gebhart/patrepeval huggingface dataset:
Characterization of a Salmon Insulin-Like Growth Factor I Promoter (1994)

We have identified four transcription initiation sites in the salmon insulin-like growth factor I (IGF-I) gene. Use of the most upstream transcription start site generates a minor mRNA species with a 5' untranslated region (UTR) of approximately 450-550 nucleotides, whereas transcription starting at the downstream initiation sites results in more abundant IGF-I mRNAs with 5'-UTRs approximately 250, 245, and 165 nucleotides in length. No consensus TATA box-like elements are present immediately upstream of the most upstream start site identified, nor is this region particularly GC-rich. Transient expression assays, however, demonstrated orientation-dependent promoter activity in a 386-nucleotide-long fragment containing the major downstream transcription start sites. Additionally, reverse transcriptase polymerase chain reaction (RT-PCR) analyses demonstrated tissue and developmental stage-specific use of the various transcription start sites identified.
Design of New Drugs for the Treatment of Alzheimer's Disease Based on Tacrine Structure (2013)

Tacrine was the first drug approved by FDA for the treatment of Alzheimer's disease. However, its use was restricted in function of side effects observed in some patients. Investigations on the structural basis by which tacrine inhibits cholinesterases activity brought new perspectives for the design of more potent analogs with fewer side effects. This review discusses the recent advances on the development of tacrine-structure-based compounds capable to target multiple molecules involved in Alzheimer's disease. Detailed information on strategies of molecular modifications commonly used in medicinal chemistry, such as bioisosterism, hybridization, dimerization and simplification is presented as well.
The Survey of Sorption Ion-Exchange Properties of Paleozoic Natural Minerals in the Static Conditions (2017)

An experimental and exploring process' results of iron's ion, manganese and ammonium sodium extraction from aqueous solution by some Ural's natural minerals in a static regime at certain physicochemical conditions: by the zeolite, montmorillonite and vermiculite in the static conditions. Values of maximum sorption capacity are estimated on a gram of natural sorbents for the present conditions. Comparison of the survey's results shows that effective sorptions from exploring natural minerals can be used as a clinoptilolite and zeolite-mineral montmorillonite type.
Bloom and Billet Mill expert system (1995)

A real-time expert system has recently been installed at British Steel Sections, Plates and Commercial Steels, Scunthorpe Works. The system is at the bloom and billet mill and has been designed to allow engineers to add and modify rules through a generic graphical rule editor. The mill has 26 soaking pits which reheat the steel prior to rolling. The expert system covers the soaking pits and the gas mixing station. It currently diagnoses operational problems with the soaking pits and generates messages which are displayed to the process operator via an existing message screen. Combustion and heat balance information is also calculated by the system for each pit every five minutes. Prior to installing the expert system, the calculations were performed manually for individual pits on an irregular basis. The on-line calculations are to be used to derive new diagnostic rules and provide supporting evidence to existing rules. (2 pages)
Is there a need for human engineering in ATO? Some case studies in transport domain (2016)

International audience
Reinforcement Learning of Musculoskeletal Control from Functional\n Simulations (2020)

To diagnose, plan, and treat musculoskeletal pathologies, understanding and\nreproducing muscle recruitment for complex movements is essential. With muscle\nactivations for movements often being highly redundant, nonlinear, and time\ndependent, machine learning can provide a solution for their modeling and\ncontrol for anatomy-specific musculoskeletal simulations. Sophisticated\nbiomechanical simulations often require specialized computational environments,\nbeing numerically complex and slow, hindering their integration with typical\ndeep learning frameworks. In this work, a deep reinforcement learning (DRL)\nbased inverse dynamics controller is trained to control muscle activations of a\nbiomechanical model of the human shoulder. In a generalizable end-to-end\nfashion, muscle activations are learned given current and desired\nposition-velocity pairs. A customized reward functions for trajectory control\nis introduced, enabling straightforward extension to additional muscles and\nhigher degrees of freedom. Using the biomechanical model, multiple episodes are\nsimulated on a cluster simultaneously using the evolving neural models of the\nDRL being trained. Results are presented for a single-axis motion control of\nshoulder abduction for the task of following randomly generated angular\ntrajectories.\n
Plasminogen Activation System (2006)

