gebhart/patrepeval huggingface dataset:
A Multiscale Data Representation for Distributed Sensor Networks (2006)

Though several wavelet-based compression solutions for wireless sensor network measurements have been proposed, no such technique has yet appreciated the need to couple a wavelet transform tolerant of irregularly sampled data with the data transport protocol governing communications in the network. As power is at a premium in sensor nodes, such a technique is necessary to reduce costly communication overhead. To this end, we present an irregular wavelet transform capable of adapting to an arbitrary, multiscale network routing hierarchy. Inspired by the Haar wavelet in the regular setting, our wavelet basis forms a tight frame adapted to the structure of the network. We demonstrate results highlighting the approximation capabilities of such a transform and the clear reduction in communication cost when transmitting a compressed snapshot of the network to an outside user.
Figure S2 from LAMC2 Regulates Key Transcriptional and Targetable Effectors to Support Pancreatic Cancer Growth (2023)

&lt;p&gt;Suppl. Figure 2. A. LAMC2 immunoblot in HPAFII after LAMC2 knockdown using 2 different sgRNAs. B. Cell proliferation assessed by MTS after LAMC2 knockdown using 2 sgRNAs. Error bars correspond to s.d. C. LAMC2 immunoblot in PM12167 after shRNA mediated Lamc2 knockdown. D. Cell proliferation assessed by MTS after shRNA mediated Lamc2 knockdown. Error bars correspond to s.d. E. Colony forming ability after shRNA mediated Lamc2 knockdown. Error bars correspond to s.d. F. Cell proliferation assessed by MTS, after shRNA-mediated LAMC2 knockdown in PATU8902 and HPAFII PDAC cell lines using a tet-inducible system. Error bars correspond to s.d.&lt;/p&gt;
Low friction in bcc metals via grain boundary sliding (2020)

Low friction is demonstrated with pure polycrystalline tantalum sliding contacts in both molecular dynamics simulations and ultrahigh vacuum experiments. This phenomenon is shown to be correlated with deformation occurring primarily through grain boundary sliding and can be explained using a recently developed predictive model for the shear strength of metals. Specifically, low friction is associated with grain sizes at the interface being smaller than a critical, material-dependent value, where a crossover from dislocation mediated plasticity to grain-boundary sliding occurs. Low friction is therefore associated with inverse Hall-Petch behavior and softening of the interface. Direct quantitative comparisons between experiments and atomistic calculations are used to illustrate the accuracy of the predictions.
Combined fiber optic sensor for colour and refractive index (CI) monitoring (2005)

Two fiber optic probes are combined for the simultaneous monitoring of colour and refractive index of a liquid. It is shown how, through modelling, the design can be adapted to cover different ranges in refractive index and light absorption.
Topographic vorticity waves forced by Antarctic dense shelf water outflows (2014)

We use numerical simulations to investigate excitation of topographic vorticity waves (TVWs) along the Antarctic continental slope by outflows of dense shelf water through troughs. Idealized models show that wave frequency depends on the amount of stretching in the ambient fluid over the outflow and on background along‐slope mean flow. Frequency is higher for steeper bottom slope, larger outflow density anomaly, and stronger westward mean flow. For weak stratification and weak westward along‐slope flows typical of the Antarctic slope, wave energy propagates eastward, in the opposite direction from phase velocity. Our results are consistent with recent observations of TVWs in the southern Weddell Sea. In a realistic simulation of the Ross Sea, TVW properties are modulated on seasonal and shorter time scales as background ocean state varies. We expect these waves to affect mixing, cross‐slope exchanges, and sea ice concentration in the vicinity of sources of dense water outflows.
Pho23 Is Associated with the Rpd3 Histone Deacetylase and Is Required for Its Normal Function in Regulation of Gene Expression and Silencing in Saccharomyces cerevisiae (2001)

