gebhart/patrepeval huggingface dataset:
Transcription factors, sucrose, and sucrose metabolic genes interact to regulate potato phenylpropanoid metabolism (2013)

Much remains unknown about how transcription factors and sugars regulate phenylpropanoid metabolism in tuber crops like potato (Solanum tuberosum). Based on phylogeny and protein similarity to known regulators of phenylpropanoid metabolism, 15 transcription factors were selected and their expression was compared in white, yellow, red, and purple genotypes with contrasting phenolic and anthocyanin profiles. Red and purple genotypes had increased phenylalanine ammonia lyase (PAL) enzyme activity, markedly higher levels of phenylpropanoids, and elevated expression of most phenylpropanoid structural genes, including a novel anthocyanin O-methyltransferase. The transcription factors Anthocyanin1 (StAN1), basic Helix Loop Helix1 (StbHLH1), and StWD40 were more strongly expressed in red and purple potatoes. Expression of 12 other transcription factors was not associated with phenylpropanoid content, except for StMYB12B, which showed a negative relationship. Increased expression of AN1, bHLH1, and WD40 was also associated with environmentally mediated increases in tuber phenylpropanoids. Treatment of potato plantlets with sucrose induced hydroxycinnamic acids, flavonols, anthocyanins, structural genes, AN1, bHLH1, WD40, and genes encoding the sucrose-hydrolysing enzymes SUSY1, SUSY4, and INV2. Transient expression of StAN1 in tobacco leaves induced bHLH1, structural genes, SUSY1, SUSY4, and INV1, and increased phenylpropanoid amounts. StAN1 infiltration into tobacco leaves decreased sucrose and glucose concentrations. In silico promoter analysis revealed the presence of MYB and bHLH regulatory elements on sucrolytic gene promoters and sucrose-responsive elements on the AN1 promoter. These findings reveal an interesting dynamic between AN1, sucrose, and sucrose metabolic genes in modulating potato phenylpropanoids.
Utilizing Gamification Approaches in Pervasive Health: How Can We Motivate Physical Activity Effectively? (2017)

Persuasive health systems such as wearable trackers and mobile applications can facilitate self-reflection on one’s physical activity. The gamification approach incorporates game design elements with persuasive systems to encourage more physical activity. However, some investigations have shown that using gamification to promote physical activity could have contradictory effects. To explore the conflicted findings in more detail, we designed and studied FitPet – an interactive virtual pet-keeping mobile game focused on encouraging physical activity. In a six-week field study, its effectiveness was evaluated and compared with two other gamification strategies, the goal-setting strategy and the use of social communities. Findings are that the social interaction strategy was the most effective intervention among these three. Contrary to prior research, goal-setting was not found to be as effective at providing motivation compared to social interaction. Although FitPet failed to promote significantly higher levels of physical activity, participants enjoyed this approach and provided design insights for future research: implementing social components and more challenging gameplay.
IC‐P‐039: Impairment of Resting‐State Functional Connectivity in The Default‐Mode Network Closely Tracks CSF Biomarkers In MCI (2016)

