gebhart/patrepeval huggingface dataset:
African Gene Flow Reduces Beta-Ionone Anosmia/Hyposmia Prevalence in Admixed Malagasy Populations (2021)

While recent advances in genetics make it possible to follow the genetic exchanges between populations and their phenotypic consequences, the impact of the genetic exchanges on the sensory perception of populations has yet to be explored. From this perspective, the present study investigated the consequences of African gene flow on odor perception in a Malagasy population with a predominantly East Asian genetic background. To this end, we combined psychophysical tests with genotype data of 235 individuals who were asked to smell the odorant molecule beta-ionone (βI). Results showed that in this population the ancestry of the OR5A1 gene significantly influences the ability to detect βI. At the individual level, African ancestry significantly protects against specific anosmia/hyposmia due to the higher frequency of the functional gene (OR ratios = 14, CI: 1.8-110, <i>p</i>-value = 0.012). At the population level, African introgression decreased the prevalence of specific anosmia/hyposmia to this odorous compound. Taken together, these findings validate the conjecture that in addition to cultural exchanges, genetic transfer may also influence the sensory perception of the population in contact.
Isolation and characterization of rhamnolipid-producing bacterial strains from a biodiesel facility (2009)

Novel strains of rhamnolipid-producing bacteria were isolated from soils at a biodiesel facility on the basis of their ability to grow on glycerol as a sole carbon source. Strains were identified as Acinetobacter calcoaceticus, Enterobacter asburiae, Enterobacter hormaechei, Pantoea stewartii, and Pseudomonas aeruginosa. The strains of the former five species were found to produce rhamnolipids in quantities the same as, or similar to, coisolated strains of P. aeruginosa. Measurements of surface tension revealed that that emulsifying properties of these strains were similar to levels displayed by rhamnolipids produced by P. aeruginosa. Results of matrix-assisted laser desorption/ionization time-of-flight MS analyses revealed that the predominant compounds made by all strains were C10-C10 mono- and dirhamnolipids. Notably, E. hormaechei and one strain of A. calcoaceticus produced rhamnolipids in amounts similar to the pseudomonads. As all strains examined were from the same taxonomic class of Proteobacteria, further examination of this group may reveal many additional species not previously known to produce rhamnolipids in addition to novel strains of species currently known to produce rhamnolipids.
Role of glycolytic intermediate in regulation: Improving lycopene production in Escherichia coli by engineering metabolic control (2001)

Metabolic engineering in the postgenomic era is expected to benefit from a full understanding of the biosynthetic capability of microorganisms as a result of the progress being made in bioinformatics and functional genomics. The immediate advantage of such information is to allow the rational design of novel pathways and the elimination of native reactions that are detrimental or unnecessary for the desired purpose. However, with the ability to manipulate metabolic pathways becoming more effective, metabolic engineering will need to face a new challenge: the reengineering of the regulatory hierarchy that controls gene expression in those pathways. In addition to constructing the genetic composition of a metabolic pathway, they propose that it will become just as important to consider the dynamics of pathways gene expression. It has been widely observed that high-level induction of a recombinant protein or pathway leads to growth retardation and reduced metabolic activity. These phenotypic characteristics result from the fact that the constant demands of production placed upon the cell interfere with its changing requirements for growth. They believe that this common situation in metabolic engineering can be alleviated by designing a dynamic controller that is able to sense the metabolic state of the cell and regulate the expression of the recombinant pathway accordingly. This approach, which is termed metabolic control engineering, involves redesigning the native regulatory circuits and applying them to the recombinant pathway. The general goal of such an effort will be to control the flux to the recombinant pathway adaptively according to the cell's metabolic state. The dynamically controlled recombinant pathway can potentially lead to enhanced production, minimized growth retardation, and reduced toxic by-product formation. The regulation of gene expression in response to the physiological state is also essential to the success of gene therapy. Here they illustrate an application of this approach for the enhanced production of lycopene in Escherichia coli. The chose lycopene as a model compound because of its potential beneficial effects on human health. Lycopene, being an effective antioxidant, has been proposed as a possible treatment for some cancers and other degenerative human conditions. As a result, the in vivo synthesis of lycopene and related carotenoids has received increasing attention, and a number of reports have described their production in recombinant microorganism.
Reachable Set Approach to Collision Avoidance for UAVs (2015)

