gebhart/patrepeval huggingface dataset:
Kinetics of substrate removal in a completely mixed anaerobic filter (1976)

Abstract A completely mixed anaerobic filter, in which the influent organic matter concentration is diluted with recirculated effluent, was found to effectively remove organic matter concentrations in high strength acidic wastewater, at a range of organic loadings and shock loads. Increases in organic loading had a substantial effect on the relative organic matter composition of the effluent and the magnitude of the fatty acid fraction showed a pattern inverse to that of the nitrogenous organics. A fixed film model was formulated which indicated that at high substrate concentrations the substrate removal rate is proportional to the square root of the substrate concentration and the specific area of the filter medium. A comparison of the biofilm model and the measured effluent concentrations tended to indicate that the substrate removal rate is primarily affected by substrate concentration, specific surface area, flow rate, and temperature of the unit.
Magnetic resonance elastography hardware design: A survey (2009)

Magnetic resonance elastography (MRE) is an emerging technique capable of measuring the shear modulus of tissue. A suspected tumour can be identified by comparing its properties with those of tissues surrounding it; this can be achieved even in deep-lying areas as long as mechanical excitation is possible. This would allow non-invasive methods for cancer-related diagnosis in areas not accessible with conventional palpation. An actuating mechanism is required to generate the necessary tissue displacements directly on the patient in the scanner and three different approaches, in terms of actuator action and position, exist to derive stiffness measurements. However, the magnetic resonance (MR) environment places considerable constraints on the design of such devices, such as the possibility of mutual interference between electrical components, the scanner field, and radio frequency pulses, and the physical space restrictions of the scanner bore. This paper presents a review of the current solutions that have been developed for MRE devices giving particular consideration to the design criteria including the required vibration frequency and amplitude in different applications, the issue of MR compatibility, actuation principles, design complexity, and scanner synchronization issues. The future challenges in this field are also described.
Twenty-One Genome Sequences from Pseudomonas Species and 19 Genome Sequences from Diverse Bacteria Isolated from the Rhizosphere and Endosphere of Populus deltoides (2012)

To aid in the investigation of the Populus deltoides microbiome, we generated draft genome sequences for 21 Pseudomonas strains and 19 other diverse bacteria isolated from Populus deltoides roots. Genome sequences for isolates similar to Acidovorax, Bradyrhizobium, Brevibacillus, Caulobacter, Chryseobacterium, Flavobacterium, Herbaspirillum, Novosphingobium, Pantoea, Phyllobacterium, Polaromonas, Rhizobium, Sphingobium, and Variovorax were generated.
Hydrogel–hydrogel composites: The interfacial structure and interaction between water and polymer chains (2008)

Abstract This work examines the interfacial structure and interaction between water and polymer chains in the hydrogel–hydrogel composites with the goal of establishing foundations for further investigation of drug diffusion from one hydrogel to another in the soft contact lens. This is based on the ability of the hydrogel–hydrogel composites to release ophthalmic drugs in a sustained manner. The hydrogel–hydrogel composites were synthesized by immersing the glycerol‐swollen particles of crosslinked N ‐vinyl‐2‐pyrrolidone (NVP) into the monomer of hydroxyethylmethacrylate (HEMA) containing initiator benzoylperoxide (BPO) that polymerizes to form a matrix in the presence of the first networks. The hydrogel–hydrogel composites were characterized by UV/Vis spectrophotometer, scanning electronic micrography (SEM), and differential scanning calorimetry (DSC). The results showed that the samples of hydrogel–hydrogel composites of the particles of crosslinked NVP and poly‐HEMA were transparent and glassy and suitable for soft contact lens. Three types of the interfacial structure, no interpenetrating interface, partly interpenetrating interface, and fully interpenetrating interface, of the hydrogel–hydrogel composites existed, and the type of the interfacial structure was determined by the degree to which the monomer of HEMA penetrated into the first networks before formation of the matrix. Different from poly‐HEMA hydrogels, the peaks near 0°C on DSC curves of the hydrogel–hydrogel composites did not split while they were kept acute, and the amount of freezable‐bound water was less. This shows that the water incorporated in the hydrogel–hydrogel composites does not strongly interact with polymer matrix, so the hydrogel–hydrogel composites cannot keep their shape during the phase transition of water. © 2008 Wiley Periodicals, Inc. J Appl Polym Sci, 2008
Safe Platooning in Automated Highway Systems Part II: Velocity Tracking Controller (1999)

