gebhart/patrepeval huggingface dataset:
Indole cell signaling occurs primarily at low temperatures in Escherichia coli (2008)

We have shown that the quorum-sensing signals acylhomoserine lactones, autoinducer-2 (AI-2) and indole influence the biofilm formation of Escherichia coli. Here, we investigate how the environment, that is, temperature, affects indole and AI-2 signaling in E. coli. We show in biofilms that indole addition leads to more extensive differential gene expression at 30 degrees C (186 genes) than at 37 degrees C (59 genes), that indole reduces biofilm formation (without affecting growth) more significantly at 25 and 30 degrees C than at 37 degrees C and that the effect is associated with the quorum-sensing protein SdiA. The addition of indole at 30 degrees C compared to 37 degrees C most significantly repressed genes involved in uridine monophosphate (UMP) biosynthesis (carAB, pyrLBI, pyrC, pyrD, pyrF and upp) and uracil transport (uraA). These uracil-related genes are also repressed at 30 degrees C by SdiA, which confirms SdiA is involved in indole signaling. Also, compared to 37 degrees C, indole more significantly decreased flagella-related qseB, flhD and fliA promoter activity, enhanced antibiotic resistance and inhibited cell division at 30 degrees C. In contrast to indole and SdiA, the addition of (S)-4,5-dihydroxy-2,3-pentanedione (the AI-2 precursor) leads to more extensive differential gene expression at 37 degrees C (63 genes) than at 30 degrees C (11 genes), and, rather than repressing UMP synthesis genes, AI-2 induces them at 37 degrees C (but not at 30 degrees C). Also, the addition of AI-2 induces the transcription of virulence genes in enterohemorrhagic E. coli O157:H7 at 37 degrees C but not at 30 degrees C. Hence, cell signals cause diverse responses at different temperatures, and indole- and AI-2-based signaling are intertwined.
The public health impact of poor sleep on severe COVID-19, influenza and upper respiratory infections (2023)

Instrumentarium Science Foundation, Academy of Finland, Signe and Ane Gyllenberg Foundation, National Institutes of Health.
Ultrasonographic Evaluation of Myometrial Thickness and Prediction of a Successful External Cephalic Version (2011)

III.
Light-induced self-written waveguide fabrication using 1550  nm laser light (2017)

Light-induced self-written (LISW) optical waveguides were fabricated for the first time, to the best of our knowledge, using a photopolymerizable resin system formed by 1550 nm pulse laser light. A two-photon absorption (TPA) chromophore with a TPA cross section of several hundred Goeppert-Mayer (GM) at 1550 nm was used. Furthermore, the optical interconnection between a single-mode fiber and a fiber Bragg grating was demonstrated by the present technique, using one-way irradiation of 1550 nm laser light through the single-mode fiber. The LISW waveguide formation using 1550 nm laser light offers a new and promising alternative route for optical interconnection in silicon photonics technology.
Complement activation and release of tumour necrosis factor alpha, interleukin-2, interleukin-6 and soluble tumour necrosis factor and interleukin-2 receptors during and after cardiopulmonary bypass in children (1995)

C3 activation products, terminal complement complex (TCC), and cytokines including interleukins 6 and 2 (IL-6, IL-2) and tumour necrosis factor-alpha (TNF), and the soluble IL-2 and TNF receptors were determined serially during and up to 48 h after open heart surgery in children. Significant increases were noted in soluble TNF and IL-2 receptor levels postoperatively (p < 0.05). No significant increase over preoperative levels was seen in the cytokines, except for IL-6 which was significantly increased postoperatively (p < 0.01), reaching a maximum 2 h postoperatively. C3 activation products and TCC levels increased significantly after weaning from cardiopulmonary bypass (p < 0.05). The IL-6 response lagged behind the complement activation. We found a significant correlation between duration of cardiopulmonary bypass and IL-6 levels 48 h postoperatively (r = 0.852, p < 0.05). We conclude that the concentration of complement activation products, IL-6 and the soluble TNF and IL-2 receptors are significantly increased after open heart surgery in children. The cytokine receptor response probably reflects some sort of regulatory mechanism.
High levels of cyclic‐di‐ GMP in plant‐associated P seudomonas correlate with evasion of plant immunity (2015)

