gebhart/patrepeval huggingface dataset:
Tissue-Specific 5′ Heterogeneity of PPARα Transcripts and Their Differential Regulation by Leptin (2013)

The genes encoding nuclear receptors comprise multiple 5'untranslated exons, which give rise to several transcripts encoding the same protein, allowing tissue-specific regulation of expression. Both human and mouse peroxisome proliferator activated receptor (PPAR) α genes have multiple promoters, although their function is unknown. Here we have characterised the rat PPARα promoter region and have identified three alternative PPARα transcripts, which have different transcription start sites owing to the utilisation of distinct first exons. Moreover these alternative PPARα transcripts were differentially expressed between adipose tissue and liver. We show that while the major adipose (P1) and liver (P2) transcripts were both induced by dexamethasone, they were differentially regulated by the PPARα agonist, clofibric acid, and leptin. Leptin had no effect on the adipose-specific P1 transcript, but induced liver-specific P2 promoter activity via a STAT3/Sp1 mechanism. Moreover in Wistar rats, leptin treatment between postnatal day 3-13 led to an increase in P2 but not P1 transcription in adipose tissue which was sustained into adulthood. This suggests that the expression of the alternative PPARα transcripts are in part programmed by early life exposure to leptin leading to persistent change in adipose tissue fatty acid metabolism through specific activation of a quiescent PPARα promoter. Such complexity in the regulation of PPARα may allow the expression of PPARα to be finely regulated in response to environmental factors.
Tunable stopband filter by using differential strains in all-fiber acoustooptical filter (2005)

This letter presents a tunable stopband filter by using an all-fiber acoustooptical tunable filter (AF-AOTF) subject to differential strains. With the proposed filter, narrow and wide tunable stopbands of 0.4-nm 12-dB bandwidth and 4-nm 12-dB bandwidth, respectively, are demonstrated by experiments. Compared to the conventional approach of simply cascading two stages of AF-AOTFs to produce the same stopband, the proposed filter has improved the tunability of stopband.
Continuous Loop Double Endobutton Reconstruction for Acromioclavicular Joint Dislocation (2015)

Excellent results were obtained and maintained over long-term follow-up. The continuous loop device eliminated the possibility of knot slippage or breakage. MRI confirmed a robust healing response. The described technique resulted in outcomes that were significantly superior to historical reports of nonsurgical outcomes, and the technique can be recommended both for acute and chronic dislocations.
RobotSculptor: Artist-Directed Robotic Sculpting of Clay (2020)

We present an interactive design system that allows users to create sculpting styles and fabricate clay models using a standard 6-axis robot arm. Given a general mesh as input, the user iteratively selects sub-areas of the mesh through decomposition and embeds the design expression into an initial set of toolpaths by modifying key parameters that affect the visual appearance of the sculpted surface finish. These parameters were identified and extracted through a series of design experiments, using a customized loop tool to cut the water-based clay material. The initialized toolpaths are fed into the optimization component of our system afterwards for optimal path planning, aiming to find the robotic sculpting motions that match the target surface, maintaining the design expression, and resolving collisions and reachability issues. We demonstrate the versatility of our approach by designing and fabricating different sculpting styles over a wide range of clay models.
AutoCLEM: An Automated Workflow for Correlative Live-Cell Fluorescence Microscopy and Cryo-Electron Tomography (2019)

Correlative light and electron microscopy (CLEM) combines the strengths of both light and electron imaging modalities and enables linking of biological spatiotemporal information from live-cell fluorescence light microscopy (fLM) to high-resolution cellular ultra-structures from cryo-electron microscopy and tomography (cryoEM/ET). This has been previously achieved by using fLM signals to localize the regions of interest under cryogenic conditions. The correlation process, however, is often tedious and time-consuming with low throughput and limited accuracy, because multiple correlation steps at different length scales are largely carried out manually. Here, we present an experimental workflow, AutoCLEM, which overcomes the existing limitations and improves the performance and throughput of CLEM methods, and associated software. The AutoCLEM system encompasses a high-speed confocal live-cell imaging module to acquire an automated fLM grid atlas that is linked to the cryoEM grid atlas, followed by cryofLM imaging after freezing. The fLM coordinates of the targeted areas are automatically converted to cryoEM/ET and refined using fluorescent fiducial beads. This AutoCLEM workflow significantly accelerates the correlation efficiency between live-cell fluorescence imaging and cryoEM/ET structural analysis, as demonstrated by visualizing human immunodeficiency virus type 1 (HIV-1) interacting with host cells.
Predictive Calculation of Neutral Beam Heating Plasmas in EAST Tokamak by NUBEAM Code for Certain Parameter Ranges (2010)

A predictive calculation is carried out for neutral beam heating of fusion plasmas in EAST by using NUBEAM code under certain plasma conditions. Results calculated are analyzed for different plasma parameters. Relations between major plasma parameters, such as density and temperature, are obtained and key physical processes in the neutral beam heating, including beam power deposition, trapped fraction, heating efficiency, and power loss, are simulated. Other physical processes, such as current-drive, toroidal rotation and neutron emission, are also discussed.
Creation of 3D Multi-Body Orthodontic Models by Using Independent Imaging Sensors (2013)