The Rpd3 histone deacetylase (HDAC) functions in a large complex containing many proteins including Sin3 and Sap30. Previous evidence indicates that the pho23, rpd3, sin3, and sap30 mutants exhibit similar defects in PHO5 regulation. We report that pho23 mutants like rpd3, sin3, and sap30 are hypersensitive to cycloheximide and heat shock and exhibit enhanced silencing of rDNA, telomeric, and HMR loci, suggesting that these genes are functionally related. Based on these observations, we explored whether Pho23 is a component of the Rpd3 HDAC complex. Our results demonstrate that Myc-Pho23 co-immunoprecipitates with HA-Rpd3 and HA-Sap30. Furthermore, similar levels of HDAC activity were detected in immunoprecipitates of HA-Pho23, HA-Rpd3, or HA-Sap30. In contrast, HDAC activity was not detected in immunoprecipitates of HA-Pho23 or HA-Sap30 from strains lacking Rpd3, suggesting that Rpd3 is the HDAC associated with these proteins. However, HDAC activity was detected in immunoprecipitates of HA-Sap30 or HA-Rpd3 from cells lacking Pho23, although levels were significantly lower than those detected in wild-type cells, indicating that Rpd3 activity is compromised in the absence of Pho23. Together, our genetic and biochemical studies provide strong evidence that Pho23 is a component of the Rpd3 HDAC complex, and is required for the normal function of this complex.
Transforming growth factor beta 1 induces methylation changes in lung fibroblasts (2019)

Idiopathic pulmonary fibrosis is a complex disease of unknown etiology. Environmental factors can affect disease susceptibility via epigenetic effects. Few studies explore global DNA methylation in lung fibroblasts, but none have focused on transforming growth factor beta-1 (TGF-β1) as a potential modifier of the DNA methylome. Here we analyzed changes in methylation and gene transcription in normal and IPF fibroblasts following TGF-β1 treatment. We analyzed the effects of TGF-β1 on primary fibroblasts derived from normal or IPF lungs treated for 24 hours and 5 days using the Illumina 450k Human Methylation array and the Prime View Human Gene Expression Array. TGF-β1 induced an increased number of gene expression changes after short term treatment in normal fibroblasts, whereas greater methylation changes were observed following long term stimulation mainly in IPF fibroblasts. DNA methyltransferase 3 alpha (DMNT3a) and tet methylcytosine dioxygenase 3 (TET3) were upregulated after 5-days TGF-β1 treatment in both cell types, whereas DNMT3a was upregulated after 24h only in IPF fibroblasts. Our findings demonstrate that TGF-β1 induced the upregulation of DNMT3a and TET3 expression and profound changes in the DNA methylation pattern of fibroblasts, mainly in those derived from IPF lungs.
A breast cancer (BC) risk model incorporating Tyrer-Cuzick version 8 (TCv8) and a polygenic risk score (PRS) for diverse ancestries. (2022)

557 Background: BC risk assessment is important for guiding personalized screening and risk-reducing interventions. TCv8 is used to estimate BC risk based on age, breast density, family cancer history and other clinical factors. Accuracy may be improved by combining TCv8 with a PRS. We developed and validated a PRS for diverse ancestries based on 149 common genetic variants (PRS-149) comprised of 56 ancestry-informative and 93 BC-associated variants. Here, we describe a BC risk model that combines PRS-149 with TCv8. Methods: Subjects had multigene panel testing for hereditary cancer and were negative for pathogenic variants in known BC susceptibility genes. A combined risk score (CRS), incorporating PRS-149 and TCv8, was developed based on 189,230 women, including 43,444 (23%) with a history of BC. Breast Imaging Reporting and Data System (BI-RADS) breast density measurements were available for 12,363 women. We used multivariable logistic regression to test breast density and PRS-149 for association with risk of BC. An independent test cohort of 6,030 BC-unaffected women with BI-RADS assessment was used to evaluate the effect of PRS-149 on risk stratification. Relative contributions of family history, breast density, other clinical factors in TCv8 and PRS-149 were examined by adding terms sequentially to an ANOVA model. We compared differences in classification of women as high (20%) or low/moderate (20%) remaining lifetime risk according to TCv8 versus CRS. Results: In the development cohort, increased breast density was significantly associated with higher risk of BC (p=3.0x10 -6 ) with an effect size consistent with TCv8. PRS-149 improved BC risk prediction over age, breast density and family history (OR per unit standard deviation: 1.41, 95% CI: 1.37 – 1.46; p: 1.8x10 -105 ). PRS-149 was weakly but significantly correlated with both family history (r=0.09) and breast density (r=0.01). After adjusting for multiple testing, no other factors were correlated with PRS-149. In the independent test cohort, PRS-149 explained 27% of CRS variability after accounting for family history, breast density and other clinical factors. Adding PRS-149 to TCv8 significantly altered risk estimates, with 16.3% (983/6,030) of patients classified differently by CRS versus TCv8. By TCv8 alone, 38.0% (2,289/6,030) of patients were classified as high-risk. Among patients who were high-risk by TCv8, 25.2% (576/2,289) were downgraded by CRS. Conclusions: This is the first BC risk model that includes breast density, family history, and a PRS based on genetically determined ancestry that is validated for diverse populations. Addition of PRS-149 improved risk prediction and substantially modified risk stratification compared to TCv8 alone. Implementation of CRS may therefore lead to improved identification of women who are likely to benefit from increased surveillance and preventive medications.
Caloric Restriction in Primates (2001)

