gebhart/patrepeval huggingface dataset:
Crosstalk between components of the innate immune system: promoting anti‐microbial defenses and avoiding immunopathologies (2008)

Because it reaches full functional efficacy rapidly upon encounter with a pathogen, the innate immune system is considered as the first line of defense against infections. The sensing of microbes or of transformed or infected cells, through innate immune recognition receptors (referred to as activating I2R2), initiates pro-inflammatory responses and innate immune effector functions. Other I2R2 with inhibitory properties bind self-ligands constitutively expressed in host. However, this dichotomy in the recognition of foreign or induced self versus constitutive self by I2R2 is not always respected in certain non-infectious conditions reminiscent of immunopathologies. In this review, we discuss that immune mechanisms have evolved to avoid inappropriate inflammatory disorders in individuals. Molecular crossregulation exists between components of I2R2 signaling pathways, and intricate interactions between cells from both innate and adaptive immune systems set the bases of controlled immune responses. We also pinpoint that, like T or B cells, some cells of the innate immune system must go through education processes to prevent autoreactivity. In addition, we illustrate how gene expression profiling of immune cell types is a useful tool to find functional homologies between cell subsets of different species and to speculate about unidentified functions of these cells in the responses to pathogen infections.
Shape metrics from curvature-scale space and curvature-tuned smoothing (1991)

This research deals with the decomposition and description of curved objects. In ongoing work, a new part description for curves and surfaces using a set of curvature-based minimization operators has been developed. The decomposition operation simultaneously performs data interpolation, data smoothing, and segmentation. The unification of these three stages results in a smoothing operation that is tightly coupled with the primitives to be used in subsequent object description. Each of the minimization operators, in addition to having a curvature tuning, has a different spatial sensitivity function. As a result, different possible descriptions of an object are produced and these capture information at multiple spatial scales. Each object is described by a small number of tokens based on differential geometric properties. The set of descriptors produced for a given object can be organized into an unusual form of nonlinear scale-space. The utility of such a scale-based description by way of two methods for the characterization (i.e., recognition) of two-dimensional objects via their multi- scale signature in terms of curvature-scale-space features is demonstrated. One method is based on graph matching by dynamic programming and the other based on statistical properties of scale space ('shape texture').
CCR2:  Characterization of the Antagonist Binding Site from a Combined Receptor Modeling/Mutagenesis Approach (2003)

We describe here a classical molecular modeling exercise that was carried out to provide a basis for the design of novel antagonist ligands of the CCR2 receptor. Using a theoretical model of the CCR2 receptor, docking studies were carried out to define plausible binding modes for the various known antagonist ligands, including our own series of indole piperidine compounds. On the basis of these results, a number of site-directed mutations (SDM) were designed that were intended to verify the proposed docking models. From these it was clear that further refinements would be necessary in the model. This was aided by the publication of a crystal structure of bovine rhodopsin, and a new receptor model was built by homology to this structure. This latest model enabled us to define ligand-docking hypotheses that were in complete agreement with the results of the SDM experiments.
External validation of the priapism impact profile in a Jamaican cohort of patients with sickle cell disease (2021)

The PIP questionnaire was successfully validated in a Jamaican cohort of SCD patients and adequately discriminated patients with active priapism from those in remission. The instrument may be utilized in routine clinical management of patients with SCD-associated priapism. Further clinical investigations are warranted in other populations.
Update of the guidelines on sudden cardiac death of the European Society of Cardiology (2003)

FIGURE 4. Deontolaimuscangioensis sp. nov., female. A. Anterior end; B. Entire female; C. Vulva region; D. Tail.
A Wideband Power Amplifier for Sub-6 GHz 5G Applications Using Second Harmonic Processing Techniques in 28nm FDSOI Technology (2022)

International audience
Piezoresistive transduction optimization of p-doped poly-Silicon NEMS (2015)