Resting-state functional MRI (rsfMRI) receives interest as a potential complement to structural imaging in MCI studies, particularly as the default-mode network (DMN) displays graded decay with disease progression. However, predictive conversion power is modest, and data on its ability to discern patients with an underlying CSF biomarker profile suggestive of incipient dementia is scant. 147 MCI patients were enrolled within WP5 of PharmaCog (E-ADNI). For all, CSFs concentrations of Aβ42, total tau (t-tau) and tau phosphorylated at residue 181 (p-tau) were measured via standardized ELISA kits. They also underwent rsfMRI at 13 sites equipped with 3.0 T scanners. A standardized sequence was utilized, having 3x3x3.5 mm resolution, TR=2.7 s, 200 volumes. Mixture model analysis established three distributions for each CSF biomarker: Aβ, Aβ/t-tau and Aβ/p-tau. Subsequent analyses were therefore conducted comparing negative, intermediate and positive groups. RsfMRI data were processed through standard preprocessing and independent-component analysis to extract the DMN. The intensity of synchronized activity (Z-scores) was measured over its constituent nodes: precuneus/posterior cingulate (PCC), left and right lateral parietal (LPC, RPC) and mediofrontal cortex (MFC), as well as for the entire network. Inferences were drawn from ANCOVAs having age, sex, education, head movement and signal-to-noise ratio as covariates. ROC curves were also calculated. Significant main effects emerged for Aβ/t-tau and Aβ/p-tau, but not Aβ alone. Averaging over the entire DMN, a graded connectivity reduction in respect to CSF status was found (p=.005 and p=.02) with significant differences between positive and negative subgroups (p=.004 and p=.01); a similar, though weaker, trend was observed separately for PCC (Aβ/t-tau only, p=.04) and LPC (p=.02 and .03). The AUC of ROC curves calculated for the entire DMN was .73 and .72 for discriminating patients in negative vs. positive Aβ/t-tau and Aβ/p-tau subgroups (p<.001). Our preliminary data suggest that DMN integrity may have significant value as a proxy of Aβ/tau CSF biomarker status in MCI. While accuracy is quantitatively small, recent technical advances are likely to increase the power of this technique.
Bacteriocines anti-listeria de leuconostoc : etude des relations structure/activite (1996)

Les bacteriocines sont des peptides ou des proteines secretes par des bacteries doues d'activite antibacterienne (a spectre etroit). A la difference des antibiotiques leur biosynthese est ribosomale et les bacteries productrices se protegent par un phenomene d'immunite qui impliquerait une proteine. Une nouvelle bacteriocine, la mesentericine y105#3#7, a ete purifiee et caracterisee a partir de deux souches de leuconostoc mesenteroides. Ce peptide de 37 residus comprend un pont disulfure et est ectif contre listeria a des concentrations nanomolaires. Nous avons synthetise la mesentericine y105#3#7 par voie chimique. La bacteriocine synthetique (rigoureusement identique au produit naturel) a ete utilisee pour etudier (i) sa structure tridimensionnelle, (ii) son spectre et son mode d'action et (iii) les motifs moleculaires impliques dans l'activite anti-listeria. La mesentericine y105 adopte une structure en helice alpha probablement au niveau du fragment 17-31. Elle est active contre certaines bacteries lactiques. Son pouvoir antibacterien varie suivant les bacteries cibles. Son mode d'action (bactericide ou bacteriostatique) est dose-dependant. Nous avons egalement montre que l'activite anti-listeria requiert l'integralite de la structure covalente. De plus, le pont disulfure semble stabiliser et/ou faciliter la formation de l'helice. Enfin, nous avons prepare un anticorps anti-peptide specifique de la proteine qui serait impliquee dans la protection de la souche productrice. Il devrait la purification de cette proteine pour l'etude du mecanisme d'immunite
Fast deformation of volume data using tetrahedral mesh rasterization (2013)

Many inherently deformable structures, such as human anatomy, are often represented using a regular volumetric discretization, e.g., in medical imaging. While deformation algorithms employ discretizations that deform themselves along with the material, visualization algorithms are optimized for regular undeformed discretizations. In this paper, we propose a method to transform highresolution volume data embedded in a deformable tetrahedral mesh. We cast volume deformation as a problem of tetrahedral rasterization with 3D texture mapping. Then, the core of our solution to volume data deformation is a very fast algorithm for tetrahedral rasterization. We perform rasterization as a massively parallel operation on target voxels, and we minimize the number of voxels to be handled using a multi-resolution culling approach. Our method allows the deformation of volume data with over 20 million voxels at interactive rates.
Hls Code Transformation Strategies And Directives Exploration For Fpga Accelerated Ecg Analysis (2018)

