function, and are accepted by clinicians. (Arch Intern Med. 1994;154:1511-1517)
TcpF Is a Soluble Colonization Factor and Protective Antigen Secreted by El Tor and Classical O1 and O139 Vibrio cholerae Serogroups (2005)

Vibrio cholerae causes diarrhea by colonizing the human small bowel and intoxicating epithelial cells. Colonization is a required step in pathogenesis, and strains defective for colonization are significantly attenuated. The best-characterized V. cholerae colonization factor is the toxin-coregulated pilus (TCP). It has been demonstrated that TCP is required for V. cholerae colonization in both humans and mice. TCP enhances bacterial interactions that allow microcolony formation and thereby promotes survival in the intestine. We have recently discovered that the TCP biogenesis apparatus also serves as a secretion system, mediating the terminal step in the extracellular secretion pathway of TcpF. TcpF was identified in classical isolates of V. cholerae O1 as a soluble factor essential for colonization in the infant mouse cholera model. In the present study, we expanded our analysis of TcpF to include the O1 El Tor and O139 serogroups and investigated how TCP and TcpF act together to mediate colonization. Additionally, we demonstrated that antibodies generated against TcpF are protective against experimental V. cholerae infection in the infant mouse cholera model. This observation, coupled with the fact that TcpF is a potent mediator of colonization, suggests that TcpF should be considered as a component of a polyvalent cholera vaccine formulation.
On the Effect of Suboptimal Estimation of Mutual Information in Feature Selection and Classification (2018)

This paper introduces a new property of estimators of the strength of statistical association, which helps characterize how well an estimator will perform in scenarios where dependencies between continuous and discrete random variables need to be rank ordered. The new property, termed the estimator response curve, is easily computable and provides a marginal distribution agnostic way to assess an estimator's performance. It overcomes notable drawbacks of current metrics of assessment, including statistical power, bias, and consistency. We utilize the estimator response curve to test various measures of the strength of association that satisfy the data processing inequality (DPI), and show that the CIM estimator's performance compares favorably to kNN, vME, AP, and H_{MI} estimators of mutual information. The estimators which were identified to be suboptimal, according to the estimator response curve, perform worse than the more optimal estimators when tested with real-world data from four different areas of science, all with varying dimensionalities and sizes.
TRIZ based interface conflict resolving strategies for modular product architectures (2011)

In product development, the chosen product architecture often possesses characteristics of both modular and integral design. Within a modular architecture, a Function-Behavior-Structure (FBS) model has been applied to describe modules and their interfaces. To resolve emerging interface conflicts, several strategies based on both modular and integral action have been formulated. The strategies encompass TRIZ methods, as they focus strongly on product innovation. The purpose of the presented study is to combine TRIZ techniques and FBS modeling while trying to solve interface conflicts at a low level of abstraction. The interface conflict resolving strategies have been applied on an industrial case study successfully.
DECOMBIO - Contribution de la combustion de la biomasse aux PM10 en vallée de l’Arve : mise en place et qualification d’un dispositif de suivi (2016)