This paper presents a thorough investigation of the longitudinal gauge factor (GF) at high doping level in columnar polycrystalline-Silicon (poly-Si) nanowire (NW) NEMS devices. It is shown that a high GF (more than 30) can be obtained with concentration about 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">20</sup> cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-3</sup> . This result is very promising for high volume, low fabrication cost NEMS devices. This high GF is due to the specific piezoresistive behavior of poly-Si when compared to c-Si. We modeled the mechanical properties of the poly-Si and compared them to electrical measurements in order to predict the optimum dopant concentration for high GF. The experimental extraction of the GF has been performed directly on NWs gauge thanks to a new non-destructive method presented in [1].
COX2 expression in prognosis and in prediction to endocrine therapy in early breast cancer patients Johanna G. H. van NesEsther M. de KruijfDana Faratian • Cornelis J. H. van de VeldeHein PutterClaire FalconerVincent T. H. B. M. Smit • Charlene KayMarc J. van de VijverPeter J. K. KuppenJohn M. S. Bartlett (2011)

In breast cancer, the prognostic impact of COX2 expression varies widely between studies. We examined the prognostic value of COX2 expression in a large cohort of breast cancer patients treated with primary surgery between 1985 and 1994 and explained the variable results of COX2 expression found in the literature. A tissue microarray was constructed of available tumour material, and ER, PgR, HER2, Ki67 and COX2 were examined by immunohistochemistry. Median follow-up was 19 years. Fifty-five percent (n = 369/677) of patients received no systemic treatment. COX2 was scored using a weighted histoscore. Analysis of COX2 expression in two groups based on the median (148; below vs. above) showed an increased hazard ratio (HR) of 1.35 (95% CI 1.05-1.75, P = 0.021) for disease-free survival (DFS) and of 1.39 (95% CI 1.03-1.82, P = 0.016) for overall survival (OS). However, COX2 did not remain independent in multivar- iate analysis. In patients with hormone receptor positive tumours, COX2 expression had a negative influence on outcome (low vs. high: DFS: HR 1.37, 95% CI 1.07-1.76, P = 0.013). This effect disappeared when endocrine ther- apy was administered (low vs. high: DFS: HR 0.93, 95% CI 0.51-1.70, P = 0.811) while it remained statistically significant when endocrine therapy was omitted (low vs. high: DFS: HR 1.48, 95% CI 1.12-1.94, P = 0.005). Our results show that COX2 plays a role in hormonal pathways. Our results can explain the results found in previously published studies.
Simultaneous multi-depth assessment of tissue oxygen saturation in thenar and forearm using near-infrared spectroscopy during a simple cardiovascular challenge (2009)

The primary findings in this study were that forearm StO2 is a more sensitive parameter to hemodynamic changes than thenar StO2 and that the depth at which StO2 is measured is of minor influence. Our data support the use of forearm StO2 as a sensitive parameter for the detection of central hypovolemia and hypovolemic shock in (trauma) patients.
ChemInform Abstract: Reassignment of Stereochemistry and Total Synthesis of the Thrombin Inhibitor Cyclotheonamide B. (1992)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Three-dimensional simulation of helix traveling-wave tube cold-test characteristics using MAFIA (2002)

Summary form only given. A critically important step in the traveling-wave tube (TWT) design process is the cold-testing of the slow-wave circuit for dispersion, beam interaction impedance and RF losses. Experimental cold-tests can be very time-consuming and expensive, thus limiting the freedom to examine numerous variations to the test circuit. This makes the need for computational methods crucial as they can lower cost, reduce tube development time and allow the freedom to introduce novel and improved designs. The cold-test parameters have been calculated for a C-Band Northrop-Grumman helix TWT slow-wave circuit using MAFIA, the three-dimensional electromagnetic finite-integration computer code. The helix model includes tape thickness, rectangular dielectric supports and material properties consistent with the actual circuit.
On condition monitoring of high frequency power GaN converters with adaptive prognostics (2018)

