gebhart/patrepeval huggingface dataset:
Earliest enamel deposits of the rat incisor examined by electron microscopy, electron diffraction, and electron probe microanalysis (1988)

In order to describe initial events in enamel mineralization and to help characterize inorganic-organic interactions in this tissue, the earliest rod and interrod enamel in mandibular incisors from normal young adult (100 gm) rats, perfused with 100% ethylene glycol, has been studied by transmission electron microscopy, selected area electron diffraction, and high-spatial-resolution electron probe microanalysis. Diffraction and probe data were correlated precisely from the same extracellular regions of the tissue. Sites were examined progressively as a function of location a) from the most recently deposited enamel adjacent to ameloblasts toward the dentin-enamel junction and b) from the apical portion of the tooth longitudinally toward its incisal end. Electron diffraction patterns consistent with that of a poorly crystalline hydroxyapatite were generated at all locations. Diffraction characteristics changed only slightly toward that of more crystalline hydroxyapatite at different locations. Earliest apical enamel generated molar Ca/P ratios in a range of 0.99-1.46 (average 1.24 +/- 0.15). Molar Ca/P ratios of the first enamel interrod elements increased from approximately 1.24 at ameloblast-enamel boundaries to approximately 1.40 at the dentin-enamel junction, small changes corresponding to those observed in electron diffraction characteristics.
Analyzing Dynamic Probabilistic Risk Assessment Data through Topology-Based Clustering (2013)

We investigate the use of a topology-based clustering technique on the data generated by dynamic event tree methodologies. The clustering technique we utilizes focuses on a domain-partitioning algorithm based on topological structures known as the Morse-Smale complex, which partitions the data points into clusters based on their uniform gradient flow behavior. We perform both end state analysis and transient analysis to classify the set of nuclear scenarios. We demonstrate our methodology on a dataset generated for a sodium-cooled fast reactor during an aircraft crash scenario. The simulation tracks the temperature of the reactor as well as the time for a recovery team to fix the passive cooling system. Combined with clustering results obtained previously through mean shift methodology, we present the user with complementary views of the data that help illuminate key features that may be otherwise hidden using a single methodology. By clustering the data, the number of relevant test cases to be selected for further analysis can be drastically reduced by selecting a representative from each cluster. Identifying the similarities of simulations within a cluster can also aid in the drawing of important conclusions with respect to safety analysis.
Segmentation Methods of Echocardiography Images for Left Ventricle Boundary Detection (2015)

Due to acoustic interferences and artifacts which are inherent in echocardiography images, automatic segmentation of anatomical structures in cardiac ultrasound images is a real challenge. This paper surveys state-of-the-art researches on echocardiography data segmentation methods, concentrating on methods techniques developed for clinical data. We present a classification of methodologies for echocardiography image segmentation. By choosing ten recent papers which have proposed innovative ideas that they proved certain clinical advantages or potential especial role to the echocardiography segmentation task. The contribution of the paper would be serving as a tutorial of the field for both clinicians and technologists, providing large number of segmentation techniques in a comprehensive and systematic manner and critically review recent approaches in terms of their performance and degree of clinical evaluation with respect to the final goal of cardiac functional analysis.
Surface pressure‐induced isothermal 2D‐ to 3D‐transitions in Langmuir films of poly(<i>ε</i>‐caprolactone)s and oligo(<i>ε</i>‐caprolactone) based polyesterurethanes (2015)

