gebhart/patrepeval huggingface dataset:
Deprotection of Homoallyl (hAllyl) Derivatives of Phenols, Alcohols, Acids, and Amines (2009)

The homoallyl moiety, (h)Allyl, is presented as a general protecting group for several functionalities. It can be chemoselectively removed via a sequential, one-pot cross-metathesis/elimination sequence.
Using Biomedical Text as Data and Representation Learning for Identifying Patients with an Osteoarthritis Phenotype in the Electronic Medical Record (2018)

IntroductionElectronic medical records (EMRs) are increasingly used in health services research. Accurate/efficient identification of a target population with a specific disease phenotype is a necessary precursor to studying the health of these individuals.&#x0D; Objectives and ApproachWe explored the use of biomedical text as inputs to supervised phenotype identification algorithms. We employed a two-stage classification approach to map the discrete, sparse high-dimensional biomedical text data to a dense low dimensional vector space using methods from unsupervised machine learning. Next we used these learned vectors as inputs to supervised machine learning algorithms for phenotype identification.&#x0D; We were able to demonstrate the applicability of the approach to identifying patients with an osteoarthritis (OA) phenotype using primary care data from the Electronic Medical Record Administrative data Linked Database (EMRALD) held at ICES.&#x0D; ResultsEMRALD contains approximately 20Gb of biomedical text data on approximately 500,000 patients. The unit of analysis for this study is the patient. We were interested in identifying OA patients using solely text data as features.&#x0D; Labelled outcome information wass available from a random sample of 7,500 patients. We divided patients into training (N=6000), validation (N=750) and test (N=750) cohorts. We learned low dimensional representations of the input text data on the entire EMRALD corpus (N=500,000). We used learned numeric vectors as inputs to supervised machine learning models for OA classification (N=6,000 training set patients).&#x0D; We compared models in terms of accuracy, sensitivity, specificity, PPV and NPV. The best learned models achieved approximately 90\% sensitivity and 80\% specificity. Classification accuracy varied as a function of learned inputs.&#x0D; Conclusion/ImplicationsWe developed an approach to phenotype identification using solely biomedical text as an input. Preliminary results suggest our two-stage ML approach has improved operating characteristics compared to existing clinically derived decision rules for OA classification. Future work will explore the generalizability of this methodology to other disease phenotypes.
A Flexible Loop as a Functional Element in the Catalytic Mechanism of Nucleoside Hydrolase from Trypanosoma vivax (2008)

The nucleoside hydrolase of Trypanosoma vivax hydrolyzes the N-glycosidic bond of purine nucleosides. Structural and kinetic studies on this enzyme have suggested a catalytic role for a flexible loop in the vicinity of the active sites. Here we present the analysis of the role of this flexible loop via the combination of a proline scan of the loop, loop deletion mutagenesis, steady state and pre-steady state analysis, and x-ray crystallography. Our analysis reveals that this loop has an important role in leaving group activation and product release. The catalytic role involves the entire loop and could only be perturbed by deletion of the entire loop and not by single site mutagenesis. We present evidence that the loop closes over the active site during catalysis, thereby ordering a water channel that is involved in leaving group activation. Once chemistry has taken place, the loop dynamics determine the rate of product release.
A High Precision Modeling Technology of Material Surface Microtopography and Its Influence on Interface Mechanical Properties (2021)

In order to accurately and effectively obtain the contact performance of the mating surface under the material surface topography characteristics, a numerical simulation method of rough surface based on the real topography characteristics and a multi-scale hierarchical algorithm of contact performance is studied in this paper. Firstly, the surface topography information of materials processed by different methods was obtained and characterized by a measuring equipment; Secondly, a non-Gaussian model considering kurtosis and skewness was established by Johnson transform based on Gaussian theory, and a rough surface digital simulation method based on real surface topography was formed; Thirdly, a multi-scale hierarchical algorithm is given to calculate the contact performance of different mating surfaces; Finally, taking the aeroengine rotor as the object, the non-Gaussian simulation method was used to simulate the mating surfaces with different topographies, and the multi-scale hierarchical algorithm was used to calculate the contact performance of different mating surfaces. Analysis results showed that the normal contact stiffness and elastic-plastic contact area between the mating surfaces of assembly 1 and assembly 2 are quite different, which further verifies the feasibility of the method. The contents of this paper allow to perform the fast and effective calculation of the mechanical properties of the mating surface, and provide a certain analysis basis for improving the surface microtopography characteristics of materials and the product performance.
Loop Shaping Control Design for a Supersonic Propulsion System Model Using Quantitative Feedback Theory (QFT) Specifications and Bounds (2010)