In this paper, we propose a reachable set based collision avoidance algorithm for unmanned aerial vehicles (UAVs). UAVs have been deployed for agriculture research and management, surveillance and sensor coverage for threat detection and disaster search and rescue operations. It is essential for the aircraft to have on-board collision avoidance capability to guarantee safety. Instead of the traditional approach of collision avoidance between trajectories, we propose a collision avoidance scheme based on reachable sets and tubes. We then formulate the problem as a convex optimization problem seeking suitable control constraint sets for participating aircraft. We have applied the approach on a case study of two quadrotors and two fix-wing aircraft collision avoidance scenario.
Investigation of the bipolar degradation of SiC MOSFET body diodes and the influence of current density (2021)

Bipolar degradation continues to be a key issue that should be taken into account in 4H-SiC devices using bipolar operation modes. The generation and expansion of recombination-induced stacking faults (SFs) in 4H-SiC devices results in a forward-voltage drift, which has been widely discussed in the literature. In this work, 1.2 kV SiC MOSFET body diodes were stressed at different current densities to investigate the influence of crystal-induced voltage drifts like bipolar degradation caused by stacking faults (SFs), expansion from pre-existing basal plane dislocations (BPDs) or conversion points. Additionally, thermomechanical failures (gate-oxide damage, front-side metallization degradation, bond-wire heel crack and lift-off) inevitably occurred due to high surge-current stress. The measurement results illustrate the spectrum of degradation by applying different current densities to the body diode of SiC MOSFETs.
Spectral tomography with diffuse near-infrared light: inclusion of broadband frequency domain spectral data (2008)

Near-infrared (NIR) region-based spectroscopy is examined for accuracy with spectral recovery using frequency domain data at a discrete number of wavelengths, as compared to that with broadband continuous wave data. Data with more wavelengths in the frequency domain always produce superior quantitative spectroscopy results with reduced noise and error in the chromophore concentrations. Performance of the algorithm in the situation of doing region-guided spectroscopy within the MRI is also considered, and the issue of false positive prior regions being identified is examined to see the effect of added wavelengths. The results indicate that broadband frequency domain data are required for maximal accuracy. A broadband frequency domain experimental system was used to validate the predictions, using a mode-locked Ti:sapphire laser for the source between 690- and 850-nm wavelengths. The 80-MHz pulsed signal is heterodyned with photomultiplier tube detection, to lower frequency for data acquisition. Tissue-phantom experiments with known hemoglobin absorption and tissue-like scatter values are used to validate the system, using measurements every 10 nm. More wavelengths clearly provide superior quantification of total hemoglobin values. The system and algorithms developed here should provide an optimal way to quantify regions with the goal of image-guided breast tissue spectroscopy within the MRI.
Charge-Transfer Perturbations Due to Interfaces on Electronic and Ionic Conductions within Composite Electrodes for Li-Ion Batteries (2018)

International audience
Master/Slave Speculative Parallelization (2002)

Master/Slave Speculative Parallelization (MSSP) is an execution paradigm for improving the execution rate of sequential programs by parallelizing them speculatively for execution on a multiprocessor. In MSSP one processor - the master - executes an approximate version of the program to compute selected values that the full program's execution is expected to compute. The master's results are checked by slave processors that execute the original program. This validation is parallelized by cutting the program's execution into tasks. Each slave uses its predicted inputs (as computed by the master) to validate the input predictions of the next task, inductively validating the entire execution. The performance of MSSP is largely determined by the execution rate of the approximate program. Since approximate code has no correctness requirements (in essence it is a software value predictor), it can be optimized more effectively than traditionally generated code. It is free to sacrifice correctness in the uncommon case to maximize performance in the common case. A simulation-based evaluation of an initial MSSP implementation achieves speedups of up to 1.7 (harmonic mean 1.25) on the SPEC2000 integer benchmarks. Performance is currently limited by the effectiveness with which our current automated infrastructure approximates programs, which can likely be improved significantly.
Baseline C-reactive protein is associated with disease progression in patients with Crohnʼs disease (2011)