Surface pressure‐induced isothermal 2D‐ to 3D‐transitions in Langmuir films of biodegradable poly( ε ‐caprolactone) (PCL) and oligo( ε ‐caprolactone) based polyester‐urethanes P(OCL‐U)s are investigated in order to gain deeper insights into the influence of the linker species on the crystallization and aggregation behavior of macromolecules in a biomimetic aqueous environment. The presence of three urethane linkers derived from 2, 2 (4), 4‐trimethyl‐hexamethylene‐diisocyanate (TMDI), hexamethylene diisocyanate (HDI) and lysine ethylester diisocyanate (LDI) induces remarkable changes in the mesoscopic structure compared to PCL Langmuir films. The pronounced changes in the morphology of the 3D structures co‐existing with the Langmuir film above a collapse surface pressure are visualized by Brewster angle microscopy (BAM). Hysteresis of the compression–expansion isotherm in the surface pressure range of the 2D‐ to 3D‐transition indicates the influence of the urethane linkers on the diffusion‐limited kinetics and on the reversibility of this phase transition. Copyright © 2015 John Wiley &amp; Sons, Ltd.
Potential Application of Induced Pluripotent Stem Cells in Cell Replacement Therapy for Parkinsons Disease (2011)

Parkinson's disease (PD), a common degenerative disease in humans, is known to result from loss of dopamine neurons in the substantia nigra and is characterized by severe motor symptoms of tremor, rigidity, bradykinsia and postural instability. Although levodopa administration, surgical neural lesion, and deep brain stimulation have been shown to be effective in improving parkinsonian symptoms, cell replacement therapy such as transplantation of dopamine neurons or neural stem cells has shed new light on an alternative treatment strategy for PD. While the difficulty in securing donor dopamine neurons and the immuno-rejection of neural transplants largely hinder application of neural transplants in clinical treatment, induced pluripotent stem cells (iPS cells) derived from somatic cells may represent a powerful tool for studying the pathogenesis of PD and provide a source for replacement therapies in this neurodegenerative disease. Yamanaka et al. [2006, 2007] first succeeded in generating iPS cells by reprogramming fibroblasts with four transcription factors, Oct4, Sox2, Klf4, and c-Myc in both mouse and human. Animal studies have further shown that iPS cells from fibroblasts could be induced into dopamine neurons and transplantation of these cells within the central nervous system improved motor symptoms in the 6-OHDA model of PD. More interestingly, neural stem cells or fibroblasts from patients can be efficiently reprogrammed and subsequently differentiated into dopamine neurons. Derivation of patient-specific iPS cells and subsequent differentiation into dopamine neurons would provide a disease-specific in vitro model for disease pathology, drug screening and personalized stem cell therapy for PD. This review summarizes current methods and modifications in producing iPS cells from somatic cells as well as safety concerns of reprogramming procedures. Novel reprogramming strategies that deter abnormal permanent genetic and epigenetic alterations are essential for propagating clinically-qualified iPS cells. Future investigations into cell transforming and reprogramming processes are needed to generate the disease-specific iPS cells for personalized regeneration medicine of PD patients by disclosing detailed reprogramming mechanisms.
Primary Hip Arthroplasty Costs Are Greater in Low-volume Than in High-volume Canadian Hospitals (2005)

Despite the widespread success of total hip arthroplasties for treatment of arthritis of the hip, the procedure continues to be targeted for cost control. Our objective was to compare the total in-hospital cost of primary total hip arthroplasties in high-volume and low-volume hospitals. Data concerning the patient-level in-hospital costs of 940 consecutive primary total hip arthroplasties were extracted from the cost accounting system of three Canadian hospitals. Mean in-hospital costs for patients having total hip arthroplasties in a high-volume institution (> or = 300 total hip arthroplasties/year) compared with two low-volume Canadian institutions (< 300 total hip arthroplasties/year) were: overhead costs 1380 US dollars +/- 35 US dollars versus 2432 US dollars +/- 49 US dollars; direct costs 3023 US dollars +/- 93 US dollars versus 4952 US dollars +/- 91 US dollars and total costs 4403 US dollars +/- 117 US dollars versus 7385 US dollars +/- 1 US dollar 38, respectively (all comparisons in US dollars). Lower overhead and direct and total costs were found for primary total hip arthroplasties done in a high-volume Canadian hospital compared with the low-volume centers. Differences in direct costs, made up in large part by the implant cost, accounted for most of the disparity. As total hip arthroplasties continue to be scrutinized for cost containment, doing the procedure in a high-volume center seems to be an effective method of controlling costs.
A Novel VLSI Divide and Conquer Array Architecture for Vector-Scalar Multiplication (2007)