This paper presents the design of a velocity tracking controller for safe vehicle maneuvering in Automated Highway Systems (AHS) in which traffic is organized into platoons of closely spaced vehicles. The notion of safety is related to the absence of collisions that exceed a given relative velocity threshold. In a companion paper, state dependent safety regions for the platoons are designed in such a way that, whenever the state of a platoon is inside these safety regions, it is guaranteed that platoon maneuvering will be safe and follow the behavior prescribed by the finite state machines that control vehicles maneuvers. Velocity profiles inside these safety regions are derived for all the single lane maneuvers and a nonlinear velocity tracking controller is designed to track these profiles. This controller attempts to complete the maneuvers with comfort in minimum time, whenever safety is not compromised. The control schemes presented in this paper were implemented and tested using AHS simulation software.
The Application of Analytical Methods to the Detection of Hidden Explosives and Explosive Devices (1997)

Abstract The detection of hidden explosives has undergone an enormous development due to an increased desire for safety and the increased terrorist attacks in the last few years. This development was made possible in particular by the rapid advances in the development of powerful analytical techniques in general. These technologies, however, must be specially adapted for the problems of explosives detection. These problems encompass, for example, the large variety of different explosives, the camouflage of explosive devices, and the complexity of the composition of suspicious objects. Frequent air‐travelers have most certainly already been confronted with a so‐called explosives detection apparatus. Baggage controls at airports are a very important and well‐known example of the application of detection technologies. This example also serves to demonstrate the high technological requirements, such as the variability of the object to be examined and a control procedure for a sealed object that must be completed with high reliability in a short period of time. The search for explosive devices or weapons cannot, however, be limited to the recognition of an external appearance with the help of X‐ray imaging. These days, explosive devices, in particular, can readily be installed and hidden in objects of daily life by the use of tiny electric and electronic elements. Therefore, in addition to the application of X‐ray imaging, the use of other technologies becomes necessary. The following article describes and discusses methods and scientific limits of explosives detection under the precondition of possible use at security checkpoints. For corrigendum see DOI: 10.1002/anie.199713711
LSTM Pose Machines (2018)

We observed that recent state-of-the-art results on single image human pose estimation were achieved by multistage Convolution Neural Networks (CNN). Notwithstanding the superior performance on static images, the application of these models on videos is not only computationally intensive, it also suffers from performance degeneration and flicking. Such suboptimal results are mainly attributed to the inability of imposing sequential geometric consistency, handling severe image quality degradation (e.g. motion blur and occlusion) as well as the inability of capturing the temporal correlation among video frames. In this paper, we proposed a novel recurrent network to tackle these problems. We showed that if we were to impose the weight sharing scheme to the multi-stage CNN, it could be re-written as a Recurrent Neural Network (RNN). This property decouples the relationship among multiple network stages and results in significantly faster speed in invoking the network for videos. It also enables the adoption of Long Short-Term Memory (LSTM) units between video frames. We found such memory augmented RNN is very effective in imposing geometric consistency among frames. It also well handles input quality degradation in videos while successfully stabilizes the sequential outputs. The experiments showed that our approach significantly outperformed current state-of-the-art methods on two large-scale video pose estimation benchmarks. We also explored the memory cells inside the LSTM and provided insights on why such mechanism would benefit the prediction for video-based pose estimations.1
Flow Activates ERK1/2 and Endothelial Nitric Oxide Synthase via a Pathway Involving PECAM1, SHP2, and Tie2 (2005)