Abstract The plasminogen activation system is a vertebrate extracellular enzyme system consisting of serine proteases, protease inhibitors of the serpin family and various binding proteins. The plasminogen activation system generates extracellular proteolytic activity for physiological and pathophysiological fibrinolysis and tissue remodelling.
(Invited) Silicon Nanostructures: A Versatile Material for Photonics (2016)

Silicon is the most common semiconductor in technology. Its main limit is the lacking of efficient light emission properties. Here quantum effects are exploited to fabricate optically active silicon photonics elements. The manuscript reports recent results obtained in different research fields spanning from bio- to integrated-photonics and nonlinear optics.
Space Station Data Systems development (1984)

The content and status of the evolving Space Station Data System (SSDS) development program are presented. High level system requirements and schedules are reviewed, and the challenges of SSDS development are discussed. Present content of the program consists of three major activities: (1) two contracted parallel Space Station Data System architecture studies; (2) the space station phase B definition studies to be awarded in early 1985; and (3) a test bed project for the evaluation and proof-of-concept of data systems technology for space station applications and for the advanced development of long-lead hardware and software for the initial and growth space station configurations. An overview of the present SSDS concept is provided, and the roles of NASA centers in this activity are summarized.
A single cell transcriptional atlas of early synovial joint development (2019)

SUMMARY Synovial joint development begins with the formation of the interzone, a region of condensed mesenchymal cells at the site of the prospective joint. Recently, lineage tracing strategies have revealed that Gdf5-lineage cells native to and from outside the interzone contribute to most, if not all, of the major joint components. However, there is limited knowledge of the specific transcriptional and signaling programs that regulate interzone formation and fate diversification of synovial joint constituents. To address this, we have performed single cell RNA-Seq analysis of 6,202 synovial joint progenitor cells from the developing murine knee joint from E12.5 to E15.5. By using a combination of computational analytics, in situ hybridization, and functional analysis of prospectively isolated populations, we have inferred the underlying transcriptional networks of the major developmental paths for joint progenitors. Our freely available single cell transcriptional atlas will serve as a resource for the community to uncover transcriptional programs and cell interactions that regulate synovial joint development.
Experimental response of framed masonry structures designed with new reinforcing details (2005)

This paper describes an experimental programme in which two one-storey single-bay specimens were tested under cyclic lateral loading. The first specimen was designed according to the normal practice for framed masonry structures, whereas new reinforcing details were provided in the second specimen, with the objective of enhancing the structural response. Special precautions were taken for the application of the lateral forces, considering that experimental and analytical results indicated that the loading system could markedly affect the structural response. Consequently, an adequate procedure should be adopted for laboratory tests in order to obtain realistic data. The most important conclusion of the experimental programme was that the response of reinforced concrete frames with masonry infills can be significantly improved by a rational design aimed at reducing the distortion of the masonry panels while the plastic deformations are concentrated in selected regions of the structure.
Gene expression profile of mouse prostate tumors reveals dysregulations in major biological processes and identifies potential murine targets for preclinical development of human prostate cancer therapy (2008)

We report a TRAMP microarray dataset of which a gene subset was validated by QRT-PCR with expression patterns consistent with previous gene-specific TRAMP studies. Concordance analysis between TRAMP and human PCa associated genes supports the utility of the model and suggests several novel molecular targets for preclinical therapy.
Supplementary Figure 7 from Homing of Human B Cells to Lymphoid Organs and B-Cell Lymphoma Engraftment Are Controlled by Cell Adhesion Molecule JAM-C (2023)

&lt;p&gt;PDF file - 3369K, JAM-B is expressed on BM endothelial cells of NOD/SCID mice&lt;/p&gt;
DisplaceNet: Recognising Displaced People from Images by Exploiting\n Dominance Level (2019)