A bstract : Caloric restriction (CR) remains the only nongenetic intervention that reproducibly extends mean and maximal life span in short‐lived mammalian species. This nutritional intervention also delays the onset, or slows the progression, of many age‐related disease processes. The diverse effects of CR have been demonstrated many hundreds of times in laboratory rodents and other short‐lived species, such as rotifers, water fleas, fish, spiders, and hamsters. Until recently, the effects of CR in longer‐lived species, more closely related to humans, remained unknown. Long‐term studies of aging in nonhuman primates undergoing CR have been underway at the National Institute on Aging (NIA) and the University of Wisconsin‐Madison (UW) for over a decade. A number of reports from the NIA and UW colonies have shown that monkeys on CR exhibit nearly identical physiological responses as reported in laboratory rodents. Studies of various markers related to age‐related diseases suggest that CR will prevent or delay the onset of cardiovascular disease, diabetes, and perhaps cancer, and preliminary data indicate that mortality due to these and other age‐associated diseases may also be reduced in monkeys on CR, compared to controls. Conclusive evidence showing that CR extends life span in primates is not presently available; however, the emerging data from the ongoing primate studies strengthens the possibility that the diverse beneficial effects of CR on aging in rodents will also apply to nonhuman primates and perhaps ultimately to humans.
Engineering of Catalytic Domain of Cellobiose Dehydrogenase and Its Application for the Direct Electron Transfer Type Enzyme Electrode (2012)

Abstract not Available.
Gouvernement et gouvernances des territoires (2006)

Spire est le dépôt institutionnel de la production scientifique de Sciences Po et contient le texte intégral des articles, ouvrages, chapitres d’ouvrages, working papers et communications dans des conférences de la communauté académique de Sciences Po.
Core-shell Nanoparticles for Anticancer Therapy (2013)

Many pharmaceutical compounds have limited availability in vivo and are thus of limited efficacy.  One potential method of improving bioavailability and creating targeted delivery vehicles of drugs is through the development of nanoparticle based formulations and surface engineering.  Here we describe a layer-by-layer (LbL) self-assembly technique used to encapsulate core charged drug particles in a polymeric nanoshell.  This approach provides a new strategy in the development of polymeric vehicles for controlled release and targeting to diseased tissues and cells.  A nanoshell composed of two biopolymers, poly-L-lysine and heparin sulfate, were assembled stepwise onto core charged drug nanoparticles.  The exterior surface of the nanoshell was functionalized with biocompatible polymers (poly(ethylene glycol)) and targeting functional moieties, such as folic acid or protein ligands. Using paclitaxel nanoparticles with a breast cancer cell line, the nanoparticles were found to be effective in the absence of an excipient such as Cremophor EL.  Strategies to create multifunctional nanoparticles and to deliver nanoparticles orally will also be discussed.
Multiple Endocrine Neoplasias in the Era of Translational Medicine (2005)

Medicine is an ever changing art, continuously adjusting to the shifting principles of philosophy and constant discoveries of science; it was beautifully said by Hippocrates: "... medicine does not do the same thing at this moment and the next..." Unabated dissemination of information is the only way that patients are assured that physicians will continue to practice medicine that reflects contemporary science. In the field of Multiple Endocrine Neoplasias (MENs), this is at least in part accomplished by biennially held International Workshops. The articles led by this editorial are the second and last installment of a collection of state-of-the-art presentations given in the course of the ninth such workshop that was held in Bethesda, MD, June 19-22, 2004. In addition to serving as an introduction to the articles that were written by some of the leaders in the field, the text of the editorial review that follows also supports the notion that MENs are poised to lead translational research in endocrinology: these disorders have benefited remarkably from the discoveries of the human genome project and are at a unique position to take advantage of new modalities in basic and clinical science.
Role of Melanin Pigment in Expression of Vibrio cholerae Virulence Factors (2008)