Blood flow modulates endothelial cell (EC) functions through specific signaling events. Previous data show that flow stimulates SHP2 translocation to cell membranes and binding to phosphotyrosine proteins. Flow-induced ERK1/2 phosphorylation depends on SHP2 phosphatase activity and SHP2 binding to phospho-PECAM1 (platelet endothelial adhesion molecule 1), suggesting that SHP2 forms a signaling module with PECAM1. We hypothesized that flow induces assembly of the multi-protein complexes with SHP2 that are required for downstream signaling. ECs were exposed to flow for 10 min, and endogenous SHP2 was immunoprecipitated. SHP2-associated proteins were analyzed by SDS-PAGE and identified by mass spectrometry. Tie2 and several known SHP2-binding proteins were identified in flow-induced SHP2 complexes. Flow significantly increased tyrosine phosphorylation of both Tie2 and PECAM1 and their association with SHP2. To evaluate their functional roles, ECs were treated with Tie2 or PECAM1 small interfering RNA (siRNA). Tie2 and PECAM1 expression decreased >80% after siRNA treatment, and flow-stimulated phosphorylation of ERK1/2, Akt, and endothelial nitric oxide synthase was significantly inhibited by Tie2 and PECAM1 siRNA. Tie2 phosphorylation by flow was significantly inhibited by PECAM1 siRNA treatment. These results establish Tie2 transactivation via PECAM1 as an early event in flow-mediated mechanotransduction and suggest an important role for a PECAM1-SHP2-Tie2 pathway in flow-mediated signal transduction.
Porcine Teschoviruses Comprise at Least Eleven Distinct Serotypes: Molecular and Evolutionary Aspects (2001)

Nucleotide sequencing and phylogenetic analysis of 10 recognized prototype strains of the porcine enterovirus (PEV) cytopathic effect (CPE) group I reveals a close relationship of the viral genomes to the previously sequenced strain F65, supporting the concept of a reclassification of this virus group into a new picornavirus genus. Also, nucleotide sequences of the polyprotein-encoding genome region or the P1 region of 28 historic strains and recent field isolates were determined. The data suggest that several closely related but antigenically and molecular distinct serotypes constitute one species within the proposed genus Teschovirus. Based on sequence data and serological data, we propose a new serotype with strain Dresden as prototype. This hitherto unrecognized serotype is closely related to porcine teschovirus 1 (PTV-1, former PEV-1), but induces type-specific neutralizing antibodies. Sequencing of field isolates collected from animals presenting with neurological disorders prove that other serotypes than PTV-1 may also cause polioencephalomyelitis of swine.
A Practical Approach for Performance Analysis of Shared-Memory Programs (2011)

Parallel programming has transcended from HPC into mainstream, enabled by a growing number of programming models, languages and methodologies, as well as the availability of multicore systems. However, performance analysis of parallel programs is still difficult, especially for large and complex programs, or applications developed using different programming models. This paper proposes a simple analytical model for studying the speedup of shared-memory programs on multicore systems. The proposed model derives the speedup and speedup loss from data dependency and memory overhead for various configurations of threads, cores and memory access policies in UMA and NUMA systems. The model is practical because it uses only generally available and non-intrusive inputs derived from the trace of the operating system run-queue and hardware events counters. Using six OpenMP HPC dwarfs from the NPB benchmark, our model differs from measurement results on average by 9% for UMA and 11% on NUMA. Our analysis shows that speedup loss is dominated by memory contention, especially for larger problem sizes. For the worst performing structured grid dwarf on UMA, memory contention accounts for up to 99% of the speedup loss. Based on this insight, we apply our model to determine the optimal number of cores that alleviates memory contention, maximizing speedup and reducing execution time.
Durability of solvent-free one-step self-etch adhesive under simulated intrapulpal pressure (2015)

Bond strength, dentin, simulated intrapulpal pressure, self-etch adhesives, solvents.
Development of A Superconducting Transformer for Rolling Stock (2006)

Having undertaken studies into a lightweight and highly efficient superconducting transformer for rolling stock, we developed a prototype with a primary winding, four secondary windings and a tertiary winding using bismuth (Bi-2223) high temperature superconducting wire. Its primary voltage is 25kV, which is widely adopted as the catenary voltage on the world's high-speed lines. We adopted liquid nitrogen cooling, the weight being 1.71t excluding the refrigerator. The maximum output available to maintain superconductivity is 3.5MVA. This paper describes the transformer details and test results.
A Tangible Information Explorer Using Vibratory Touch Screen (2012)