A novel VLSI array architecture for vector-scalar multiplication is introduced. It is based on a parameterized divide and conquer algorithm that uses optimal partitioning and redundancy removal for simultaneous computation of partial sums. Two variations of the proposed Parameterized Vector-Scalar Multiplier Architecture (PVSMA), namely PVSMA-A and PVSMA-AT, are implemented and compared to the parallel implementation with carry-save array multipliers. PVSMA-A is optimized for area (A), and is shown to achieve significant area (A) savings at the cost of increased operational delay (T). PVSMA-AT is optimized for area-time product (AT), and is shown to achieve significant area-time product (AT) savings and a smaller operational delay (T) at the cost of smaller area (A) savings.
Calibration laws based on multiple linear regression applied to matrix‐assisted laser desorption/ionization Fourier transform ion cyclotron resonance mass spectrometry (2008)

Operation of any mass spectrometer requires implementation of mass calibration laws to translate experimentally measured physical quantities into a m/z range. While internal calibration in Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS) offers several attractive features, including exposure of calibrant and analyte ions to identical experimental conditions (e.g. space charge), external calibration affords simpler pulse sequences and higher throughput. The automatic gain control method used in hybrid linear trap quadrupole (LTQ) FT-ICR-MS to consistently obtain the same ion population is not readily amenable to matrix-assisted laser desorption/ionization (MALDI) FT-ICR-MS, due to the heterogeneous nature and poor spot-to-spot reproducibility of MALDI. This can be compensated for by taking external calibration laws into account that consider magnetic and electric fields, as well as relative and total ion abundances. Herein, an evaluation of external mass calibration laws applied to MALDI-FT-ICR-MS is performed to achieve higher mass measurement accuracy (MMA).
Myopia Outcome Study of Atropine in Children (MOSAIC): an investigator-led, double-masked, placebo-controlled, randomised clinical trial protocol [version 1; peer review: 2 approved, 1 approved with reservations] (2019)

Background: The Myopia Outcome Study of Atropine in Children (MOSAIC) aims to explore the efficacy, safety, acceptability and mechanisms of action of 0.01% unpreserved atropine for myopia control in a European population. Methods: MOSAIC is an investigator-led, double-masked, placebo-controlled, randomised clinical trial (RCT) investigating the efficacy, safety and mechanisms of action of 0.01% atropine for managing progression of myopia. During Phase 1 of the trial, 250 children aged 6-16 years with progressive myopia instil eye drops once nightly in both eyes from randomisation to month 24. From month 24 to 36 participants are re-randomised in Phase 2 of the trial, into continued 0.01% atropine, and washout, at 1:1 ratio for those participants initially randomised to the intervention arm (n=167), during which any potential rebound effects on cessation of treatment will be monitored. All participants initially assigned to the placebo (n=83) crossover to the intervention arm of the study for Phase 2, and from month 24 to 36, instil 0.01% atropine eye drops in both eyes once nightly. Further treatment and monitoring beyond 36 months is planned (Phase 3) and will be designed dependent on the outcomes of Phase 1. Results: The primary outcome measure is cycloplegic spherical equivalent refractive error progression at 24 months. Secondary outcome measures include axial length change as well as the rebound, safety and acceptability profile of 0.01% atropine. Additional analyses will include the mechanisms of action of 0.01% atropine for myopia control. Conclusions: The generalisability of results from previous clinical trials investigating atropine for myopia control is limited by the predominantly Asian ethnicity of previous study populations. MOSAIC is the first RCT to explore the efficacy, safety and mechanisms of action of unpreserved 0.01% atropine in a predominantly White population.
Tactical Study of Care Originating in the Prehospital Environment (Tacscope) (2016)