Every year millions of men, women and children are forced to leave their\nhomes and seek refuge from wars, human rights violations, persecution, and\nnatural disasters. The number of forcibly displaced people came at a record\nrate of 44,400 every day throughout 2017, raising the cumulative total to 68.5\nmillion at the years end, overtaken the total population of the United Kingdom.\nUp to 85% of the forcibly displaced find refuge in low- and middle-income\ncountries, calling for increased humanitarian assistance worldwide. To reduce\nthe amount of manual labour required for human-rights-related image analysis,\nwe introduce DisplaceNet, a novel model which infers potential displaced people\nfrom images by integrating the control level of the situation and conventional\nconvolutional neural network (CNN) classifier into one framework for image\nclassification. Experimental results show that DisplaceNet achieves up to 4%\ncoverage-the proportion of a data set for which a classifier is able to produce\na prediction-gain over the sole use of a CNN classifier. Our dataset, codes and\ntrained models will be available online at\nhttps://github.com/GKalliatakis/DisplaceNet.\n
Characteristic evaluation of the flowmeter using the Wells turbine for measurement of respiration (2003)

A new turbine flowmeter for measurement of respiration using a bi-directional air turbine, the Wells turbine, which is suitable for wave energy conversion is proposed. Characteristics of the turbine flowmeter have been experimentally evaluated using a test equipment simulating respiration. From the results the following conclusions were obtained: Using this turbine flowmeter, the measurement of the period and the respiratory rate of respiration is possible The possibility of univocally obtaining a flow rate of an unsteady flow from the value of an angular velocity and acceleration of the turbine's rotation was shown by using the characteristic curve made beforehand.
Synthesis and Solution Properties of Double Hydrophilic Poly(ethylene oxide)-block-poly(2-ethyl-2-oxazoline) (PEO-b-PEtOx) Star Block Copolymers (2013)

We demonstrate the synthesis of star-shaped poly(ethylene oxide)-block-poly(2-ethyl-2-oxazoline) [PEOm-b-PEtOxn]x block copolymers with eight arms using two different approaches, either the “arm-first” or the “core-first” strategy. Different lengths of the outer PEtOx blocks ranging from 16 to 75 repeating units were used, and the obtained materials [PEO28-b-PEtOxx]8 were characterized via size exclusion chromatography (SEC), nuclear magnetic resonance spectroscopy (NMR), and Fourier-transform infrared spectroscopy (FT-IR) measurements. First investigations regarding the solution behavior in water as a non-selective solvent revealed significant differences. Whereas materials synthesized via the “core-first” method seemed to be well soluble (unimers), aggregation occurred in the case of materials synthesized by the “arm-first” method using copper-catalyzed azide-alkyne click chemistry.
Particulates and the Airways: Basic Biological Mechanisms of Pulmonary Pathogenicity (1998)

Abstract With strong evidence that materials such as silica and asbestos are associated with irreversible lung disease, efforts have been made to identify abrasive substitute materials for silica and produce various synthetic vitreous fibers as substitutes for asbestos. With the introduction of new materials, questions concerning potential health effects are raised. A clear understanding of the mechanisms by which certain inhaled particles induce lung damage and subsequent disease is vital to the ability to predict the relative safety of new materials, as well as, to provide appropriate measures for the safe use of old materials currently grouped together as particulates not otherwise classified/regulated. The following is a brief review of mechanisms currently thought to be important in the development and progression of particle-induced lung disease.
An overview of aerosol particle sensors for size distribution measurement (2007)

Fine aerosols are generally referred to airborne particles of diameter in submicron or nanometer size range. Measurement capabilities are required to gain understanding of these particle dynamics. One of the most important physical and chemical parameters is the particle size distribution. The aim of this article is to give an overview of recent development of already existing sensors for particle size distribution measurement based on electrical mobility determination. Available instruments for particle size measurement include a scanning mobility particle sizer (SMPS), an electrical aerosol spectrometer (EAS), an engine exhaust particle sizer (EEPS), a bipolar charge aerosol classifier (BCAC), a fast aerosol spectrometer (FAS) a differential mobility spectrometer (DMS), and a CMU electrical mobility spectrometer (EMS). The operating principles, as well as detailed physical characteristics of these instruments and their main components consisting of a particle charger, a mobility classifier, and a signal detector, are described. Typical measurements of aerosol from various sources by these instruments compared with an electrical low pressure impactor (ELPI) are also presented.
Sol-Gel Applications in Textile Finishing Processes (2017)