This paper covers the propulsion system component modeling and controls development of an integrated mixed compression inlet and turbojet engine that will be used for an overall vehicle Aero-Propulso-Servo-Elastic (APSE) model. Using previously created nonlinear component-level propulsion system models, a linear integrated propulsion system model and loop shaping control design have been developed. The design includes both inlet normal shock position control and jet engine rotor speed control for a potential supersonic commercial transport. A preliminary investigation of the impacts of the aero-elastic effects on the incoming flow field to the propulsion system are discussed, however, the focus here is on developing a methodology for the propulsion controls design that prevents unstart in the inlet and minimizes the thrust oscillation experienced by the vehicle. Quantitative Feedback Theory (QFT) specifications and bounds, and aspects of classical loop shaping are used in the control design process. Model uncertainty is incorporated in the design to address possible error in the system identification mapping of the nonlinear component models into the integrated linear model.
Iron-sulfur clusters of hydrogenase I and hydrogenase II of Clostridium pasteurianum. (1989)

The iron and acid-labile sulfide contents and the electron paramagnetic resonance (EPR) properties of hydrogenase I (bidirectional) and hydrogenase II (uptake) of Clostridium pasteurianum (strain W5) have been determined on the basis of quantitative amino acid analyses. The iron and acid-labile sulfide values are approximately 20 and 18 atoms per molecule of hydrogenase I and 14 and 11 atoms per molecule of hydrogenase II, respectively. These amounts are substantially greater than previously reported values, which relied on protein concentration determined by colorimetric assay. The oxidized hydrogenases exhibit unusual EPR signals that originate from a novel type of iron-sulfur center, termed the hydrogenase or H cluster, which covalently binds the inhibitor CO. This EPR signal represents approximately one unpaired electron per molecule in each enzyme with and without bound CO, which is consistent with the presence of one oxidized H cluster (S = 1/2) per enzyme molecule. The two enzymes also contain ferredoxin-type four-iron centers or F clusters. The EPR signals from the F clusters observed in the reduced forms of hydrogenase I and hydrogenase II account for approximately four and one unpaired electron per molecule, respectively. We conclude from the iron determinations and the EPR results, together with a reevaluation of previous spectroscopic data, that in both hydrogenases the H cluster probably comprises six iron atoms. Mechanistic models of the two hydrogenases are presented that account for their cluster compositions and the dramatic differences in their catalytic activities.
Investigation of the Washout Effect in a Magnetically Driven Axial Blood Pump (2008)

For a long-term implementation of the magnetically driven CircuLite blood pump system, it is extremely important to be able to ensure a minimum washout flow in order to avoid dangerous stagnation regions in the gap between the impeller and the motor casing as well as near the pivot-axle area at the holes in the impeller's hub. In general, stagnation zones are prone to thrombus formation. Here, the optimal impeller/motor gap width will be determined and the washout flow for different working conditions will be quantitatively calculated. The driving force for this secondary flow is mainly the strong pressure difference between both ends of the gap. Computational fluid dynamics (CFD) and digital particle image velocimetry (DPIV) will be used for this analysis.
Impact of microfluidic processing on bacterial ribonucleic acid expression (2015)