Electrocardiogram analysis has been established as a key factor for analysing and assessing the health status of a person. The ECG analysis flow is complex, relies on machine learning algorithms such as Support Vector Machines classifier and in an effort to be executed in real-time Hardware acceleration is required. In this paper we focus on utilizing High Level Synthesis capabilities to produce efficient SVM hardware accel- erators, targeting ECG analysis. Our case study is arrhythmia detection using MIT-BIH ECG signal medical database. We show that as a first step, the original code under acceleration can be re-structured in order to create instances which are efficiently transformed into a HW accelerator. As a second step, an exploration is performed on the transformed code in order to determine which HLS directives produce the best outcome in terms of various performance and resources utilization metrics. Our combined analysis shows that we can achieve results of up to 94% execution latency gain compared to the original SVM code and the designer is provided with the infrastructure necessary in order to decide the best trade-off between gains in latency versus increase in utilized FPGA HW resources.
Utilization of Accumulated Log Data of On-Demand Bus Operation (2009)

This paper describes the utilization of log data accumulated from the On-demand Bus Operation. On-Demand Bus is a Demand Responsive Transit service where users are transported by the vehicles after they reserve their seats, and that the vehicles will not move if there is no reservation. Log data is accumulated in the operating server when customers avail of the service. A single record of Log data consists of the passenger’s status (sex/age/address/answers to questionnaire), and On-demand Bus use data (origin/destination/boarding time/reservation time/tool used in reservation). These data can be analyzed from the micro aspect focused on individual data to the macro aspect which deals with the characteristics of the populace. In looking at the micro aspect view, the recommendation service which promotes use of the On-demand Bus and helps passengers with easy reservation is developed. In a larger scale or the macro aspect view, sensing the mobility of the population is proposed.
Microoptodes for Ammonia Sensing in the ppb-Range (2006)

Microoptodes to determine ammonia in the ppb-range by utilization of polymer coatings blended with a fluorescent pH-indicator and a crown ether were developed. They can be applied in gas and in aqueous environments.
Membrane plasticity induced by <i>myo</i>-inositol derived archaeal lipids: chemical synthesis and biophysical characterization (2023)

Archaeal membrane lipids have specific structures that allow Archaea to withstand extreme conditions of temperature and pressure. In order to understand the molecular parameters that govern such resistance, the synthesis of 1,2-di-<i>O</i>-phytanyl-<i>sn-glycero</i>-3-phosphoinositol (DoPhPI), an archaeal lipid derived from <i>myo</i>-inositol, is reported. Benzyl protected <i>myo</i>-inositol was first prepared and then transformed to phosphodiester derivatives using a phosphoramidite based-coupling reaction with archaeol. Aqueous dispersions of DoPhPI alone or mixed with DoPhPC can be extruded and form small unilamellar vesicles, as detected by DLS. Neutron, SAXS, and solid-state NMR demonstrated that the water dispersions could form a lamellar phase at room temperature that then evolves into cubic and hexagonal phases with increasing temperature. Phytanyl chains were also found to impart remarkable and nearly constant dynamics to the bilayer over wide temperature ranges. All these new properties of archaeal lipids are proposed as providers of plasticity and thus means for the archaeal membrane to resist extreme conditions.
Basic study of heat flow in fusion welding. Progress report to the US Department of Energy, October 1, 1980-October 1, 1982 (1981)

Progress is reported in an investigation whose purpose is the development of a fundamental understanding of heat and fluid flow in fusion welding operations and of the role played by heat and fluid flow in determining the mechanical and structural properties of the welds produced. To date, a good quantitative description has been developed of the temperature profiles for electroslag welding systems and an understanding has been derived of factors that determine the size of the heat-affected zone (HAZ). Mathematical models of heat and fluid flow in the weld pool and of the temperature distribution in weldments using a moving heat source were developed. Experiments were performed to determine the effects of welding process parameters on the size and shape of the weld pool and of the HAZ. An unexpected finding was that the size of the HAZ was not markedly dependent on any of the welding process parameters. (LCL)
Sample Complexity of Power System State Estimation using Matrix Completion (2019)

The following topics are dealt with: power engineering computing; smart power grids; power grids; distributed power generation; power system security; optimisation; learning (artificial intelligence); security of data; power generation economics; pricing.
Image Zoom Completion (2016)

