gebhart/patrepeval huggingface dataset:
Role of the Streptococcus suis serotype 2 capsular polysaccharide in the interactions with dendritic cells is strain-dependent but remains critical for virulence (2018)

Streptococcus suis serotype 2 is an important porcine bacterial pathogen and zoonotic agent responsible for sudden death, septic shock, and meningitis. However, serotype 2 strains are heterogeneous, composed of a multitude of sequence types (STs) whose distribution greatly varies worldwide. Of the virulence factors presently described for S. suis, the capsular polysaccharide (CPS) is a critical factor implicated in a multitude of functions, including in impairment of phagocytosis and innate immune cell activation by masking underlying bacterial components. However, these roles have been described using Eurasian ST1 and ST7 strains, which greatly differ from North American ST25 strains. Consequently, the capacity of the CPS to mask surface antigens and putative virulence factors in non-Eurasian strains remains unknown. Herein, the role of the S. suis serotype 2 CPS of a prototype intermediate virulent North American ST25 strain, in comparison with that of a virulent European ST1 strain, with regards to interactions with dendritic cells, as well as virulence during the systemic phase of infection, was evaluated. Results demonstrated that the CPS remains critical for virulence and development of clinical disease regardless of strain background, due to its requirement for survival in blood. However, its role in the interactions with dendritic cells is strain-dependent. Consequently, certain key characteristics associated with the CPS are not necessarily applicable to all S. suis serotype 2 strains. This indicates that though certain factors may be important for S. suis serotype 2 virulence, strain background could be as determining, reiterating the need in using strains from varying backgrounds in order to better characterize the S. suis pathogenesis.
Title: Proposal to form a Project on Architectures and Signaling for Configurable All-Optical Networks (2001)

Long-reach optics and configurable all-optical networks provide economic benefits for carriers in terms of both capital and operating expenses by significantly reducing the amount of equipment required in the network. Such networks are currently entering the marketplace, and there is a desire in the OIF and other standards organizations to generalize their respective architectural models to include all- optical networks. This contribution is a proposal for initiating a new project in the OIF to address the specific features of all-optical networks as they relate to signaling for automatic provisioning and restoration of optical paths. Since an all-optical network naturally forms a domain, another important aspect of this project relates to the more general problem of establishing connections across multi-domain networks.
Screening and familial characterization of copy‐number variations in NR5A1 in 46,XY disorders of sex development and premature ovarian failure (2013)

The NR5A1 gene encodes for steroidogenic factor 1, a nuclear receptor that regulates proper adrenal and gonadal development and function. Mutations identified by NR5A1 sequencing have been associated with disorders of sex development (DSD), ranging from sex reversal to severe hypospadias in 46,XY patients and premature ovarian failure (POF) in 46,XX patients. Previous reports have identified four families with a history of both 46,XY DSD and 46,XX POF carrying segregating NR5A1 sequence mutations. Recently, three 46,XY DSD sporadic cases with NR5A1 microdeletions have been reported. Here, we identify the first NR5A1 microdeletion transmitted in a pedigree with both 46,XY DSD and 46,XX POF. A 46,XY individual with DSD due to gonadal dysgenesis was born to a young mother who developed POF. Array CGH analysis revealed a maternally inherited 0.23 Mb microdeletion of chromosome 9q33.3, including the NR5A1 gene. Based on this finding, we screened patients with unexplained 46,XY DSD (n = 11), proximal hypospadias (n = 21) and 46,XX POF (n = 36) for possible NR5A1 copy-number variations (CNVs) via multiplex ligation-dependent probe amplification (MLPA), but did not identify any additional CNVs involving NR5A1. These data suggest that NR5A1 CNVs are an infrequent cause of these disorders but that array CGH and MLPA are useful genomic screening tools to uncover the genetic basis of such unexplained cases. This case is the first report of a familial NR5A1 CNV transmitting in a pedigree, causing both the male and female phenotypes associated with NR5A1 mutations, and the first report of a NR5A1 CNV associated with POF.
Characteristics of Progesterone Changes in Women with Subtle Progesterone Rise in Recombinant Follicle-Stimulating Hormone and Gonadotropin-Releasing Hormone Antagonist Cycle (2010)