Bacterial transcriptomics is widely used to investigate gene regulation, bacterial susceptibility to antibiotics, host-pathogen interactions, and pathogenesis. Transcriptomics is crucially dependent on suitable methods to isolate and detect bacterial RNA. Microfluidics offer ways of creating integrated point-of-care systems, analysing a sample from preparation, and RNA isolation to detection. A critical requirement for on-chip diagnostics to deliver on their promise is that mRNA expression is not altered via microfluidic sample processing. This article investigates the impact of the use of microfluidics upon RNA expression of bacteria isolated from blood, a key step towards proving the suitability of such systems for further development.
Magnetoplasmonic structures with broken spatial symmetry for light control at normal incidence (2020)

As magnetized media by their nature have broken time reciprocity, the spatial symmetry of a material is also crucial and it imposes some restrictions on observed optical phenomena. Thus, for the normal incidence of light the spatial inversion symmetry makes transmitted and reflected light insensitive to the direction of the in-plane magnetization of the sample. To avoid this limitation, we propose here an approach based on a magnetoplasmonic structure with broken spatial symmetry. Combination of the specially designed spatial asymmetry with magnetism in the presence of optical losses provides a different effect, the transverse magnetophotonic transmittance effect, notable magnetooptical modulation of the optical transmittance at normal incidence enhanced by surface plasmon excitation. As the phenomenon is sensitive to asymmetry, it can serve as a powerful tool to study spin waves and currents in magnonic and optospintronic devices. The approach to marry the concepts of magnetoplasmonics and a lack of spatial symmetry is promising for the design of nanophotonics devices with outstanding properties.
An Adaptive Guidance System for Robotic Walking Aids (2008)

In the last years, several robotic walking aids to assist elderly users with mobility constraints and thus to react to the growing number of elderly persons in our society have been developed. In order to ensure good support for the user, the robotic walker should adapt to the motion of the user while at the same time not losing the target out of sight. Even though some of the existing active robotic walkers are able to guide their user to a target, during guidance, the input of the user is not considered sufficiently. Therefore a new adaptive guidance system for robotic walkers has been developed. It is able to lead the walking aid user to a given target while considering his inputs during guidance and adapting the path respectively. The guidance system has been implemented on the mobile robot assistant Care-O-bot II and a field test was done in an old people’s residence proving the correct function and usefulness of the guidance system.
Definition of a VR-Based Protocol to Treat Social Phobia (2003)

Social phobia is an anxiety disorder that is accessible to two forms of treatment yielding scientifically validated results: drugs and cognitive-behavioral therapies. Graded exposure to feared social situations is fundamental to obtain an improvement of the anxious symptoms. Traditionally, exposure therapies are done either in vivo or by imagining the situations. In vivo exposure is sometimes difficult to control and many patients have some difficulties in using imagination. Virtual reality (VR) seems to bring significant advantages. It allows exposures to numerous and varied situations. This paper reports the definition of a clinical protocol whose purpose is to assess the efficiency of a VR therapy compared to a CBT and to the absence of treatment for social phobic patients. It explains the illness' diagnosis and its usual treatments. It exposes all the architecture of the study, the assessment tools, the content and unfold of the therapy sessions. It finally reports first results of a clinical trial in a between-group design in 10 patients suffering from social phobia. The virtual environments used in the treatment reproduce four situations that social phobics feel the most threatening: performance, intimacy, scrutiny and assertiveness. With the help of the therapist, the patient learns adapted cognitions and behaviors with the aim of reducing her or his anxiety in the corresponding real situations. The novelty of our work is to address a group of situations that the phobic patient is most likely to experience and to treat patients according to a precise protocol.
Photocatalytic degradation of carbofuran in TiO_2 aqueous solution： Kinetics using design of experiments and mechanism by HPLC/MS/MS (2013)

carbofuran 的 photocatalytic 降级动力学被中央合成设计第一次基于反应表面方法论优化。三个变量， TiO2 集中，起始的 pH 值和 carbofuran 的集中，被选择在独立变量上决定降级效率的依赖。反应表面方法论建模结果显示 carbofuran 的降级效率被起始的 pH 价值和 carbofuran 的集中高度影响。然后，九降级中介被 HPLC/MS/MS 检测。carbofuran 的边疆电子密度被计算在氢氧根激进分子和光穴攻击的 carbofuran 上预言活跃地点。点费用被用来阐明 TiO2 催化剂上的化学吸着模式在 photocatalytic 过程期间。由联合试验性的结果和计算数据， carbofuran 的 photocatalytic 降级小径被建议，包括氢氧根激进分子和氨基甲酸酯方面链的劈开的增加。
QAngaroo (MedHop + WikiHop) - Constructing Datasets for Multi-hop Reading Comprehension Across Documents (2018)