The plant innate immune system employs plasma membrane-localized receptors that specifically perceive pathogen/microbe-associated molecular patterns (PAMPs/MAMPs). This induces a defence response called pattern-triggered immunity (PTI) to fend off pathogen attack. Commensal bacteria are also exposed to potential immune recognition and must employ strategies to evade and/or suppress PTI to successfully colonize the plant. During plant infection, the flagellum has an ambiguous role, acting as both a virulence factor and also as a potent immunogen as a result of the recognition of its main building block, flagellin, by the plant pattern recognition receptors (PRRs), including FLAGELLIN SENSING2 (FLS2). Therefore, strict control of flagella synthesis is especially important for plant-associated bacteria. Here, we show that cyclic-di-GMP [bis-(3'-5')-cyclic di-guanosine monophosphate], a central regulator of bacterial lifestyle, is involved in the evasion of PTI. Elevated cyclic-di-GMP levels in the pathogen Pseudomonas syringae pv. tomato (Pto) DC3000, the opportunist P. aeruginosa PAO1 and the commensal P. protegens Pf-5 inhibit flagellin synthesis and help the bacteria to evade FLS2-mediated signalling in Nicotiana benthamiana and Arabidopsis thaliana. Despite this, high cellular cyclic-di-GMP concentrations were shown to drastically reduce the virulence of Pto DC3000 during plant infection. We propose that this is a result of reduced flagellar motility and/or additional pleiotropic effects of cyclic-di-GMP signalling on bacterial behaviour.
A compact model for thin SOI LIGBTs: description, experimental verification and system application (2005)

A complete physical model for the lateral IGBT in thin silicon on insulator technology is presented for the first time. The model is oriented to circuit simulators and is implemented in Pspice. Model results are compared against experimental results and Medici numerical simulations. Numerical convergence performance of the model is verified through the simulation of a half bridge circuit and a complete flyback switch mode power supply.
Diamond Meta-Surfaces for High Power Laser Applications (2018)

Over the past decade optical quality CVD diamond has found its way into many high -power laser applications. In these demanding high -power applications, diamond is able to succeed due to its extraordinary physical properties. The highest thermal conductivity of any known material, low absorption over a broad spectrum, and exceptional strength all contribute towards an excellent optical material. As diamond is a high refractive index material, a solution is generally needed to manage Fresnel reflections from polished diamond surfaces. This is especially important for high -power laser applications, where even just a few percent of total power reflected must be carefully handled. Currently the industry standard solution is to apply thin film coatings to the polished diamond surfaces, and for many applications this is a perfectly adequate solution. In fact it has been shown that thin film coated diamond windows greatly outperform similar thin film coated windows [1]. For the most demanding and highest power density applications, applications that are pushing the boundaries of technology, thin film coatings can be a limitation. This is due to the relatively poor thermal properties of the coating materials; at high enough power -density the rate of heat generation through absorption overwhelms the ability of the coating to dissipate heat, leading to thermal runaway and often catastrophic failures. Laser Induced Damage Threshold (LIDT), a common measure of an optic's power handling capability, describes the power density at which this tipping point occurs. Thankfully nature has demonstrated an alternative solution towards eliminating reflections. Close inspection of the eyes of moths reveals a tightly packed array of conical structures on a sub -micron scale. In nature these tightly packed arrays eliminate reflections that otherwise may give the moth away to predators. Likewise, in demanding laser applications this "moth -eye" solution can be applied to eliminate Fresnel reflections. The advantage to this approach is that the LIDT of a moth -eye optic is limited by only the material properties of the optic itself, rather than by the material properties of a thin film coating. Given diamond's extraordinary material properties, the moth -eye approach is especially advantageous when creating a diamond optic.
Impaired Muscle Mitochondrial Function in Familial Partial Lipodystrophy (2021)