ATC is substantially associated with greater injury severity, MT, and mortality. Prehospital identification of MT casualties may expedite triage and evacuation, and enable remote damage control resuscitation to delay ATC onset and improve outcomes.
Discovery of 5-Phenyl-<i>N</i>-(pyridin-2-ylmethyl)-2-(pyrimidin-5-yl)quinazolin-4-amine as a Potent<i>I</i><sub>Kur</sub>Inhibitor (2016)

A new series of phenylquinazoline inhibitors of Kv 1.5 is disclosed. The series was optimized for Kv 1.5 potency, selectivity versus hERG, pharmacokinetic exposure, and pharmacodynamic potency. 5-Phenyl-N-(pyridin-2-ylmethyl)-2-(pyrimidin-5-yl)quinazolin-4-amine (13k) was identified as a potent and ion channel selective inhibitor with robust efficacy in the preclinical rat ventricular effective refractory period (VERP) model and the rabbit atrial effective refractory period (AERP) model.
Synthesis, Characterization, and Plasma Lipoprotein Association of a Nucleus-Targeted Boronated Porphyrin (2004)

The efficacy of binary cancer therapies such as BNCT and PDT depends critically on the subcellular localization site of the sensitizer. This work presents the synthesis and plasma lipoprotein binding properties of the first reported binary conjugate of a boronated porphyrin with a peptide nuclear localization sequence. The porphyrin-NLS conjugate associates in vitro predominantly with low density lipoproteins. Such association provides a potentially selective entry pathway into malignant cells that overexpress the LDL receptor.
Energy-efficient Traffic Allocation in SDN-based Backhaul Networks: Theory and Implementation (2016)

5G networks are expected to be highly energy efficient, with a 10 times lower consumption than today's systems. An effective way to achieve such a goal is to act on the backhaul network by controlling the nodes operational state and the allocation of traffic flows. To this end, in this paper we formulate energy-efficient flow routing on the backhaul network as an optimization problem. In light of its complexity, which impairs the solution in large-scale scenarios, we then propose a heuristic approach. Our scheme, named EMMA, aims to both turn off idle nodes and concentrate traffic on the smallest possible set of links, which in its turn increases the number of idle nodes. We implement EMMA on top of ONOS and derive experimental results by emulating the network through Mininet. Our results show that EMMA provides excellent energy saving performance, which closely approaches the optimum. In larger network scenarios, the gain in energy consumption that EMMA provides with respect to the simple benchmark where all nodes are active, is extremely high, reaching almost 1 under medium-low traffic load.
Optimization of User Selection and Bandwidth Allocation for Federated Learning in VLC/RF Systems (2021)

Limited radio frequency (RF) resources restrict the number of users that can participate in federated learning (FL) thus affecting FL convergence speed and performance. In this paper, we first introduce visible light communication (VLC) as a supplement to RF in FL and build a hybrid VLC/RF communication system, in which each indoor user can use both VLC and RF to transmit its FL model parameters. Then, the problem of user selection and bandwidth allocation is studied for FL implemented over a hybrid VLC/RF system aiming to optimize the FL performance. The problem is first separated into two subproblems. The first subproblem is a user selection problem with a given bandwidth allocation, which is solved by a traversal algorithm. The second subproblem is a bandwidth allocation problem with a given user selection, which is solved by a numerical method. The final user selection and bandwidth allocation are obtained by iteratively solving these two subproblems. Simulation results show that the proposed FL algorithm that efficiently uses VLC and RF for FL model transmission can improve the prediction accuracy by up to 10% compared with a conventional FL system using only RF.
Distribution of magnesium in coral skeleton (2004)