There is no doubt that in the future, a need for higher switching frequency is inevitable to extract the full benefits of reliable Gallium Nitride (GaN) device characteristics. Along with the reliability enhancement for GaN-based power converters, it is essential to monitor a precursor signature identification for diagnostics/prognostics techniques. With the availability of the most granular information deduced from advanced devices, a new data-driven scheme is proposed for system monitoring and possible lifetime extension of 400W power GaN converters at 100kHz. The approach relies on the real-time R <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">ds</sub> ( <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">on</sub> ) data extraction from the power converter, and calibration of an adaptive model using multi-physics co-simulations under thermal cycling. More specifically, the focus is on deploying machine learning algorithms to exploit for the parameter estimation in power electronics engineering reliability.
Identification of residual ischemia, infarction, and microvascular impairment in revascularized myocardial infarction using 64‐slice MDCT (2008)

This study aimed to assess the potential of 64-slice MDCT in characterizing revascularized infarcted myocardium at the cellular and microvascular levels. Pigs (n = 7) underwent 2 h left anterior descending coronary artery occlusion/reperfusion. In acute (2-4 h) and subacute (1 week) infarction, first-pass perfusion (FPP) (1 ml/kg of 300 mg/ml Omnipaque) was performed using a cine (rotation time 60 s/bpm) non-ECG gated sequence (mAS/kV = 100/120). Delayed contrast enhanced images (DE) (mAS/kV = 650/120) were acquired every 2 min for 10 min to determine the kinetics of Omnipaque and to define infarcted myocardium and microvascular impairment (representing microvascular obstruction and/or no- or low-reflow phenomenon). Maximum upslope, maximum attenuation and time to the peak were measured from FPP plots. 2,3,5-Triphenyltetrazolium-chloride (TTC) was used to define true infarction in the excised hearts. Hyperenhanced myocardium on DE was measured and compared with TTC. The contrast media caused minor beam hardening and X-ray scatter on FPP. The above-mentioned perfusion parameters significantly differed between remote and acute infarction. Infarcted myocardium showed two patterns of enhancement on DE, hyperenhanced rim representing the perfused infarction and hypoenhanced core representing a microvascular impaired region, with significantly different attenuation. The extent of infarction on DE-MDCT decreased over the course of 1 week and did not differ from TTC. Post-processed FPP semi-quantitative images showed a decline in myocardial blood volume and flow in acute revascularized infarction. In conclusion, modern MDCT has the potential to identify residual ischemia on FPP and microvascular impairment and infarction on DE images.
Matrix decompositions and latent semantic indexing (2008)

Class-tested and coherent, this textbook teaches classical and web information retrieval, including web search and the related areas of text classification and text clustering from basic concepts. It gives an up-to-date treatment of all aspects of the design and implementation of systems for gathering, indexing, and searching documents; methods for evaluating systems; and an introduction to the use of machine learning methods on text collections. All the important ideas are explained using examples and figures, making it perfect for introductory courses in information retrieval for advanced undergraduates and graduate students in computer science. Based on feedback from extensive classroom experience, the book has been carefully structured in order to make teaching more natural and effective. Slides and additional exercises (with solutions for lecturers) are also available through the book's supporting website to help course instructors prepare their lectures.
Nonlinear Optical Loop Mirror Switch (NOLM) for Coding High Repetition Mode-Locked Semiconductor Laser Pulses (1997)

A high frequency (33 GHz) optical pulse train from a monolithic mode-locked semiconductor laser at λ = 1554 nm was modulated by pulses from a low repetition rate (1 GHz) gain-switched distributed feedback laser (DFB) at a different wavelength λ = 1542 nm by using a nonlinear optical loop mirror (NOLM). This technique provides a scheme of optical coding of a high repetition rate optical pulse source and can simultaneously perform N × 1 multi-wavelength conversion.
A novel variant of the MHC‐linked hsp70, hsp70‐hom, is associated with rheumatoid arthritis (2000)