We identified the mutated gene locus in a pigment-overproducing Vibrio cholerae mutant of strain A1552. The deduced gene product is suggested to be an oxidoreductase based on partial homology to putative homogentisate 1,2-dioxygenase in Pseudomonas aeruginosa and Mesorhizobium loti, and we propose that the gene VC1345 in the V. cholerae genome be denoted hmgA in accordance with the nomenclature for other species. The hmgA::mini-Tn5 mutant showed a nonpigmented phenotype after complementation with a plasmid clone carrying the WT hmgA(+) locus. Microarray transcription analysis revealed that expression of hmgA and the neighboring genes encoding a postulated two-component sensor system was growth phase dependent. Results from quantitative reverse transcription-PCR analysis showed that hmgA operon expression was reduced in the rpoS mutant, but pigment production by the WT V. cholerae or the hmgA mutant was not detectably influenced by the stationary-phase regulator RpoS. The pigmented mutant showed increased UV resistance in comparison with the WT strain. Interestingly, the pigment-producing mutant expressed more toxin-coregulated pilus and cholera toxin than WT V. cholerae. Moreover, the hmgA mutant showed a fivefold increase in the ability to colonize the intestines of infant mice. A possible mechanism by which pigment production might cause induction of the ToxR regulon due to generation of hydrogen peroxide was supported by results from tests showing that externally supplied H(2)O(2) led to higher TcpA levels. Taken together, our findings suggest that melanin pigment formation may play a role in V. cholerae virulence factor expression.
Modeling Plasma-to-Interstitium Glucose Kinetics from Multitracer Plasma and Microdialysis Data (2015)

We have demonstrated that, in steady-state condition, the glucose plasma-to-ISF kinetics can be modeled with a linear two-compartment model and that the "equilibration time" between the two compartments can be estimated with precision. Future studies will assess plasma-to-interstitium glucose kinetics during glucose and insulin perturbations in both healthy and T1DM subjects.
Electrified Deceleration Cylinder Cutoff Engine Control Benefits and Strategies (2021)

&lt;div class="section abstract"&gt;&lt;div class="htmlview paragraph"&gt;Cylinder deactivation is a fuel consumption and CO&lt;sub&gt;2&lt;/sub&gt; reduction technology for internal combustion engines that deactivates cylinders at light to moderate loads, allowing the remaining firing cylinders to operate near optimum efficiency. Dynamic Skip Fire (DSF) uses full-authority cylinder deactivation that allows any cylinder of the engine to be deactivated in sequence. In previous SAE papers, both DSF technology and the synergies between DSF and electrification (eDSF) have been described.&lt;/div&gt;&lt;div class="htmlview paragraph"&gt;Recent engine technology includes deactivation mechanisms that do not effectively incorporate individual cylinder control. Nevertheless, it is still quite possible to improve the efficiency of engines equipped with these ganged-deactivation mechanisms. By grouping all cylinders into a deactivation mode, no air is pumped through the cylinders as it would be during the corresponding conventional operation that deactivates fuel alone. The engine equipped with deactivating cylinders can eliminate pumping work and provide more opportunity to recuperate electrical energy from the vehicle, as well as prevent oxygen saturation of the exhaust aftertreatment system.&lt;/div&gt;&lt;div class="htmlview paragraph"&gt;This paper presents the substantial benefits of this approach, showing both simulated and experimental fuel economy improvements for a C-segment vehicle exceeding 5% in the WLTC class 3 drive cycle. It discusses control strategies for managing transitions in and out of deactivation to achieve customer-pleasing NVH and drivability. Finally, the value proposition is presented for this electrified deceleration cylinder cutoff (eDCCO) system, also known as Hybrid++.&lt;/div&gt;&lt;/div&gt;
Dual energy CT Angiographie der Becken Bein Region bei peripherer Verschlusskrankheit (2009)