Ion micro‐probe imaging of the aragonite skeleton of Pavona clavus , a massive reef‐building coral, shows that magnesium and strontium are distributed very differently. In contrast to strontium, the distribution of magnesium is strongly correlated with the fine‐scale structure of the skeleton and corresponds to the layered organization of aragonite fibers surrounding the centers of calcification, which have up to ten times higher magnesium concentration. This indicates a strong biological control over the magnesium composition of all structural components within the skeleton. Magnesium may be used by the coral to actively control the growth of the different skeletal crystal components.
Development of a novel multiplexed optoelectronic nose for analysis of volatile organic compounds (2017)

International audience
Three-Dimensional Numerical Simulations of Circular Cylinders Undergoing Two Degree-of-Freedom Vortex-Induced Vibrations (2006)

In an effort to gain a better understanding of the VIV phenomena, we present three-dimensional numerical simulations of VIV of circular cylinders. We consider operating conditions that correspond to high Reynolds number flow, low structural damping, and allow for two-degree of freedom motion. The numerical implementation makes use of overset (Chimera) grids, in a multiple block environment where the workload associated with the blocks is distributed among multiple processors working in parallel. The three-dimensional grids around the cylinder are allowed to undergo arbitrary motions with respect to fixed background grids, eliminating the need for tedious grid regeneration at every time step.
Yield estimation in vineyards by visual grape detection (2011)

The harvest yield in vineyards can vary significantly from year to year and also spatially within plots due to variations in climate, soil conditions and pests. Fine grained knowledge of crop yields can allow viticulturists to better manage their vineyards. The current industry practice for yield prediction is destructive, expensive and spatially sparse - during the growing season sparse samples are taken and extrapolated to determine overall yield. We present an automated method that uses computer vision to detect and count grape berries. The method could potentially be deployed across large vineyards taking measurements at every vine in a non-destructive manner. Our berry detection uses both shape and visual texture and we can demonstrate detection of green berries against a green leaf background. Berry detections are counted and the eventual harvest yield is predicted. Results are presented for 224 vines (over 450 meters) of two different grape varieties and compared against the actual harvest yield as groundtruth. We calibrate our berry count to yield and find that we can predict yield of individual vineyard rows to within 9.8% of actual crop weight.
Visualization of Transient Protein-Protein Interactions that Promote or Inhibit Amyloid Assembly (2014)

In the early stages of amyloid formation, heterogeneous populations of oligomeric species are generated, the affinity, specificity, and nature of which may promote, inhibit, or define the course of assembly. Despite the importance of the intermolecular interactions that initiate amyloid assembly, our understanding of these events remains poor. Here, using amyloidogenic and nonamyloidogenic variants of β2-microglobulin, we identify the interactions that inhibit or promote fibril formation in atomic detail. The results reveal that different outcomes of assembly result from biomolecular interactions involving similar surfaces. Specifically, inhibition occurs via rigid body docking of monomers in a head-to-head orientation to form kinetically trapped dimers. By contrast, the promotion of fibrillation involves relatively weak protein association in a similar orientation, which results in conformational changes in the initially nonfibrillogenic partner. The results highlight the complexity of interactions early in amyloid assembly and reveal atomic-level information about species barriers in amyloid formation.
Hydrogen Sulfide in Pharmacotherapy, Beyond the Hydrogen Sulfide-Donors (2020)

Hydrogen sulfide (H<sub>2</sub>S) is one of the important biological mediators involved in physiological and pathological processes in mammals. Recently developed H<sub>2</sub>S donors show promising effects against several pathological processes in preclinical and early clinical studies. For example, H<sub>2</sub>S donors have been found to be effective in the prevention of gastrointestinal ulcers during anti-inflammatory treatment. Notably, there are well-established medicines used for the treatment of a variety of diseases, whose chemical structure contains sulfur moieties and may release H<sub>2</sub>S. Hence, the therapeutic effect of these drugs may be partly the result of the release of H<sub>2</sub>S occurring during drug metabolism and/or the effect of these drugs on the production of endogenous hydrogen sulfide. In this work, we review data regarding sulfur drugs commonly used in clinical practice that can support the hypothesis about H<sub>2</sub>S-dependent pharmacotherapeutic effects of these drugs.