We consider the problem of recovering a high-resolution image from a pair consisting of a complete low-resolution image and a high-resolution but incomplete one. We refer to this task as the image zoom completion problem. After discussing possible contexts in which this setting may arise, we introduce a nonlocal regularization strategy, giving full details concerning the numerical optimization of the corresponding energy and discussing its benefits and shortcomings. We also derive two total variation-based algorithms and evaluate the performance of the proposed methods on a set of natural and textured images. We compare the results and get with those obtained with two recent state-of-the-art single-image super-resolution algorithms.
Oxford domed lateral unicompartmental knee arthroplasty (2020)

Domed lateral UKA provides a good alternative to total knee arthroplasty (TKA) in the management of lateral compartment OA. Although dislocation is relatively easy to treat successfully, the dislocation rate of 4% is high. It is recommended that the stability of the bearing is assessed intraoperatively. If the bearing can easily be displaced, the fixed rather than the mobile bearing version of the Oxford lateral tibial component should be inserted instead. Younger age, heavier weight, high activity, and patellofemoral erosions did not detrimentally affect outcome, so should not be considered contraindications. Cite this article: <i>Bone Joint J</i> 2020;102-B(8):1033-1040.
Sensitive detection of transgenic plant marker gene persistence in soil microcosms (1996)

Abstract Genetic engineering offers the opportunity to generate plants with useful new traits conferred by genes originating from a variety of organisms. The objectives of this study were to establish methods for investigating persistence of recombinant plant marker DNA after introduction into soil and to collect data from controlled laboratory test systems. As a model system, we studied the stability of DNA encoding recombinant neomycin phosphotransferase II (rNPT‐II), a neomycin/kanamycin resistance marker, used in plant genetic engineering. The recombinant nature of the target (i.e. fusion of nopaline synthase promoter and NPT‐II coding region) allowed us to design a rNPT‐II‐specific PCR primer pair. DNA preparation and quantitative PCR protocols were established. Effects of temperature and moisture, on DNA persistence in soil were determined in two laboratory test systems. In the first system, purified plasmid DNA was added to soil and incubated under controlled conditions. Up to 0.08% of the rNPT‐II target sequences were detectable after 40 days. In the second system, fresh leaf tissue of transgenic tobacco was ground, added to soil, and incubated under controlled conditions. After 120 days, up to 0.14% of leaf tissue‐derived genomic rNPT‐II sequences were detectable. Under most experimental conditions, leaf tissue‐derived and plasmid DNA were initially degraded at a high rate. A small proportion of the added DNA resisted degradation and was detectable for several months. We hypothesize that this DNA may have been adsorbed to soil particles and was protected from complete degradation.
HIV-1 Vaccine Trials: Evolving Concepts and Designs (2012)

An effective prophylactic HIV-1 vaccine is needed to eradicate the HIV/AIDS pandemic but designing such a vaccine is a challenge. Despite many advances in vaccine technology and approaches to generate both humoral and cellular immune responses, major phase-II and -III vaccine trials against HIV/AIDS have resulted in only moderate successes. The modest achievement of the phase-III RV144 prime-boost trial in Thailand re-emphasized the importance of generating robust humoral and cellular responses against HIV. While antibody-directed approaches are being pursued by some groups, others are attempting to develop vaccines targeting cell-mediated immunity, since evidence show CTLs to be important for the control of HIV replication. Phase-I and -IIa multi-epitope vaccine trials have already been conducted with vaccine immunogens consisting of known CTL epitopes conserved across HIV subtypes, but have so far fallen short of inducing robust and consistent anti-HIV CTL responses. The concepts leading to the development of T-cell epitope-based vaccines, the outcomes of related clinical vaccine trials and efforts to enhance the immunogenicity of cell-mediated approaches are summarized in this review. Moreover, we describe a novel approach based on the identification of SIV and FIV antigens which contain conserved HIV-specific T-cell epitopes and represent an alternative method for developing an effective HIV vaccine against global HIV isolates.
Prediction of myocardial infarction versus cardiac death by gated myocardial perfusion SPECT: risk stratification by the amount of stress-induced ischemia and the poststress ejection fraction. (2001)