Most Reading Comprehension methods limit themselves to queries which can be answered using a single sentence, paragraph, or document. Enabling models to combine disjoint pieces of textual evidence would extend the scope of machine comprehension methods, but currently no resources exist to train and test this capability. We propose a novel task to encourage the development of models for text understanding across multiple documents and to investigate the limits of existing methods. In our task, a model learns to seek and combine evidence — effectively performing multihop, alias multi-step, inference. We devise a methodology to produce datasets for this task, given a collection of query-answer pairs and thematically linked documents. Two datasets from different domains are induced, and we identify potential pitfalls and devise circumvention strategies. We evaluate two previously proposed competitive models and find that one can integrate information across documents. However, both models struggle to select relevant information; and providing documents guaranteed to be relevant greatly improves their performance. While the models outperform several strong baselines, their best accuracy reaches 54.5% on an annotated test set, compared to human performance at 85.0%, leaving ample room for improvement.
Fast and comprehensive analysis of secondary metabolites in cocoa products using ultra high‐performance liquid chromatography directly after pressurized liquid extraction (2016)

Fast methods for the extraction and analysis of various secondary metabolites from cocoa products were developed and optimized regarding speed and separation efficiency. Extraction by pressurized liquid extraction is automated and the extracts are analyzed by rapid reversed-phase ultra high-performance liquid chromatography and normal-phase high-performance liquid chromatography methods. After extraction, no further sample treatment is required before chromatographic analysis. The analytes comprise monomeric and oligomeric flavanols, flavonols, methylxanthins, N-phenylpropenoyl amino acids, and phenolic acids. Polyphenols and N-phenylpropenoyl amino acids are separated in a single run of 33 min, procyanidins are analyzed by normal-phase high-performance liquid chromatography within 16 min, and methylxanthins require only 6 min total run time. A fourth method is suitable for phenolic acids, but only protocatechuic acid was found in relevant quantities. The optimized methods were validated and applied to 27 dark chocolates, one milk chocolate, two cocoa powders and two food supplements based on cocoa extract.
An efficient polymer moist-electric generator (2019)

An efficient polymer moist-electric generator is developed on the basis of conventional polyelectrolyte membrane to output considerable electric power under moisture.
Le contrat de pôle en pratique (2008)

Le contrat de pole est, avec le projet de pole, l'etape fondatrice du pole prevue par l'ordonnance du 2 mai 2005 portant sur la nouvelle gouvernance. L'elaboration de ce contrat, sa negociation avec les directions fonctionnelles de l'hopital et sa signature constituent une innovation considerable dans l'organisation hospitaliere. Retour d'experience.
A Multi-Granularity Power Modeling Methodology for Embedded Processors (2010)

With power becoming a major constraint for multiprocessor embedded systems, it is becoming important for designers to characterize and model processor power dissipation. It is critical for these processor power models to be useable across various modeling abstractions in an electronic system level (ESL) design flow, to guide early design decisions. In this paper, we propose a unified processor power modeling methodology for the creation of power models at multiple granularity levels that can be quickly mapped to an ESL design flow. Our experimental results based on applying the proposed methodology on the OpenRISC and MIPS processors demonstrate the usefulness of having multiple power models. The generated models range from very high-level two-state and architectural/instruction set simulator models that can be used in transaction level models, to extremely detailed cycle-accurate models that enable early exploration of power optimization techniques. These models offer a designer tremendous flexibility to trade off estimation accuracy with estimation/simulation effort.
Filling the Gap: Silicon Terahertz Integrated Circuits Offer Our Best Bet (2019)