A subtle Prog rise may occur as early as cycle day 8 in r-FSH/GnRH antagonist cycles.
Self-Stabilization of an Actively Mode-Locked Semiconductor-Based Fiber-Ring Laser for Ultralow Jitter (2007)

Noise characteristics are studied for a self-stabilized laser utilizing the interplay between the intracavity dispersion and the optical frequency shift. The noise suppression bandwidth of this scheme is from 0 to ~100 KHz and showed the reduction of residual timing jitter (integrated from 0.9 Hz to 1 MHz) from 2.2fs to 660 attosecond which represents, to our knowledge, the lowest timing jitter reported for an actively mode-locked laser
Inhibition of Simian Virus 40 DNA Synthesis by Frog Virus 3 (1974)

SUMMARY The replication of simian virus 40 (SV40) DNA is arrested by superinfection with frog virus 3 (FV3). Most of the SV40 DNA molecules synthesized before infection by FV3 become nicked or fragmented. These events take place at 37 °C, a restrictive temperature for FV3 growth.
Low level image processing operators on FPGA: implementation examples and performance evaluation (2002)

This work deals with evaluation of hardware implementations of image processing algorithms for real time applications, using SRAM based field-programmable gate arrays. We discuss a generic architectural model adapted to this domain and to the technology characteristics. A method to evaluate the area costs and timing performances of architectures implemented on such a model is presented. A feasibility study of a pre-processing chain in an image-recognition system is presented.
Determining the conformation of surface species by DNPeEnhanced solid-state NMR (2014)

International audience
Plant Seed Species Identification from Chemical Fingerprints: A High-Throughput Application of Direct Analysis in Real Time Mass Spectrometry (2015)

Plant species identification based on the morphological features of plant parts is a well-established science in botany. However, species identification from seeds has largely been unexplored, despite the fact that the seeds contain all of the genetic information that distinguishes one plant from another. Using seeds of genus Datura plants, we show here that the mass spectrum-derived chemical fingerprints for seeds of the same species are similar. On the other hand, seeds from different species within the same genus display distinct chemical signatures, even though they may contain similar characteristic biomarkers. The intraspecies chemical signature similarities on the one hand, and interspecies fingerprint differences on the other, can be processed by multivariate statistical analysis methods to enable rapid species-level identification and differentiation. The chemical fingerprints can be acquired rapidly and in a high-throughput manner by direct analysis in real time mass spectrometry (DART-MS) analysis of the seeds in their native form, without use of a solvent extract. Importantly, knowledge of the identity of the detected molecules is not required for species level identification. However, confirmation of the presence within the seeds of various characteristic tropane and other alkaloids, including atropine, scopolamine, scopoline, tropine, tropinone, and tyramine, was accomplished by comparison of the in-source collision-induced dissociation (CID) fragmentation patterns of authentic standards, to the fragmentation patterns observed in the seeds when analyzed under similar in-source CID conditions. The advantages, applications, and implications of the chemometric processing of DART-MS derived seed chemical signatures for species level identification and differentiation are discussed.
NEPTUNE: An under-sea plate scale observatory (2003)

The NEPTUNE project will establish a linked array of undersea observatories on the Juan de Fuca tectonic plate. The NEPTUNE infrastructure, consisting of fiber-optic/power cable and junction boxes, will provide significant amounts of power and an Internet communications link to sensors and sensor networks on, above, and below the seafloor. This observatory will provide a new kind of research platform for real-time, long-term, plate-scale studies in the ocean and Earth sciences.
A 4.1Mpix 280fps stacked CMOS image sensor with array-parallel ADC architecture for region control (2017)