Touch panel displays are becoming available for implementing futuristic human computer interaction (HCI) methods and are proven to be a useful infrastructure for creating intuitive HCI. In spite of their popularity, there are some drawbacks. The most serious one is their hardness to operate especially for the weak in information technology such as elderly and blind users. A tactile feedback function has a potential ability for enabling them to make full use of the devices. We propose an approach for effectively designing user-friendly HCI based on the tactile feedback. We exemplify our approach through the design and development of a practical application, a haptic web browser. It allows even the weak users to intuitively explore various web pages without heavily depending on the visual information. While the system targets at supporting the weak, the touch interactions are quite useful means for general public to improve the stability and the degree of satisfaction in web browsing operations. The proposed system uses a touch panel haptic display for helping the users to operate with intuitive touch sensations.
Effects of Extracellular Matrix on the Expression of Specific Ovarian Proteins1 (1990)

A unique ovarian follicle cell culture system has been established to analyze the effects of extracellular matrix (ECM) on early granulosa cell differentiation. Primary and early secondary follicles isolated from ovaries of sexually immature rabbits were grown on poly-D-lysine or Englebreth-Holm-Swarm basement membrane biomatrix substrata (EHS) in serum-free, hormonally defined medium. Granulosa cells from these follicles were examined for growth pattern characteristics and for secretory protein synthesis by two-dimensional (2D) PAGE. Whereas some proteins were synthesized by cells on either matrix, the expression of other secreted proteins was markedly affected by the ECM used. Secretion of zona pellucida (ZP) proteins was demonstrated by ELISA assays and immunoblots of one-dimensional (1D) and 2D-PAGE separations of secreted proteins probed with monoclonal and epitope-selected antibodies. Expression of two ZP proteins was altered by ECM: 55-kDa endo-beta-galactosidase (EBGD)-treated ZP glycoprotein (55-kDaEBGD) was secreted by cells grown on either ECM, but a greater amount of 75-kDaEBGD was secreted by cells grown on poly-D-lysine. These studies are the first to show that granulosa cells from early-stage follicles express ZP proteins in vitro in the absence of oocytes, although proper post-translational modification may not occur. They also demonstrate the dramatic effect of ECM on the expression of these and other secretory proteins.
Similarity Searching in Large Image DataBases (1994)

We propose a method to handle approximate searching by image content in large image databases. Image content is represented by attributed relational graphs holding features of objects and relationships between objects. The method relies on the assumption that a fixed number of &quot;labeled&quot; or &quot;expected&quot; objects (e.g., &quot;heart&quot;, &quot;lungs&quot; etc.) are common in all images of a given application domain in addition to a variable number of &quot;unexpected&quot; or &quot;unlabeled&quot; objects (e.g., &quot;tumor&quot;, &quot;hematoma&quot; etc.). The method can answer queries by example such as &quot;find all X-rays that are similar to Smith&apos;s X-ray&quot;. The stored images are mapped to points in a multidimensional space and are indexed using state-of-the-art database methods (R-trees). The proposed method has several desirable properties: (a) Database search is approximate so that all images up to a pre-specified degree of similarity (tolerance) are retrieved, (b) it has no &quot;false dismissals&quot; (i.e., all images qualifying query selection criteri...
Surface Analysis by X-ray Photoelectron Spectroscopy of Sol−Gel Silica Modified with Covalently Bound Peptides (2007)