In the chapter, sol‐gel applications in textile finishing process such as flame retardancy, water, oil repellency, ultraviolet (UV) protection, self‐cleaning, and antibacterial and antiwrinkle processes are reviewed. Sol‐gel technology is well known in materials, metallurgy, ceramic, and glass industry since 1960 and has been researched in textile industry in the last decade. Sol‐gel technology has some advantages when compared to conventional textile finishing process. Sol‐gel technology, which is a method applied to the inorganic metal alkoxide or metal salts to organic textile materials, could impart the high, durable activity and multifunctional properties to different textile materials in the same bath at one step using low concentration of precursors. In addition, sol‐gel technology presents alternatively economical, ecological, and environmental friendly process due to one‐step application, using low concentration of chemicals, nonhalogenated chemicals, and nonformaldehyde release when compared to conventional processes.
Matrix metalloproteinase-8 deficiency increases joint inflammation and bone erosion in the K/BxN serum-transfer arthritis model (2010)

Lack of Mmp-8 is accompanied by exacerbated synovial inflammation and bone erosion in the K/BxN serum-transfer arthritis model, indicating that this Mmp has a protective role in arthritis.
Modélisation et diagnostic de la machine asynchrone à cage en présence de défauts. Synthèse de plusieurs méthodes (2005)

International audience
Cover Picture: Plasma Process. Polym. 9∕2016 (2016)

Front Cover: The time-dependent contact angle drop during plasma afterglow activation of polymers can be described by exponential decay processes. Fitted parameters enable the comparison of different discharge configurations and therefore allow adjusting treatment conditions to process requirements. Further on, they facilitate to study the influence of experimental settings on activation process. Further details can be found in the article by G. Oberbossel et al. on page 937.
Alterations in homologous recombination repair genes in prostate cancer brain metastases (2022)

Abstract Improved survival rates for prostate cancer through more effective therapies have also led to an increase in the diagnosis of metastases to infrequent locations such as the brain. Here we investigate the repertoire of somatic genetic alterations present in brain metastases from 51 patients with prostate cancer brain metastases (PCBM). We highlight the clonal evolution occurring in PCBM and demonstrate an increased mutational burden, concomitant with an enrichment of the homologous recombination deficiency mutational signature in PCBM compared to non-brain metastases. Focusing on known pathogenic alterations within homologous recombination repair genes, we find 10 patients (19.6%) fulfilling the inclusion criteria used in the PROfound clinical trial, which assessed the efficacy of PARP inhibitors (PARPi) in homologous recombination deficient prostate cancer. Eight (15.7%) patients show biallelic loss of one of the 15 genes included in the trial, while 5 patients (9.8%) harbor pathogenic alterations in BRCA1/2 specifically. Uncovering these molecular features of PCBM may have therapeutic implications, suggesting the need of clinical trial enrollment of PCBM patients when evaluating potential benefit from PARPi.
MR-guided RF thermal ablation of the kidney in a porcine model. (1999)

MR-guided RF thermal ablation in the porcine kidney was found to be feasible, but minor complications occurred. Induced thermal lesion size was best monitored using turbo STIR images. In the future, RF ablation may offer an alternative treatment option for renal cancer.
In Vitro and In Vivo Evaluation of a Bio-Inspired Adhesive for Bone Fixation (2023)