Increased muscularity in FPL is not due to increased muscle protein synthesis and is likely due to reduced muscle protein degradation. Impaired mitochondrial function and altered gene expression likely explain the metabolic abnormalities and skeletal muscle dysfunction in FPL subjects.
UV to NIR optical properties of IP-Dip, IP-L, and IP-S after two-photon polymerization determined by spectroscopic ellipsometry (2019)

The polymers IP-Dip, IP-L, and IP-S are among the most commonly used photo-resists employed for the rapid prototyping of optical components using two-photon polymerization. Despite the widespread use of these polymers, measured data on their optical properties is scarce. Recently, the refractive index n of these polymers has been determined in the visible and nearinfrared spectral range. However, the accurate optical properties including extinction coefficient kappa in the ultraviolet spectral range have not been reported yet. Here we report on accurate, ellipsometric measurements of the complex dielectric functions of two-photon polymerized IP-Dip, IP-L, and IP-S in the spectral range from 210 nm to 1500 nm. Model dielectric functions composed of oscillators with Lorentz, Gaussian, and Tauc-Lorentz broadenings are presented for all investigated polymers. (C) 2019 Optical Society of America under the terms of the OSA Open Access Publishing Agreement
Gel Compression Considerations for Chromatography Scale-Up for Protein C Purification (1997)

Abstract Protein C is a vitamin K dependent glycoprotein which is synthesized by the liver [1]. It is the zymogen of a serine protease which acts as an anticoagulant by inhibiting activated factors V and VIII thus enhancing fibrinolysis. An increased risk for the development of venous thrombosis has been attributed to Protein C deficiency[2]. This work is to establish theoretical and experimental relationships for the scale up of Immobilized Metal Affinity Chromatography (IMAC) and Immuno Affinity Chromatography for the low cost production of large quantities of Protein C. Gel matrices for Protein C separation are being analyzed to determine the relationship between the materials properties of the gel and column collapse characteristics.
Higher Order Modulations and GSM/EDGE Radio Access Network Evolution (2006)

The GSM/EDGE radio access network (GERAN) is continuously evolving to support higher peak data rates and to improve coverage. The evolution process is controlled by Third Generation Partnership Project (3GPP) specification work, within the technical specification group (TSG) GERAN and its working groups. One of the proposals how to increase the radio network performance is the usage of higher order modulations such as quadrature amplitude modulation (QAM). That could be seen as a straight step when compared to the introduction of the additional 8-PSK modulation in 3GPP Release 99. The performance evaluation of higher order modulation namely 16-QAM in GSM environment is presented. A comparison with other candidates such as the dual symbol rate is discussed. The effects of transceiver and receiver impairments, frequency hopping, and power amplifier non-linearity are examined separately with the help of a link layer simulator. The obtained results are compared with 3GPP objectives approved on the 24 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">th</sup> TSG GERAN meeting
SAM: Squeeze-and-Mimic Networks for Conditional Visual Driving Policy Learning (2020)

We describe a policy learning approach to map visual inputs to driving controls conditioned on turning command that leverages side tasks on semantics and object affordances via a learned representation trained for driving. To learn this representation, we train a squeeze network to drive using annotations for the side task as input. This representation encodes the driving-relevant information associated with the side task while ideally throwing out side task-relevant but driving-irrelevant nuisances. We then train a mimic network to drive using only images as input and use the squeeze network's latent representation to supervise the mimic network via a mimicking loss. Notably, we do not aim to achieve the side task nor to learn features for it; instead, we aim to learn, via the mimicking loss, a representation of the side task annotations directly useful for driving. We test our approach using the CARLA simulator. In addition, we introduce a more challenging but realistic evaluation protocol that considers a run that reaches the destination successful only if it does not violate common traffic rules. A video summarizing this work is available at this https URL , and code is available at this https URL .
The Role of Chlorin—Chlorine Interaction in the Crystal structure of a Highly Volatile Molecule: Trans-3,4-Dichlorotetrahydrothiophene (1990)

Abstract The present work deals with the synthesis and spectroscopic (NMR, IR) and structural characterization of trans-3,4-dichlorotetrahydrothiophene (TDTHT). This compound is solid, but highly volatile, at room temperature and is constituted of only one conformer, in contrast with the liquid phase where both conformers coexist. The solid phase seems to be stabilized by a very short C1 … C1 interaction (∼3.3Å).
Hematopoietic progenitor cell expression of the H-CAM (CD44) homing- associated adhesion molecule (1990)