A 4.1Mpix 280fps stacked CMOS image sensor with array-parallel ADC architecture is developed for region control applications. The combination of an active reset scheme and frame correlated double sampling (CDS) operation cancels Vth variation of pixel amplifier transistors and kTC noise. The sensor utilizes a floating diffusion (FD) based back-illuminated (BI) global shutter (GS) pixel with 4.2e-rms readout noise. An intelligent sensor system with face detection and high resolution region-of-interest (ROI) output is demonstrated with significantly low data bandwidth and low ADC power dissipation by utilizing a flexible area access function.
Demonstration that the shear force required to separate short double-stranded DNA does not increase significantly with sequence length for sequences longer than 25 base pairs (2008)

We have measured the shear force for short double-stranded DNA sequences pulled by either the 3'3' or 5'5' ends and find that the shear force is independent of the pulling technique. For the 50% GC sequences examined, the force is a linear function of DNA length up to 20 base pairs (bp); however, we show that, as predicted by deGennes, the shear force approaches an asymptotic value in the limit where the number of base pairs approaches infinity, where the shear force for a 32 bp sequence is within 5% of the asymptotic value of 61.4 pN . Fits to deGennes' theory suggest that the shear force is distributed over fewer than 10 bp at the end of the sequence, with the rest of the sequence experiencing negligible shear force. The single base pair rupture force and the ratio of the backbone spring constant to the base pair spring constant determined from fits of the data to deGennes' theory are consistent with ab initio predictions.
Detection of Visible and Latent Fingerprints Using Micro‐X‐ray Fluorescence Elemental Imaging* (2005)

Using micro-X-ray fluorescence (MXRF), a novel means of detecting fingerprints was examined in which the prints were imaged based on their elemental composition. MXRF is a nondestructive technique. Although this method requires a priori knowledge about the approximate location of a print, it offers a new and complementary means for detecting fingerprints that are also left pristine for further analysis (including potential DNA extraction) or archiving purposes. Sebaceous fingerprints and those made after perspiring were detected based on elements such as potassium and chlorine present in the print residue. Unique prints were also detected including those containing lotion, saliva, banana, or sunscreen. This proof-of-concept study demonstrates the potential for visualizing fingerprints by MXRF on surfaces that can be problematic using current methods.
A nonlinear full order observer for oscillator tracking (2015)

We present a class of nonlinear observers that track oscillator states from observations of the complex envelope. We first identify core state variables that are observable and provide a general observer structure for estimating these state variables, that results in globally uniformly asymptotically stable observers. We provide a specialization that induces the 2-norm of the state estimation error to monotonically decline to zero, and has an intuitively appealing structure that has parallels to full order observers of Linear Time Invariant systems.
Observation of Field‐Effect Transistor Behavior at Self‐Organized Interfaces (2004)

Ultrathin, conformal semiconductor– dielectric bilayers can be fabricated in one step by self-organization (see Figure), without exposing the critical interface to ambient contamination. Low-voltage polymer field-effect transistors using a fluorene–triarylamine copolymer as the p-channel semiconductor and 40–60 nm thick crosslinked bisbenzocyclobutene derivative as the gate dielectric are shown to be robust and reproducible.
Sympathetic Reinnervation Is Required for Mammalian Cardiac Regeneration (2015)

These findings demonstrate that the profound regenerative capacity of the neonatal mammalian heart requires sympathetic innervation. As such, these data offer significant insights into an underlying basis for inadequate adult regeneration after myocardial infarction, a situation where nerve growth is hindered by age-related influences and scar tissue.
Ultrasensitive measurement of both SARS-CoV2 RNA and serology from saliva (2021)

Abstract Tests for COVID-19 generally measure SARS-CoV2 viral RNA from nasal swabs or antibodies against the virus from blood. It has been shown, however, that both viral particles and antibodies against those particles are present in saliva, which is more accessible than both swabs and blood. We present methods for highly sensitive measurements of both viral RNA and serology from the same saliva sample. We developed an efficient saliva RNA extraction method and combined it with an ultrasensitive serology test based on Single Molecule Array (Simoa) technology. We apply our test to the saliva of patients who presented to the hospital with COVID-19 symptoms, some of whom tested positive with a conventional RT-qPCR nasopharyngeal swab test. We demonstrate that combining viral RNA detection by RT-qPCR with serology identifies more patients as infected than either method alone. Our results suggest the utility of combining viral RNA and serology testing from saliva, a single easily accessible biofluid.
Air–water flow in a vertical pipe: experimental study of air bubbles in the vicinity of the wall (2008)