The three major histocompatibility complex (MHC)-linked hsp70s have been screened for variation in their 28 kDa C-terminal regions by direct nucleotide sequencing of the corresponding DNA fragments. No amino acid variation was detected in the major heat-inducible hsp70 (encoded by hsp70-1 and hsp70-2), although previously unreported silent mutations were identified in all three of the MHC-linked hsp70 genes. A novel coding polymorphism, a G to A transition, was identified at nucleotide 2763 of hsp70-hom (hom-2763). This dimorphism results in a glutamic acid to lysine alteration at position 602 in the C-terminal domain of hsp70-hom. The frequencies of the A-2763 and G-2763 alleles were calculated to be 27% and 73%, respectively. The hom-2763 dimorphism was characterised in 81 HLA-homozygous cell lines using an ARMS-PCR assay and A-2763 was found to be in strong linkage disequilibrium with DRB1*04 (Pc=1.31 x 10(-7), following Bonferoni's correction). Analysis of 60 rheumatoid arthritis (RA) families, each with an affected sib-pair, revealed an association between hsp70-hom A-2763 and RA using both the transmission disequilibrium test (TDT) and the transmission to sib-pair (Tsp) test (P=0.0038 and P=0.013, respectively). This association may be due to linkage disequilibrium with HLA-DR alleles, but could represent an additional risk factor for RA in the MHC class III region.
Association of Cardiovascular Health Metrics With Risk of Transition to Hypertension in Non-Hypertensive Young Adults (2022)

CVH metrics can stratify the risk for hypertension in non-hypertensive adults aged 20-39 years. These findings have important public health implications for the screening and prevention of hypertension. Improving CVH metrics may prevent the risk of developing hypertension in young adults.
On a new cylindrical harmonic representation for spherical waves (1999)

An exact series representation is presented for integrals whose integrands are products of cosine and spherical wave functions, where the argument of the cosine term can be any integral multiple n of the azimuth angle /spl phi/. This series expansion is shown to have the following form: I(n)=e/sup -jkR0//R/sub 0/ /spl delta//sub no/-jk /spl Sigma//sub m=1//sup /spl infin// C(m,n)(k/sup 2//spl rho//spl rho/0)/m! h/sub m//sup (2)/(kR/sub 0/)/(kR/sub 0/)/sup m/. It is demonstrated that in the special cases n=0 and n=1, this series representation corresponds to existing expressions for the cylindrical wire kernel and the uniform current circular loop vector potential, respectively. A new series representation for spherical waves in terms of cylindrical harmonics is then derived using this general series representation. Finally, a closed-form far-field approximation is developed and is shown to reduce to existing expressions for the cylindrical wire kernel and the uniform current loop vector potential as special cases.
Novel Strategies for the Design of New Potent and Selective Human A3 Receptor Antagonists: An Update (2006)

A computer-aided approach has been developed in order to understand the molecular pharmacology of human A3R, and specifically, to lead to the discovery and structural refinement of new, potent and selective human A3R antagonists. This review focuses on our combined target-based and ligand-based drug design strategy, recently applied to provide more accurate information about the recognition mode on human A3R of some pyrazolotriazolopyrimidine and triazoloquinoxalinone analogs. The 3D rhodopsin-based homology model of human A3R has represented the starting point of our approach. A high throughput molecular docking method on the considered antagonists has allowed us to generate a receptor-based pharmacophore model. A novel "Y-shaped" pharmacophore binding motif has been proposed for both pyrazolotriazolopyrimidine and triazoloquinoxalinone derivatives. Moreover, related receptor-based 3D-QSAR analysis has been carried out to provide a suitable tool for prediction of the antagonists binding affinity on human A3R.
Folding of polyglutamine chains (2008)

Long polyglutamine chains have been associated with a number of neurodegenerative diseases. These include Huntington's disease, where expanded polyglutamine (PolyQ) sequences longer than 36 residues are correlated with the onset of symptoms. In this paper we study the folding pathway of a 54-residue PolyQ chain into a beta-helical structure. Transition path sampling Monte Carlo simulations are used to generate unbiased reactive pathways between unfolded configurations and the folded beta-helical structure of the polyglutamine chain. The folding process is examined in both explicit water and an implicit solvent. Both models reveal that the formation of a few critical contacts is necessary and sufficient for the molecule to fold. Once the primary contacts are formed, the fate of the protein is sealed and it is largely committed to fold. We find that, consistent with emerging hypotheses about PolyQ aggregation, a stable beta-helical structure could serve as the nucleus for subsequent polymerization of amyloid fibrils. Our results indicate that PolyQ sequences shorter than 36 residues cannot form that nucleus, and it is also shown that specific mutations inferred from an analysis of the simulated folding pathway exacerbate its stability.
Comprehensive Peptide Ion Structure Studies Using Ion Mobility Techniques: Part 1. An Advanced Protocol for Molecular Dynamics Simulations and Collision Cross-Section Calculation (2017)