Ziele: Der Vergleich von zwei verschiedenen CT Angiographie (CTA) Nachverarbeitungsalgorithmen, dual energy bone removal und konventionelles bone removal, mit dem Goldstandard DSA in der Diagnostik der peripheren Verschlusskrankheit der Becken Bein Region. Methode: 20 Patienten unterzogen sich einer selektiven DSA und dual energy CTA (DE CTA) des Beckens und der Beine. Die Daten der CTA wurden sowohl im dual energy bone removal Modus als auch mit einem herkömmlichen bone removal Algorithmus (InSpace) an einem externen Arbeitsplatz (Syngo MMWP VA 21A, Siemens AG, Medical Solutions, Forchheim, Germany) zu MIPs nachverarbeitet. Es erfolgte die Berechnung der Sensitivität, Spezifität und Treffgenauigkeit der Stenosegrade. Zwei Subanalysen untersuchten die Abhängigkeit des Stenosegrads vom Kalzifizierungsgrad der Gefäßwand und der anatomischen Lokalisation. Ergebnis: Es wurden insgesamt 359 Gefäßsegmente evaluiert. Im Vergleich zur DSA ergaben sich im dual energy bone removal Modus eine Sensitivität, Spezifität und Treffgenauigkeit von 97.2%, 94.1% und 94.7%. Mit dem herkömmlichen Nachverarbeitungsprogramm (InSpace) betrugen die Sensitivität 77.1%, die Spezifität 70.7% und die Treffgenauigkeit 72.0%. Die besten Ergebnisse zeigten sich am Oberschenkel. Bei stark verkalkten Gefäßsegmenten erwies sich die dual energy Technik deutlich robuster, hier fielen die Sensitivität, die Spezifität und die Treffgenauigkeit nicht unter 90% während der konventionelle bone removal Algorithmus einen starken Abfall der Sensitivität, Spezifität und Treffgenauigkeit unter 74% aufwies. Schlussfolgerung: Die Nachverarbeitung der Becken-Bein DE CTA im dual energy bone removal Modus ist dem konventionellen bone removal (InSpace), insbesondere bei stark verkalkten Gefäßsegmenten, deutlich überlegen. Die Ergebnisse im Vergleich zum Goldstandard DSA belegen, dass die DE-CTA eine zuverlässige und robuste Methode zur Diagnostik der peripheren Verschlusskrankheit der Becken Bein Region bietet.
Agent-Based Distributed Security Constrained Optimal Power Flow (2016)

The need for the coordination of distributed energy resources in the future electric power system provides motivation to move from the current highly centralized control of resources toward a more distributed control structure. This paper presents an agent-based fully distributed dc security constrained optimal power flow (DC-SCOPF) approach. The algorithm is based on a multi-agent system, in which geographically distributed network entities are designated as agents with local sensing, communication, and computation abilities as envisioned for a smart grid. This distributed approach is based on solving the first order optimality conditions associated with DC-SCOPF formulation through an iterative process. At each iteration, each agent updates a few local variables through simple computations, and exchanges information with its neighboring agents. In particular, the updates for each agent incorporate local information such as the Lagrange multipliers, as well as enforcing the supply/demand balance through a local innovation term. Also, the performance is evaluated using the IEEE test systems with 14 and 57 buses and a 944-bus system consisting of eight IEEE 118-bus systems. Finally, analytical arguments concerning the convergence of the proposed method to the optimal solution of the DC-SCOPF are provided.
Structural vaccinology to thwart antigenic variation in microbial pathogens (2011)

Pathogenic microbes evolve continuously to adapt to the immune responses of their infected hosts. For some pathogens, this presents a formidable challenge, because host adaptive immune responses may neutralize key virulence attributes of the microbe, thereby establishing immunity to subsequent infection (1). Under such immune selection, microbes evolve variants with altered antigenic but unaltered functional properties, thereby restoring virulence for invasion of hosts with neutralizing immunity because of prior exposure with another isolate of the same pathogen (2). How then can one find the key protective antigens of microbes, and what technologies may be applied to thwart their evasive strategies? Answers to these queries are provided in a paper by Nuccitelli et al. (3) in PNAS. Large-scale DNA sequencing of microbial genomes combined with bioinformatic analyses of their predicted products provide access to the genetic information of all isolated variants of a pathogen (4). Reverse vaccinology involves the exhaustive testing of recombinant translational products as vaccine candidates in search of subunits that elicit specific protective immunity in animal models (Fig. 1). Applied to the Gram-positive pathogen Streptococcus agalactiae, these approaches led to the identification of pilus genes that are critically important for the disease process but display variation among different isolates (5). Combining structural biology approaches with domain mapping of protective epitopes, Nuccitelli et al. (3) string together six antigenic variants of the same functional unit into a single recombinant antigen that elicits antibody-mediated vaccine protection against all of S. agalactiae isolates examined.