This study deals with the influence of bubbles on a vertical air–water pipe flow, for gas-lift applications. The effect of changing the bubble size is of particular interest as it has been shown to affect the pressure drop over the pipe. Local measurements on the bubbles characteristics in the wall region were performed, using standard techniques, such as high-speed video recording and optical fibre probe, and more specific techniques, such as two-phase hot film anemometry for the wall shear stress and conductivity measurement for the thickness of the liquid film at the wall. The injection of macroscopic air bubbles in a pipe flow was shown to increase the wall shear stress. Bubbles travelling close to the wall create a periodic perturbation. The injection of small bubbles amplifies this effect, because they tend to move in the wall region; hence, more bubbles are travelling close to the wall. A simple analysis based on a two-fluid set of equations emphasised the importance of the local gas fraction fluctuations on the wall shear stress.
Real-time autonomous surveillance for vector-borne pathogens. (2017)

Abstract not provided.
Resibufogenin Administration Prevents Oxidative Stress in a Rat Model of Human Preeclampsia (2010)

Background and Objectives. Marinobufagenin (MBG) is a cardiotonic steroid that is increased in preeclampsia. An analog of MBG, resibufogenin (RBG), prevents the development of preeclampsia in a rat model. Oxidative stress is a concomitant of endothelial dysfunction in the latter disorder. The objective of the current studies was to evaluate the status of oxidative stress in a rat model of preeclampsia. Methods. We measured the aortic AT1 receptor expression and urinary excretion of 8-isoprostane (8IP) in rats rendered “preeclamptic” and compared the findings to those obtained in normal pregnant animals, pregnant rats injected with MBG, and preeclamptic rats treated with RBG. Results. Aortic AT1 receptor expression and the urinary excretion of 8IP were significantly augmented in “preeclamptic” and MBG-injected pregnant rats compared to normal pregnant animals. RBG prevented evidence of oxidative stress in “preeclamptic” rats. Conclusion. MBG is involved in the causation of oxidative stress in our rat model and RBG attenuates this change.
Nitrogen-Doped Single-Walled Carbon Nanotube Thin Films Exhibiting Anomalous Sheet Resistances (2011)

Nitrogen-doped single-walled carbon nanotubes (N-SWCNTs) were synthesized using a floating catalyst aerosol chemical vapor deposition method, with carbon monoxide as the carbon source, ammonia as the nitrogen source, and iron particles derived from evaporated iron as the catalyst. The material was deposited on various substrates as grown directly from the gas phase as films and subsequently characterized by Raman and optical absorption spectroscopies, sheet resistance measurements, electron microscopy, energy-loss spectroscopy, and X-ray photoelectron spectroscopy.The sheet resistance measurements revealed that the doped films had unexpectedly high resistances. This stands in contrast to the case of N-MWCNT films, where decreased resistance has been reported with N-doping. To understand this effect, we developed a resistor network model, which allowed us to disentangle the contribution of bundle−bundle contacts when combined with data on undoped films. Assuming doping does not significantly change the contacts, the increased resistances of the doped films are likely due to enhanced carrier scattering by defect sites in the nanotubes. This work represents the first experimental report on macroscopic N-SWCNT thin films.
Simultaneous in Situ X-ray Scattering and Infrared Imaging of Polymer Extrusion in Additive Manufacturing (2019)