Elevated C-reactive protein (CRP), a marker of inflammation, is known to correlate with Crohn's disease (CD) activity1,2 and to be a predictor of disease relapse in CD.3,4 However, in patients with moderate or severe CD it is not known whether CRP is associated with disease progression. This post hoc analysis evaluated the association of baseline (BL) CRP and change in CDAI over time in patients with moderate (CDAI>220 to ≤300) to severe (CDAI>300) CD who were randomized to the placebo group in the CHARM trial5 (N=238). Patients received open-label adalimumab (ADA) induction (week 0: 80mg; week 2: 40mg) followed by blinded weekly placebo treatment from weeks 4-56, with switch to open-label ADA allowed after week 12 for disease flare. This analysis grouped patients by CD severity and BL CRP (severe, high: CDAI>300, CRP≥10mg/L; severe, low: CDAI>300, CRP<10mg/L; moderate, high: CDAI≤300, CRP≥10mg/L; moderate, low: CDAI≤300, CRP<10mg/L). Mean CDAI scores at each visit from weeks 4-56 were calculated for each subgroup, using last observation carried forward (after week 4) to handle dropouts or switch to ADA. Mean CDAI decreased from BL in all subgroups after ADA induction (Week 4, Table). By week 56, the mean CDAI in all subgroups had increased compared with week 4, and was greater in patients who had higher CRP versus lower CRP at BL (244 vs 223, 306 vs 260, for moderate and severe groups, respectively). In patients with moderate CD and high CRP, week 12 and week 56 CDAI approached that of patients with severe CD and low CRP, despite BL differences in CDAI of over 90 points (week 12: 235 vs 243; week 56: 244 vs 260). ORs (95% Confidence Intervals) ORs (95% Confidence Intervals) This post hoc analysis of disease activity and CRP demonstrates that an elevated BL CRP in patients with moderate or severe CD is associated with higher disease scores after one year. Disease activity over time in patients with moderate CD and higher CRP behaved similarly to that of patients with severe CD and lower CRP.
Free‐Breathing Volumetric Liver and Proton Density Fat Fraction Quantification in Pediatric Patients Using Stack‐of‐Radial MRI With Self‐Gating Motion Compensation (2020)

2 TECHNICAL EFFICACY STAGE: 2.
Multielectrode Spectroscopy Enables Rapid and Sensitive Molecular Profiling of Extracellular Vesicles (2022)

Detecting protein markers in extracellular vesicles (EVs) is becoming a useful tool for basic research and clinical diagnoses. Most EV protein assays, however, require lengthy processes-conjugating affinity ligands onto sensing substrates and affixing EVs with additional labels to maximize signal generation. Here, we present an iPEX (impedance profiling of extracellular vesicles) system, an all-electrical strategy toward fast, multiplexed EV profiling. iPEX adopts one-step electropolymerization to rapidly functionalize sensor electrodes with antibodies; it then detects EV proteins in a label-free manner through impedance spectroscopy. The approach streamlines the entire EV assay, from sensor preparation to signal measurements. We achieved (i) fast immobilization of antibodies (<3 min) per electrode; (ii) high sensitivity (500 EVs/mL) without secondary labeling; and (iii) parallel detection (quadruple) in a single chip. A potential clinical utility was demonstrated by directly analyzing plasma samples from glioblastoma multiforme patients.
Search-Based Serving Architecture of Embeddings-Based Recommendations (2019)