We explored the expression of a lymphocyte homing-associated cell adhesion molecule (H-CAM, CD44) on hematopoietic progenitors. We demonstrate that immature myeloid and erythroid leukemic cell lines stain intensely with monoclonal antibodies Hermes-1 and Hermes-3, which define distinct epitopes on lymphocyte surface H-CAM, a glycoprotein involved in lymphocyte interactions with endothelial cells. Using fluorescence-activated cell sorting (FACS), human marrow cells were fractionated into Hermeshi, Hermesmed, and Hermeslo populations according to the expression of both the Hermes-1 and Hermes-3 epitopes. Granulocyte-macrophage colony-forming unit and erythroid burst-forming unit precursors were found predominantly in the brightly positive fractions. Two-color FACS analysis confirmed that the My10 (CD34) positive populations of cells in bone marrow, which contain most of the progenitor cell activity, are brightly positive for Hermes-1. Finally, we demonstrate that among bone marrow cells, the highest levels of H-CAM are expressed on myeloid and erythroid progenitors as well as mature granulocytes and lymphocytes. Thus we provide evidence that molecules related or identical to the H-CAM homing receptor are expressed on marrow progenitor cells. H-CAM may contribute to progenitor cell interactions with marrow endothelial and stromal cell elements important to the maintenance and regulation of hematopoiesis.
Narrow-linewidth low-noise multiwatt power operation of tunable compact (2010)

International audience
Modeling the evolved gas species from cashew nut shells pyrolysis (2006)

Cashew nut shells are important biomass wastes abundant in most of the tropical countries. As biomass feedstock, they are important energy sources that can play an important role as fuel for energy generation through the ordinary thermochemical processes. However, although this potential as fuel, cashew nut shells are still rarely and weakly studied. In fact, studies on pyrolysis, gasification or combustion of cashew nut shells are not commonly found as it happens with wood related biomasses. On the other hand, it is known that pyrolysis plays a key role in any thermochemical conversion of biomass. In fact, biomass pyrolysis is a complex process that influences any of the three main thermochemical conversion processes of biomass into useful energy. This is due to the fact that pyrolysis characteristics do determine the char quality in which gasification and combustion are heavily dependent. Therefore, characterization of pyrolysis process is essential in thermochemical conversion processes. This makes the study of pyrolysis as mandatory in biomass fuels research. In this study, cashew nut shells are pyrolysed at three different low heating rates (10, 30 and 100°C/mn) using thermogravimetric analyser coupled with Fourier transform infrared spectrometer (TG-FTIR). Gas and tar evolution rates as well as yields and pyrolysis kinetics are obtained and compared with the data available in the literature for wood pellets and Miscanthus Giganteus under the same testing conditions. Further, these results are used as reference data for modeling pyrolysis at high heating rates as l,000and 10,000°C/s. The modeling aims at predicting yields and evolution rates of the pyrolysis products.
Is Premorbid Glenoid Anatomy Altered in Patients with Glenohumeral Osteoarthritis? (2013)

The glenoid vault model may be a clinically useful tool to estimate patient-specific premorbid glenoid anatomy, which may help in preoperative or intraoperative surgical planning for total shoulder arthroplasty.
P-141 Association Between Week 8 Mayo Subscores and Hospitalisation Rates in Adalimumab-treated Patients with Ulcerative Colitis from ULTRA1 and ULTRA2 (2013)