La vallee de l’Arve (Haute-Savoie), et plus generalement les vallees alpines, sont regulierement soumises a des phenomenes de pollution atmospherique, caracterises entre autres par des depassements frequents du seuil de 50 μg.m-3 en concentration journaliere des PM10 (45 jours en 2012, 58 en 2013 et 46 en 2014). Cette situation a conduit a l’etablissement d’un Plan de Protection de l’Atmosphere (PPA) sur une grande partie de la vallee de l’Arve. Dans ce contexte, une operation pilote (Fonds Air Bois), visant a reduire significativement les emissions de particules fines liees a l’utilisation du chauffage au bois, doit contribuer a terme a une amelioration de la qualite de l’air sur ce perimetre. Le programme de recherche DECOMBIO (DEconvolution de la contribution de COMbustion de la BIOmasse aux PM10, finance par le programme Primequal) a ete mis en place afin de proposer et valider des outils d’evaluation de cette operation. Depuis novembre 2013, trois sites representatifs de l’ensemble de la vallee de l’Arve (Marnaz, Passy et Chamonix) ont ainsi ete instrumentes afin d’etudier la composition chimique des particules et de realiser un suivi sur toute la periode du Fonds Air Bois de l’evolution des concentrations en carbone suie (Black Carbon, BC), permettant ainsi d’evaluer la part « biomasse » des emissions. Au cours de la premiere annee du projet, des prelevements sur filtres ont permis une speciation chimique detaillee des PM10. La quantification de nombreux marqueurs de differentes sources permet de faire ressortir des processus regionaux, ou au contraire tres locaux, impactant la qualite de l’air de la vallee, et de quantifier les contributions d’une dizaine de sources d’emission. Les mesures continues du BC par Aethalometre (AE33) sur les trois sites permettent une deconvolution directe de deux sources de BC (fuel fossile note BCff et combustion biomasse note BCwb). Ce suivi a mis en evidence la contribution tres importante de la combustion de la biomasse, pouvant atteindre presque 50 % du BC, notamment a Passy. La confrontation des deux types de mesures de traceurs de la combustion de biomasse (recherche de traceurs moleculaires sur filtre et mesure continue du BCwb par AE33) est discutee afin de valider l’utilisation des Aethalometres en vallees alpines et de determiner les facteurs de conversion les plus appropries pour deduire la part de PM10 issue de la combustion de biomasse (PM10wb) a partir des mesures de BCwb. A terme, la methodologie utilisee permettra la determination en continu de la fraction de la contribution PM10wb, et de suivre sur le long terme l’impact des mesures de changement de dispositifs de chauffage au bois par le Fonds Air Bois.
Exonuclease III (XthA) Enforces In Vivo DNA Cloning of Escherichia coli To Create Cohesive Ends (2018)

<i>Escherichia coli</i> has an ability to assemble DNA fragments with homologous overlapping sequences of 15 to 40 bp at each end. Several modified protocols have already been reported to improve this simple and useful DNA cloning technology. However, the molecular mechanism by which <i>E. coli</i> accomplishes such cloning is still unknown. In this study, we provide evidence that the <i>in vivo</i> cloning of <i>E. coli</i> is independent of both RecA and RecET recombinases but is dependent on XthA, a 3' to 5' exonuclease. Here, <i>in vivo</i> cloning of <i>E. coli</i> by XthA is referred to as <i>in vivo</i><i>E. coli</i> cloning (iVEC). We also show that iVEC activity is reduced by deletion of the C-terminal domain of DNA polymerase I (PolA). Collectively, these results suggest the following mechanism of iVEC. First, XthA resects the 3' ends of linear DNA fragments that are introduced into <i>E. coli</i> cells, resulting in exposure of the single-stranded 5' overhangs. Then, the complementary single-stranded DNA ends hybridize each other, and gaps are filled by DNA polymerase I. Elucidation of the iVEC mechanism at the molecular level would further advance the development of <i>in vivo</i> DNA cloning technology. Already we have successfully demonstrated multiple-fragment assembly of up to seven fragments in combination with an effortless transformation procedure using a modified host strain for iVEC.<b>IMPORTANCE</b> Cloning of a DNA fragment into a vector is one of the fundamental techniques in recombinant DNA technology. Recently, an <i>in vitro</i> recombination system for DNA cloning was shown to enable the joining of multiple DNA fragments at once. Interestingly, <i>E. coli</i> potentially assembles multiple linear DNA fragments that are introduced into the cell. Improved protocols for this <i>in vivo</i> cloning have realized a high level of usability, comparable to that by <i>in vitro</i> recombination reactions. However, the mechanism of <i>in vivo</i> cloning is highly controversial. Here, we clarified the fundamental mechanism underlying <i>in vivo</i> cloning and also constructed a strain that was optimized for <i>in vivo</i> cloning. Additionally, we streamlined the procedure of <i>in vivo</i> cloning by using a single microcentrifuge tube.
Détection de parole superposée distante à l’aide d’une antenne de microphones (2022)

International audience
Incorporation of Current ICRP Recommendations in the GENMOD Internal Dosimetry Code (1998)

Journal Article Incorporation of Current ICRP Recommendations in the GENMOD Internal Dosimetry Code Get access R.B. Richardson, R.B. Richardson Search for other works by this author on: Oxford Academic PubMed Google Scholar D.W. Dunford D.W. Dunford Search for other works by this author on: Oxford Academic PubMed Google Scholar Radiation Protection Dosimetry, Volume 79, Issue 1-4, 1 October 1998, Pages 375–378, https://doi.org/10.1093/oxfordjournals.rpd.a032430 Published: 01 October 1998
Molecular Polygons Probe the Role of Intramolecular Strain in the Photophysics of π‐Conjugated Chromophores (2017)