Over the past 10 years, many recommendation techniques have been based on embedding users and items in latent vector spaces, where the inner product of a (user,item) pair of vectors represents the predicted affinity of the user to the item. A wealth of literature has focused on the various modeling approaches that result in embeddings, and has compared their quality metrics, learning complexity, etc. However, much less attention has been devoted to the issues surrounding productization of an embeddings-based high throughput, low latency recommender system. In particular, how the system might keep up with the changing embeddings as new models are learnt. This paper describes a reference architecture of a high-throughput, large scale recommendation service which leverages a search engine as its runtime core. We describe how the search index and the query builder adapt to changes in the embeddings, which often happen at a different cadence than index builds. We provide solutions for both id-based and feature-based embeddings, as well as for batch indexing and incremental indexing setups. The described system is at the core of a Web content discovery service that serves tens of billions recommendations per day in response to billions of user requests.
Prediction of sustained harmonic walking in the free-living environment using raw accelerometry data (2018)

We propose a simple approach for the detection of SHW and estimation of IWF, based on Fourier decomposition.
Genome-wide discovery of somatic regulatory variants in diffuse large B-cell lymphoma (2018)

Diffuse large B-cell lymphoma (DLBCL) is an aggressive cancer originating from mature B-cells. Prognosis is strongly associated with molecular subgroup, although the driver mutations that distinguish the two main subgroups remain poorly defined. Through an integrative analysis of whole genomes, exomes, and transcriptomes, we have uncovered genes and non-coding loci that are commonly mutated in DLBCL. Our analysis has identified novel cis-regulatory sites, and implicates recurrent mutations in the 3' UTR of NFKBIZ as a novel mechanism of oncogene deregulation and NF-κB pathway activation in the activated B-cell (ABC) subgroup. Small amplifications associated with over-expression of FCGR2B (the Fcγ receptor protein IIB), primarily in the germinal centre B-cell (GCB) subgroup, correlate with poor patient outcomes suggestive of a novel oncogene. These results expand the list of subgroup driver mutations that may facilitate implementation of improved diagnostic assays and could offer new avenues for the development of targeted therapeutics.
A brief guide to polymer nomenclature (IUPAC Technical Report) (2012)

The universal adoption of an agreed nomenclature has never been more important for the description of chemical structures in publishing and online searching. The International Union of Pure and Applied Chemistry (IUPAC) and Chemical Abstracts Service (CAS) make similar recommendations. The main points are shown here with references to original documents. Further details can be found in the IUPAC Purple Book.
Reversion of tumor phenotype in surface transplants of skin SCC cells by scaffold-induced stroma modulation (2006)

Interactions between cancer cells and the tissue microenvironment play an essential role in controlling tumor development and progression. Here, we report that stromal modulation induced by a biodegradable meshwork (Hyalograft 3D) inhibited tumor vascularization and invasion of the locally invasive low-grade malignant human HaCaT-ras II-4 keratinocytes in a surface xenotransplantation assay. The scaffold caused formation of an active granulation tissue that shifted to a fibrotic-type connective tissue with accumulation of myofibroblasts and collagen bundles. Most importantly, in transplants with scaffolds, the epithelial-stromal border was normalized developing an ultrastructurally complete basement membrane (BM) including hemidesmosomes. The observed reversion of the tumor phenotype was not due to decreased tumor cell proliferation but correlated with (i) normalization of epidermal differentiation, (ii) condensation of extracellular matrix (ECM) and (iii) reduction of peritumoral protease activity Furthermore, inhibited invasion was paralleled by eliminated tumor vascularization. This was substantiated by a diminished endothelial VEGF-receptor (VEGFR) expression and, in turn, by a concomitant increase in the ECM components thrombospondin-1 (TSP-1) and endostatin, known to impair angiogenesis. Even in transplants of the metastatic high-grade malignant HaCaT-ras A-5RT3 keratinocytes the anti-invasive effect of the scaffold-modulated stroma prevailed. Tumor vascularization and invasion was reduced and the epithelial tissue partially normalized including formation of stretches of BM. This clearly demonstrates that the scaffold-modulated connective tissue not only blocks tumor invasion but reverts the tumor phenotype. These novel findings underline the controlling function of tumor stroma and open new strategies of cancer therapy by targeting tumor stroma elements.
Effects of malignancy and interleukin-2 infusion on gut macromolecular permeability (1995)

Gut permeability to polyethylene glycol 3350 is enhanced in advanced malignancy. High-dose interleukin-2 therapy does not further increase permeability of the gut.
Ultra-sharp asymmetric Fano-like resonance spectrum on Si photonic platform (2019)