Chemical surface characterization of biologically modified sol-gel derived silica is critical but somewhat limited. This work demonstrates the ability of x-ray photoelectron spectroscopy (XPS) to characterize the surface chemistry of peptide modified sol-gel thin films based on the example of four different free peptide-silanes, denoted RGD, NID, KDI ,and YIG. The N 1s and C 1s peaks were found to be good fingerprints of the peptides, whereas O 1s overlapped with the signal of substrate oxygen and, therefore, the O 1s peak was not informative in the case of the thin films. The C 1s peak was fitted and the contribution of the residual hydrocarbons was sorted out. The curve-fitting procedure of the C 1s peak accounted for the different chemical states of carbon atoms in the peptide structure. The curve-fitting procedure was validated by analyzing free peptides in the powder form and was then applied to the characterization of the peptide-modified thin films. The XPS measured ratio between nitrogen and carbon for the peptide thin film was similar to the corresponding value calculated from the peptide structures. Angle resolved XPS confirmed the surface nature of peptides in modified thin films. The coverage and thickness of the peptides on the thin film surface depended on the peptide sequence. The coverage was in the range of 10% of a monolayer, and the layer thickness varied from 10 to 30 A. We believe that the different thicknesses and surface coverage are due to the local structure of the peptides, with the RGD and NID peptides taking a globule conformation and the YIG and KDI peptides adopting a more linear structure.
New insights into structure-function relationships of oxalyl CoA decarboxylase from Escherichia coli (2010)

The gene yfdU from Escherichia coli encodes a putative oxalyl coenzyme A decarboxylase, a thiamine diphosphate-dependent enzyme that is potentially involved in the degradation of oxalate. The enzyme has been purified to homogeneity. The kinetic constants for conversion of the substrate oxalyl coenzyme A by the enzyme in the absence and presence of the inhibitor coenzyme A, as well as in the absence and presence of the activator adenosine 5′-diphosphate, were determined using a novel continuous optical assay. The effects of these ligands on the solution and crystal structure of the enzyme were studied using small-angle X-ray scattering and X-ray crystal diffraction. Analyses of the obtained crystal structures of the enzyme in complex with the cofactor thiamine diphosphate, the activator adenosine 5′-diphosphate and the inhibitor acetyl coenzyme A, as well as the corresponding solution scattering patterns, allow comparison of the oligomer structures of the enzyme complexes under various experimental conditions, and provide insights into the architecture of substrate and effector binding sites. Structured digital abstract • MINT-7717846: EcODC (uniprotkb:P0AFI0) and EcODC (uniprotkb:P0AFI0) bind (MI:0407) by X-ray scattering (MI:0826) • MINT-7717834: EcODC (uniprotkb:P0AFI0) and EcODC (uniprotkb:P0AFI0) bind (MI:0407) by X-ray crystallography (MI:0114)
Epithelial-Mesenchymal Transition-Derived Cells Exhibit Multilineage Differentiation Potential Similar to Mesenchymal Stem Cells   (2010)

The epithelial-to-mesenchymal transition (EMT) is an embryonic process that becomes latent in most normal adult tissues. Recently, we have shown that induction of EMT endows breast epithelial cells with stem cell traits. In this report, we have further characterized the EMT-derived cells and shown that these cells are similar to mesenchymal stem cells (MSCs) with the capacity to differentiate into multiple tissue lineages. For this purpose, we induced EMT by ectopic expression of Twist, Snail, or transforming growth factor-beta in immortalized human mammary epithelial cells. We found that the EMT-derived cells and MSCs share many properties including the antigenic profile typical of MSCs, that is, CD44(+), CD24(-), and CD45(-). Conversely, MSCs express EMT-associated genes, such as Twist, Snail, and mesenchyme forkhead 1 (FOXC2). Interestingly, CD140b (platelet-derived growth factor receptor-beta), a marker for naive MSCs, is exclusively expressed in EMT-derived cells and not in their epithelial counterparts. Moreover, functional analyses revealed that EMT-derived cells but not the control cells can differentiate into alizarin red S-positive mature osteoblasts, oil red O-positive adipocytes and alcian blue-positive chondrocytes similar to MSCs. We also observed that EMT-derived cells but not the control cells invade and migrate towards MDA-MB-231 breast cancer cells similar to MSCs. In vivo wound homing assays in nude mice revealed that the EMT-derived cells home to wound sites similar to MSCs. In conclusion, we have demonstrated that the EMT-derived cells are similar to MSCs in gene expression, multilineage differentiation, and ability to migrate towards tumor cells and wound sites.