Compared to metallic hardware, an effective bone adhesive can revolutionize the treatment of clinically challenging situations such as comminuted, articular, and pediatric fractures. The present study aims to develop such a bio-inspired bone adhesive, based upon a modified mineral-organic adhesive with tetracalcium phosphate (TTCP) and phosphoserine (OPS) by incorporating nanoparticles of polydopamine (nPDA). The optimal formulation, which was screened using in vitro instrumental tensile adhesion tests, was found to be 50%<sub>mol</sub>TTCP/50%<sub>mol</sub>OPS-2%<sub>wt</sub>nPDA with a liquid-to-powder ratio of 0.21 mL/g. This adhesive has a substantially stronger adhesive strength (1.0-1.6 MPa) to bovine cortical bone than the adhesive without nPDA (0.5-0.6 MPa). To simulate a clinical scenario of autograft fixation under low mechanical load, we presented the first in vivo model: a rat fibula glued to the tibia, on which the TTCP/OPS-nPDA adhesive (n = 7) was shown to be effective in stabilizing the graft without displacement (a clinical success rate of 86% and 71% at 5 and 12 weeks, respectively) compared to a sham control (0%). Significant coverage of newly formed bone was particularly observed on the surface of the adhesive, thanks to the osteoinductive property of nPDA. To conclude, the TTCP/OPS-nPDA adhesive fulfilled many clinical requirements for the bone fixation, and potentially could be functionalized via nPDA to offer more biological activities, e.g., anti-infection after antibiotic loading.
WeedGait: Unobtrusive Smartphone Sensing of Marijuana-Induced Gait impairment By Fusing Gait Cycle Segmentation and Neural Networks (2019)

The use of marijuana is now legal for medical purposes in 39 of the 50 United States. Eleven of these 39 states have also legalized marijuana for non-medical usage. Marijuana impairs the motor skills of users, making Driving Under the Influence of Marijuana (DUIM) a growing public health concern. There are currently few accessible and accurate methods to assess the impairment levels of drivers who have used marijuana. Current assessment methods include self-reports and testing urine, oral fluid, and blood. However, self-reports are often biased and biological tests are cumbersome to perform in situ. In this paper, we investigate whether dose-dependent changes in participants gait (walk) can be detected using data gathered from their smartphone motion sensors (accelerometer and gyroscope). We envision WeedGait, a smartphone sensing system that will assess the gait of marijuana users passively and warn them when they are too impaired to drive safely. To the best of our knowledge, this is the first study on using smartphones to assess marijuana-induced gait impairment. Gait data was collected from 10 subjects and pre-processing steps included low pass filtering, step cycle detection and segmentation, and normalization. We present a novel gait analysis approach that analyzes normalized, single-step segments to achieve higher accuracy than prior approaches. We compared the classification results of various machine and deep learning models, and found that Long Short Time Memory (LSTM) and Support Vector Machines performed best, discriminating the gait of subjects after smoking either marijuana with 3% or 7.2% THC versus smoking a placebo marijuana cigarette with an accuracy of 92.1%. These results suggest that smartphone-based marijuana testing is more accurate than urine-based tests but slightly less accurate than oral fluid based testing. Moreover, smartphone sensing of marijuana is completely passive and hence more convenient, which facilitates pervasive testing in natural settings and could have massive impact due to the near-ubiquity of smartphones.
Dynamic basis of fidelity and speed in translation: Coordinated multistep mechanisms of elongation and termination (2017)

As the universal machine that transfers genetic information from RNA to protein, the ribosome synthesizes proteins with remarkably high fidelity and speed. This is a result of the accurate and efficient decoding of mRNA codons via multistep mechanisms during elongation and termination stages of translation. These mechanisms control how the correct sense codon is recognized by a tRNA for peptide elongation, how the next codon is presented to the decoding center without change of frame during translocation, and how the stop codon is discriminated for timely release of the nascent peptide. These processes occur efficiently through coupling of chemical energy expenditure, ligand interactions, and conformational changes. Understanding this coupling in detail required integration of many techniques that were developed in the past two decades. This multidisciplinary approach has revealed the dynamic nature of translational control and uncovered how external cellular factors such as tRNA abundance and mRNA modifications affect the synthesis of the protein product. Insights from these studies will aid synthetic biology and therapeutic approaches to translation.