In this paper, we report the generation of an ultra-sharp asymmetric resonance spectrum through Fano-like interference. This generation is accomplished by weakly coupling a high-quality factor (Q factor) Fabry-Pérot (FP) cavity and a low-Q factor FP cavity through evanescent waves. The high-Q FP cavity is formed by Sagnac loop mirrors, whilst the low-Q one is built by partially transmitting Sagnac loop reflectors. The working principle has been analytically established and numerically modelled by using temporal coupled-mode-theory (CMT), and verified using a prototype device fabricated on the 340 nm silicon-on-insulator (SOI) platform, patterned by deep ultraviolet (DUV) lithography. Pronounced asymmetric resonances with slopes up to 0.77 dB/pm have been successfully measured, which, to the best of our knowledge, is higher than the results reported in state-of-the-art devices in on-chip integrated Si photonic studies. The established theoretical analysis method can provide excellent design guidelines for devices with Fano-like resonances. The design principle can be applied to ultra-sensitive sensing, ultra-high extinction ratio switching, and more applications.
BMP-2 (and partially GDF-5) coating significantly accelerates and augments bone formation close to hydroxyapatite/tricalcium-phosphate/brushite implant cylinders for tibial bone defects in senile, osteopenic sheep (2023)

Bilateral defects (diameter 8 mm) in the medial tibial head of senile, osteopenic female sheep (n = 48; 9.63 ± 0.10 years; mean ± SEM) were treated with hydroxyapatite (HA)/beta-tricalcium phosphate (β-TCP)/dicalcium phosphate dihydrate (DCPD; brushite) cylinders coated with BMP-2 (25 or 250 micrograms) or growth differentiation factor (GDF)-5 (125 or 1250 micrograms; left side); cylinders without BMP served as controls (right side). Three, 6, and 9 months post-operation (n = 6 each group), bone structure and formation were analyzed in vivo by X-ray and ex vivo by osteodensitometry, histomorphometry, and micro-computed tomography (micro-CT) at 3 and 9 months. Semi-quantitative X-ray evaluation showed significantly increasing bone densities around all implant cylinders over time. High-dose BMP-2-coated cylinders (3 and 9 months) and low-dose GDF-5-coated cylinders (3 and 6 months) demonstrated significantly higher densities than controls (dose-dependent for BMP-2 at 3 months). This was confirmed by osteodensitometry at 9 months for high-dose BMP-2-coated cylinders (and selected GDF-5 groups), and was again dose-dependent for BMP-2. Osteoinduction by BMP-2 was most pronounced in the adjacent bone marrow (dynamic histomorphometry/micro-CT). BMP-2 (and partially GDF-5) significantly increased the bone formation in the vicinity of HA/TCP/DCPD cylinders used to fill tibial bone defects in senile osteopenic sheep and may be suitable for surgical therapy of critical size, non-load-bearing bone defects in cases of failed tibial head fracture or defect healing.
Optical performance test and validation of microcameras in multiscale, gigapixel imagers (2014)

Wide field-of-view gigapixel imaging systems capable of diffraction-limited resolution and video-rate acquisition have a broad range of applications, including sports event broadcasting, security surveillance, astronomical observation, and bioimaging. The complexity of the system integration of such devices demands precision optical components that are fully characterized and qualified before being integrated into the final system. In this work, we present component and assembly level characterizations of microcameras in our first gigapixel camera, the AWARE-2. Based on the results of these measurements, we revised the optical design and assembly procedures to construct the second generation system, the AWARE-2 Retrofit, which shows significant improvement in image quality.
Effects of Humidity on Solid Oxide Fuel Cell Cathodes (2015)

This report summarizes results from experimental studies performed by a team of researchers assembled on behalf of the Solid-state Energy Conversion Alliance (SECA) Core Technology Program. Team participants employed a variety of techniques to evaluate and mitigate the effects of humidity in solid oxide fuel cell (SOFC) cathode air streams on cathode chemistry, microstructure, and electrochemical performance.