In situ wide-angle X-ray scattering together with infrared imaging was performed during three-dimensional material extrusion printing and correlated with the development of the crystalline structure and subsequent thermomechanical properties. Identical samples were printed with nozzle motion either along the short axis or the long axis. The short axis mode had higher thermal retention, which resulted in later onset of crystal structure. The longer time spent at temperatures between the glass transition and the melting point produced samples with higher degree of crystallinity but also significantly increased brittleness. The tracer diffusion coefficient <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mrow><mml:mi>D</mml:mi> <mml:mo>(</mml:mo> <mml:mi>T</mml:mi> <mml:mo>)</mml:mo></mml:mrow> </mml:math> , together with its temperature dependence, was measured using neutron reflectivity, and the total interdiffusion length between filaments was then calculated using <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mrow><mml:mi>D</mml:mi> <mml:mo>(</mml:mo> <mml:mi>T</mml:mi> <mml:mo>)</mml:mo></mml:mrow> </mml:math> for each temperature point, as determined by the measured thermal profiles. This allowed us to define the time/temperature plane that yielded the minimum diffusion length <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mrow><mml:mtext>Δ</mml:mtext> <mml:mi>L</mml:mi></mml:mrow> </mml:math> that provides mechanical integrity of the printed features ( <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mrow><mml:mtext>Δ</mml:mtext> <mml:mi>L</mml:mi></mml:mrow> </mml:math> less than the radius of gyration of the poly(l-lactide)). The model was probed by printing structures at four nozzle temperatures and measuring the time dependence of the thermal profiles at filaments in the horizontal and vertical positions. The data indicated that the thermal retention was anisotropic, where higher values were obtained in the horizontal plane. Mechanical measurements indicated large differential increases in the torsional strength, corresponding to the direction with increased thermal retention.
Evaluation of the inotropic function at rest and the effect of enoximone in heart transplanted recipients. Assessment by left ventricular endsystolic pressure volume relationship. (1992)

Denervation of the heart involves an alteration (density, distribution of beta 1-beta 2-types) of beta-adrenoceptors in long-term follow-up. To elucidate the influence of these changes on left ventricular contractility and to provide an effective alternative treatment to re-transplantation in cases of chronic rejection (coronary vasculopathy-CVP, unspecific myocardial allograft failure-UMAF) a clinical study on 19 male transplant recipients after orthotopic heart transplantation without CVP and UMAF in the non-rejecting state was undertaken. Six male patients served as a control group to compare the systolic function at rest. Left ventricular end-systolic pressure-volume relationships (ESPVR) (k-slope) were registered and computer measured using a conductance catheter-technique under conditions of a transiently occluded vena cava and at a fixed heart rate (atrial pacing) in all patients (n = 25). In the transplanted patient group the acute response of enoximone (0.75 mg/kg) administered intravenously was recorded. The position of the ESPVR in the transplanted hearts were not different as compared to the data obtained from the non-transplanted hearts at rest. The k-slope increased from the baseline data after the acute infusion of enoximone in the transplanted hearts. The dosage of enoximone used produced a significant leftward shift in the ESPVR in most patients (89%). In addition, 42% of the patients showed an insignificant drop in left ventricular systolic pressure. Thus, the baseline contractile characteristics of the heart transplant recipients without chronic rejection and in the non-rejecting state is not obviously different from those in non-transplanted patients at rest independent of the time since operation.(ABSTRACT TRUNCATED AT 250 WORDS)
The Multiple Inhibitory Mechanisms of GEM 91®, a gag Antisense Phosphorothioate Oligonucleotide, for Human Immunodeficiency Virus Type 1 (1997)

GEM 91 (gene expression modulator) is a 25-mer oligonucleotide phosphorothioate complementary to the gag initiation site of HIV-1. GEM 91 has been studied in various in vitro cell culture models to examine inhibitory effects on different stages of HIV-1 replication. Experiments were focused on the binding of virions to the cell surface, inhibition of virus entry, reverse transcription (HIV DNA production), inhibition of steady state viral mRNA levels, inhibition of virus production from chronically infected cells, and inhibition of HIV genome packaging within virions. Experiments were also performed in vitro in an attempt to generate strains of HIV with reduced sensitivity to GEM 91. We observed sequence-dependent inhibition of virus entry/reverse transcription and a reduction in steady state viral RNA levels. We also observed sequence-independent inhibition of virion binding to cells and inhibition of virus production by chronically infected cells. Using in vitro methods that were successful in generating HIV strains with reduced sensitivity to AZT, we were unable to generate strains with reduced sensitivity to GEM 91.