The definition for the frequency range of a terahertz wave varies in the literature. Some refer to terahertz as the spectrum between 300 GHz (λ = 1 mm) and 3 THz (λ = 0.1 mm) to distinguish it from its millimeter-wave counterpart (30-300 GHz). Others adopt a decimal pattern and a loosely defined frequency range from 100 GHz to 10 THz. Based on the latter definition, probably the earliest documented endeavor to reach terahertz frequency was published in a paper in Physical Review in 1923 [1]. In this nearly century-old work, authors Nichols and Tear generated a 0.17-THz signal using a spark-gap oscillator, detected it with a radiometer vane, and analyzed the spectrum through a Boltzmann interferometer.
Leader election algorithms for mobile ad hoc networks (2000)

We present two new leader election algorithms for mobile ad hoc networks. The algorithms ensure that eventually each connected component of the topology graph has exactly one leader. The algorithms are based on a routing algorithm called TORA [5], which in turn is based on an algorithm by Gafni and Bertsekas [3]. The algorithm require nodes to communicate with only their current neighbors, making it well suited to the ad hoc environment. The first algorithm is for a single topology change and is provided with a proof of correctness. The second algorithm tolerates multiple concurrent topology changes.
Pan-genomic perspective on the evolution of the Staphylococcus aureus USA300 epidemic (2016)

<i>Staphylococcus aureus</i> USA300 represents the dominant community-associated methicillin-resistant <i>S. aureus</i> lineage in the USA, where it is a major cause of skin and soft tissue infections. Previous comparative genomic studies have described the population structure and evolution of USA300 based on geographically restricted isolate collections. Here, we investigated the USA300 population by sequencing genomes of a geographically distributed panel of 191 clinical <i>S. aureus</i> isolates belonging to clonal complex 8 (CC8), derived from the Tigecycline Evaluation and Surveillance Trial program. Isolates were collected at 12 healthcare centres across nine USA states in 2004, 2009 or 2010. Reconstruction of evolutionary relationships revealed that CC8 was dominated by USA300 isolates (154/191, 81 %), which were heterogeneous and demonstrated limited phylogeographic clustering. Analysis of the USA300 core genomes revealed an increase in median pairwise SNP distance from 62 to 98 between 2004 and 2010, with a stable pattern of above average d<i>N</i>/d<i>S</i> ratios. The phylogeny of the USA300 population indicated that early diversification events led to the formation of nested clades, which arose through cumulative acquisition of predominantly non-synonymous SNPs in various coding sequences. The accessory genome of USA300 was largely homogenous and consisted of elements previously associated with this lineage. We observed an emergence of SCC<i>mec</i> negative and ACME negative USA300 isolates amongst more recent samples, and an increase in the prevalence of ϕSa5 prophage. Together, the analysed <i>S. aureus</i> USA300 collection revealed an evolving pan-genome through increased core genome heterogeneity and temporal variation in the frequency of certain accessory elements.
Applications and experiments with eblocks - electronic blocks for basic sensor-based systems (2005)

Building a sensor-based system typically requires some programming and electronics expertise. However, some applications require only basic logic transformations and/or state maintenance of sensor information. This paper describes a set of electronic blocks, called eBlocks, that enable non-experts to build basic small-scale sensor-based systems. Each block performs a particular sensing, logic/state, or output function. A user builds a system by connecting blocks together. Each block contains a hidden microprocessor executing a pre-determined low-power compute and communication protocol. A difference between eBlocks and widely known sensor-network nodes is that each eBlock has a specific easy-to-understand function, and thus does not require programming. Further, eBlocks are designed to be connected in particular configurations to create an end application, while traditional nodes form a wireless network that must be programmed to form an application. Our physical prototypes can last for several years or more on a 9-volt battery, or can receive power from wall outlets. We describe the domain of applications for which eBlocks are suitable, including being used to build complete systems or to interface with existing sensor-network compute nodes, and we summarize the eBlock compute/communication protocol. We describe experiments, involving hundreds of users of varying levels of expertise, that demonstrate how systems that otherwise would have taken weeks or more to build can be built by non-experts in just a few minutes using eBlocks.