Abstract π‐Conjugated segments, chromophores, are the electronically active units of polymer materials used in organic electronics. To elucidate the effect of the bending of these linear moieties on elementary electronic properties, such as luminescence color and radiative rate, we introduce a series of molecular polygons. The π‐system in these molecules becomes so distorted in bichromophores (digons) that these absorb and emit light of arbitrary polarization: any part of the chain absorbs and emits radiation with equal probability. Bending leads to a cancellation of transition dipole moment (TDM), increasing excited‐state lifetime. Simultaneously, fluorescence shifts to the red as radiative transitions require mixing of the excited state with vibrational modes. However, strain can become so large that excited‐state localization on shorter units of the chain occurs, compensating TDM cancellation. The underlying correlations between shape and photophysics can only be resolved in single molecules.
ChemInform Abstract: PHOSPHORUS HETEROCYCLE SYNTHESIS USING RPX2.ALX3 ADDITION TO 1,4‐DIENES PART 1 (1974)

Abstract Bei der Reaktion des Diens (I) mit dem Dichlorphenylphosphin‐Aluminiumchlorid‐ Komplex entstehen als Hauptprodukte das Phosphatricyclodecan (II) und das Phosphinylchlorid (IV) (als Hydrolysat eines Cyclohexen‐Dichlorphenylphosphin‐Addukts).
Interactions of Symbiotic Partners Drive the Development of a Complex Biogeography in the Squid-Vibrio Symbiosis (2020)

Microbes live in complex microniches within host tissues, but how symbiotic partners communicate to create such niches during development remains largely unexplored. Using confocal microscopy and symbiont genetics, we characterized the shaping of host microenvironments during light organ colonization of the squid <i>Euprymna scolopes</i> by the bacterium <i>Vibrio fischeri</i> During embryogenesis, three pairs of invaginations form sequentially on the organ's surface, producing pores that lead to interior compressed tubules at different stages of development. After hatching, these areas expand, allowing <i>V. fischeri</i> cells to enter and migrate ∼120 μm through three anatomically distinct regions before reaching blind-ended crypt spaces. A dynamic gatekeeper, or bottleneck, connects these crypts with the migration path. Once <i>V. fischeri</i> cells have entered the crypts, the bottlenecks narrow, and colonization by the symbiont population becomes spatially restricted. The actual timing of constriction and restriction varies with crypt maturity and with different <i>V. fischeri</i> strains. Subsequently, starting with the first dawn following colonization, the bottleneck controls a lifelong cycle of dawn-triggered expulsions of most of the symbionts into the environment and a subsequent regrowth in the crypts. Unlike other developmental phenotypes, bottleneck constriction is not induced by known microbe-associated molecular patterns (MAMPs) or by <i>V. fischeri</i><i>-</i>produced bioluminescence, but it does require metabolically active symbionts. Further, while symbionts in the most mature crypts have a higher proportion of live cells and a greater likelihood of expulsion at dawn, they have a lower resistance to antibiotics. The overall dynamics of these distinct microenvironments reflect the complexity of the host-symbiont dialogue.<b>IMPORTANCE</b> The complexity, inaccessibility, and time scales of initial colonization of most animal microbiomes present challenges for the characterization of how the bacterial symbionts influence the form and function of tissues in the minutes to hours following the initial interaction of the partners. Here, we use the naturally occurring binary squid-vibrio association to explore this phenomenon. Imaging of the spatiotemporal landscape of this symbiosis during its onset provides a window into the impact of differences in both host-tissue maturation and symbiont strain phenotypes on the establishment of a dynamically stable symbiotic system. These data provide evidence that the symbionts shape the host-tissue landscape and that tissue maturation impacts the influence of strain-level differences on the daily rhythms of the symbiosis, the competitiveness for colonization, and antibiotic sensitivity.
A Novel Method for Removal of Human Immunodeficiency Virus: Filtration with Porous Polymeric Membranes (1989)

We propose a new method to rid solutions of a virus by using a novel regenerated multilayered structured cellulose membrane (BMM). When the filtrate of human immunodeficiency virus (HIV) preparation was obtained through BMM it showed no infectivity. Electron microscopic observation revealed that HIV was completely caught by the multilayers of the BMM. Conveniently, BMM was seldomly found to adsorb protein molecules and also to have a high filtration rate. These characteristics may have a use in the removal of other variously sized pathogenic agents from plasma.