To determine the association between week 8 Mayo subscore (MS) values for rectal bleeding (RB), stool frequency (SF), endoscopy, and physicians global assessment (PGA) and hospitalisation incidence rates (IR) for adalimumab (ADA)-treated patients (pts) with moderately to severely active ulcerative colitis (UC) enrolled in ULTRA 11 and ULTRA 2.2 All-cause and UC-related hospitalisations occurring from wks 8 to 52 were examined for 160/80 mg-ADA randomised pts in ULTRA 1 and ULTRA 2. ADA-treated pts received 160/80 mg ADA at weeks 0/2, followed by 40 mg ADA every other week (eow) to week 52. ULTRA 1 had an 8-week double-blind (DB) phase followed by an open-label (OL) phase to week 52, during which pts could move to weekly (ew) ADA for inadequate response. In the 52-week DB trial ULTRA 2, pts with inadequate response could receive OL 40 mg eow beginning at week 12 followed by 40 mg ew. All hospitalisations occurring during DB or OL were analyzed. Hospitalisation IR (the number of pts with hospitalisations over pt-yrs at risk) were calculated for each MS value as assessed at wk 8. Spearman correlation coefficients were calculated between the MS and IR for each category. Pts were censored at first hospitalisation. The table shows IRs for all-cause and UC-related hospitalisations by week 8 MS category. Significant correlations were seen for SF subscores and all-cause hospitalisations and for RB and PGA subscores with UC-related hospitalisations. Week 8 endoscopy subscores were not significantly correlated with hospitalisation IRs (R2 = 0.64, P = 0.20 for each category). The IRs for both categories of hospitalisations were similar for pts with a week 8 endoscopy subscore of 0 or 1. For ADA-treated pts with moderately to severely active UC, SF subscore at week 8 was strongly correlated with all-cause hospitalisation risk, whereas week 8 endoscopy subscore trended to correlate with hospitalisation risk. References: 1. Reinisch W, et al. 2011. Gut;60:780 2. Sandborn WJ, et al. 2012. Gastroenterology;142:257.
Oxidative stress in Lactococcus lactis. (2003)

Lactococcus lactis, the most extensively characterized lactic acid bacterium, is a mesophilic- and microaerophilic-fermenting microorganism widely used for the production of fermented food products. During industrial processes, L. lactis is often exposed to multiple environmental stresses (low and high temperature, low pH, high osmotic pressure, nutrient starvation and oxidation) that can cause loss or reduction of bacterial viability, reproducibility, as well as organoleptic and/or fermentative qualities. Among these stress factors, oxidation can be considered one of the most deleterious to the cell, causing cellular damage at both molecular and metabolic levels. During the last two decades, considerable efforts have been made to improve our knowledge of oxidative stress in L. lactis. Many genes involved with both oxidative stress resistance and control mechanisms have been identified; functionally they seem to overlap. The finding of new genes, and a better understanding of the molecular mechanisms of stress resistance in L. lactis and other lactic acid bacterium, will lead to the construction and isolation of stress-resistant strains. Such strains could be exploited for both traditional and probiotic uses.
Scattering-parameter models and representations for microwave mixers (2005)

We present straightforward models and representations for RF and image mixers, and develop simple rules for transforming electrical problems involving mixers and signals at several frequencies into equivalent single-frequency problems. We show how those models, representations, and rules can be applied to mixer characterization with vector network analyzers, and how they relate to more general descriptions based on scattering parameters currently in use.
Chemoprevention of lung cancer: from concept to reality. (2003)

Among all cancer, lung cancer is the leading cause of cancer death in the western world. The poor lung cancer survival figures argue powerfully for new approaches to control this disease such as chemoprevention, that has been defined as the use of agents that reverse, suppress or prevent lung carcinogenesis. Over 80% of lung cancers are attributed to tobacco and carcinogens from cigarette smoke form the unquestionable link between nicotine addiction and lung cancer. Confoundedly epidemiological studies show that not more than 15% of heavy smokers will ultimately develop lung cancer. The fact that 85% of heavy smokers will not develop lung cancer points to differences in susceptibility. Dietary and genetically determined factors seem to play an important role in modulating individual susceptibility and are closely linked to the chemoprevention approach. Developments in tumor biology and chest radiology have given rise to optimism regarding to earlier diagnosis and improved possibilities for the management of preneoplastic- and early invasive lesions. The current article summarizes the chemoprevention efforts in lung cancer during the last two decades and identifies novel strategies for chemoprevention studies in high-risk individuals based on the developments in molecular targeted therapies and developments in response evaluation by using intermediate biomarker endpoints.