Poststress EF is the best predictor of CD, whereas the amount of ischemia is the best predictor of nonfatal MI. Integration of perfusion and function data improves stratification of patients into low, intermediate, and high risk of CD.
Role of Peptide Backbone in T Cell Recognition (1999)

T cells recognize self and nonself peptides presented by molecules of the MHC. Amino acid substitutions in the antigenic peptide showed that T cell specificity is highly degenerate. Recently, determination of the crystal structure of several TCR/MHC-peptide complexes suggested that the peptide backbone may significantly contribute to the interaction with the TCR. To directly investigate the role of the peptide backbone in T cell recognition, we performed a methylene-amino scan on the backbone of an antigenic peptide and measured the capacity of such pseudopeptides to bind their cognate MHC molecule, to sensitize target cells for T cell lysis, and to stimulate IL-2 secretion by two T cell hybridomas. For one of these pseudopeptides, we prepared fluorescent tetramers of MHC molecules and compared the staining of two T cell hybridomas. Our results demonstrate that the peptide backbone has an important contribution to TCR binding and suggest that some interactions between the peptide backbone and the TCR may be partially conserved. We discuss this finding in the perspective of TCR plasticity and T cell function.
Augmenting Cybersecurity in Autonomous Vehicles: Innovative Recommendations for Aspiring Entrepreneurs (2020)

Autonomous and connected vehicles are a collection of smart components such as sensors, Radar/Lidar, Electronic Control Units (ECUs), and cameras programmed through voluminous lines of codes, which enable a seamless communication system between the user, vehicle, and infrastructure. The concept of autonomous vehicles is gaining significant traction in the global markets, generating higher revenues, and witnessing high market penetration, thus attracting entrepreneurs to make new and disruptive innovations. However, the underlying technology and communication system of autonomous and connected vehicles are prone to the cybersecurity threats, which circumvent any product that uses sensors, transmits data over the network, and can be controlled through a remote computer or a mobile application. In this article, we attempt to outline the concerns that an aspiring entrepreneur should be aware of before entering into the autonomous vehicle industry, followed by innovative recommendations that can guide addressing the article's issues. The presented recommendations and guidelines are based on the cybersecurity principles of confidentiality, integrity, and availability.
Chemical clustering and visualization applied to macromolecular crystallography (2014)

Many bioscience fields employ high-throughput methods to screen multiple biochemical conditions. The analysis of these becomes tedious without a degree of automation. Crystallization, a rate limiting step in biological X-ray crystallography, is one of these fields. Screening of multiple potential crystallization conditions (cocktails) is the most effective method of probing a proteins phase diagram and guiding crystallization but the interpretation of results can be consuming. To aid this empirical approach a cocktail distance coefficient was developed to quantitatively compare macromolecule crystallization conditions and outcome. These coefficients were evaluated against an existing similarity metric developed for crystallization, the C6 metric, using both virtual crystallization screens and by comparison of two related 1,536-cocktail high-throughput crystallization screens. Hierarchical clustering was employed to visualize one of these screens and the crystallization results from an exopolyphosphatase-related protein from Bacteroides fragilis, (BfR192) overlaid on this clustering. This demonstrated a strong correlation between certain chemically related clusters and crystal lead conditions. While this analysis was not used to guide the initial crystallization optimization, it led to the re-evaluation of unexplained peaks in the electron density map of the protein and the insertion and correct placement of a sodium, potassium and phosphate atoms in the structure. With these in place, the resulting structure of the putative active site demonstrated features consistent with active sites of other phosphatases which are involved in binding the phosphoryl moieties of nucleotide triphosphates. The new distance coefficient appears to be robust in this application and coupled with hierarchical clustering and the overlay of crystallization outcome reveals information of biological relevance. While tested with a single example the potential applications appear promising.