Collision cross-section (CCS) measurements with a linear drift tube have been utilized to study the gas-phase conformers of a model peptide (acetyl-PAAAAKAAAAKAAAAKAAAAK). Extensive molecular dynamics (MD) simulations have been conducted to derive an advanced protocol for the generation of a comprehensive pool of in-silico structures; both higher energy and more thermodynamically stable structures are included to provide an unbiased sampling of conformational space. MD simulations at 300 K are applied to the in-silico structures to more accurately describe the gas-phase transport properties of the ion conformers including their dynamics. Different methods used previously for trajectory method (TM) CCS calculation employing the Mobcal software [1] are evaluated. A new method for accurate CCS calculation is proposed based on clustering and data mining techniques. CCS values are calculated for all in-silico structures, and those with matching CCS values are chosen as candidate structures. With this approach, more than 300 candidate structures with significant structural variation are produced; although no final gas-phase structure is proposed here, in a second installment of this work, gas-phase hydrogen deuterium exchange data will be utilized as a second criterion to select among these structures as well as to propose relative populations for these ion conformers. Here the need to increase conformer diversity and accurate CCS calculation is demonstrated and the advanced methods are discussed. Graphical Abstract ᅟ.
Effects of normal human fibroblast mitochondrial DNA on segregation of HeLaTG Mitochondrial DNA and on tumorigenicity of HeLaTG cells. (1986)

We isolated hybrids and cybrids using HeLaTG cells and human normal primary fibroblasts to examine the functional differences between the mitochondrial genomes of tumor and normal cells with respect to their possible involvement in the regulation of tumorigenicity. Hybrids contained mitochondrial DNA (mtDNA) predominantly from the fibroblast parent and their tumorigenicity was suppressed completely. Then, cytoplasmic transmission of primary fibroblast mtDNA to HeLaTG cells was carried out using toxin-antitoxin selection. Two cybrid clones containing a HeLaTG nucleus only and more than 60% of transmitted fibroblast mtDNA were isolated and injected into nude mice to test their tumorigenicity. They formed tumors when 2 X 10(6) cells were injected, whereas no tumors were formed after injection of 5 X 10(5) cells (a concentration at which HeLaTG subclones formed tumors). These cybrids were cultivated in normal medium for two additional months and the content of fibroblast mtDNA increased gradually, resulting in HeLaTG mtDNA eventually being lost from both cybrid clones. We again examined their tumorigenicity and found that they recovered tumorigenicity completely. These results indicate that tumorigenicity of HeLaTG cells could not be suppressed by replacing their mitochondrial genomes with those of normal primary fibroblasts. Further, the partial suppression of tumorigenicity observed in the cybrid clones was temporary and may be due to cytoplasmic factors other than the mitochondrial genomes. Although we can find no difference between the mitochondrial genomes of normal and tumor cells regarding the regulation of tumorigenicity, the segregation pattern of the mtDNA in the cybrids was of interest: in the absence of any mitochondrial selection, HeLaTG mtDNA was lost while fibroblast mtDNA was retained, even though the nuclear component of these cybrids was from the HeLaTG cells. Thus, there should be some functional differences between the mitochondrial genomes of HeLaTG cells and primary fibroblasts that are responsible for the preferential segregation of HeLaTG mtDNA from the cybrids.
Sol-gel-derived double-layered nanocrystal memory (2006)

The authors have used the sol-gel spin-coating method to fabricate a coexisting hafnium silicate and zirconium silicate double-layered nanocrystal (NC) memories. From transmission electron microscopic and x-ray photoelectron spectroscopic analyses, the authors determined that the hafnium silicate and zirconium silicate NCs formed after annealing at 900°C for 1min. When using channel hot electron injection for charging and band-to-band tunneling-induced hot hole injection for discharging, the NC memories exhibited superior Vth shifting because of the higher probability for trapping the charge carrier.