In the field of dental health care, plaster models combined with 2D radiographs are widely used in clinical practice for orthodontic diagnoses. However, complex malocclusions can be better analyzed by exploiting 3D digital dental models, which allow virtual simulations and treatment planning processes. In this paper, dental data captured by independent imaging sensors are fused to create multi-body orthodontic models composed of teeth, oral soft tissues and alveolar bone structures. The methodology is based on integrating Cone-Beam Computed Tomography (CBCT) and surface structured light scanning. The optical scanner is used to reconstruct tooth crowns and soft tissues (visible surfaces) through the digitalization of both patients' mouth impressions and plaster casts. These data are also used to guide the segmentation of internal dental tissues by processing CBCT data sets. The 3D individual dental tissues obtained by the optical scanner and the CBCT sensor are fused within multi-body orthodontic models without human supervisions to identify target anatomical structures. The final multi-body models represent valuable virtual platforms to clinical diagnostic and treatment planning.
Building a Fine-Grained Entity Typing System Overnight for a New X (X = Language, Domain, Genre) (2016)

Recent research has shown great progress on fine-grained entity typing. Most existing methods require pre-defining a set of types and training a multi-class classifier from a large labeled data set based on multi-level linguistic features. They are thus limited to certain domains, genres and languages. In this paper, we propose a novel unsupervised entity typing framework by combining symbolic and distributional semantics. We start from learning general embeddings for each entity mention, compose the embeddings of specific contexts using linguistic structures, link the mention to knowledge bases and learn its related knowledge representations. Then we develop a novel joint hierarchical clustering and linking algorithm to type all mentions using these representations. This framework doesn't rely on any annotated data, predefined typing schema, or hand-crafted features, therefore it can be quickly adapted to a new domain, genre and language. Furthermore, it has great flexibility at incorporating linguistic structures (e.g., Abstract Meaning Representation (AMR), dependency relations) to improve specific context representation. Experiments on genres (news and discussion forum) show comparable performance with state-of-the-art supervised typing systems trained from a large amount of labeled data. Results on various languages (English, Chinese, Japanese, Hausa, and Yoruba) and domains (general and biomedical) demonstrate the portability of our framework.
Nitrogen dioxide, sulfur dioxide, and ammonia detector for remote sensing of vehicle emissions (2006)

A remote sensor for measuring on-road vehicles passing the sensor in real time is described. This sensor expands upon previous technology that measured carbon monoxide, carbon dioxide, and exhaust hydrocarbons in the IR and nitric oxide in the UV. The design adds the capability to measure nitrogen dioxide in the UV with one spectrometer and to measure SO2 and NH3 along with NO in a second UV spectrometer. With these units operating side by side, the major mobile source precursors to secondary aerosol production can be measured simultaneously and in real time. Detection limits for NO2, SO2, and NH3 are 1.2, 0.72, and 0.78 g pollutant per kilogram of fuel, respectively.
Effects of Airfoil’s Polar Data in the Stall Region on the Estimation of Darrieus Wind Turbine Performance (2016)

Interest in vertical-axis wind turbines (VAWTs) is experiencing a renaissance after most major research projects came to a standstill in the mid 90’s, in favour of conventional horizontal-axis turbines (HAWTs). Nowadays, the inherent advantages of the VAWT concept, especially in the Darrieus configuration, may outweigh their disadvantages in specific applications, like the urban context or floating platforms. To enable these concepts further, efficient, accurate, and robust aerodynamic prediction tools and design guidelines are needed for VAWTs, for which low-order simulation methods have not reached yet a maturity comparable to that of the Blade Element Momentum Theory for HAWTs’ applications. The two computationally efficient methods that are presently capable of capturing the unsteady aerodynamics of Darrieus turbines are the Double Multiple Streamtubes (DMS) Theory, based on momentum balances, and the Lifting Line Theory (LLT) coupled to a free vortex wake model. Both methods make use of tabulated lift and drag coefficients to compute the blade forces. Since the incidence angles range experienced by a VAWT blade is much wider than that of a HAWT blade, the accuracy of polars in describing the stall region and the transition towards the “thin plate like” behaviour has a large effect on simulation results. This paper will demonstrate the importance of stall and post-stall data handling in the performance estimation of Darrieus VAWTs. Using validated CFD simulations as a baseline, comparisons are provided for a blade in VAWT-like motion based on a DMS and a LLT code employing three sets of post-stall data obtained from a wind tunnel campaign, XFoil predictions extrapolated with the Viterna-Corrigan model and a combination of them. The polar extrapolation influence on quasi-steady operating conditions is shown and azimuthal variations of thrust and torque are compared for exemplary tip-speed ratios (TSRs). In addition, the major relevance of a proper dynamic stall model into both simulation methods is highlighted and discussed.
A Cylindricity Error Evaluation Algorithm Based on Mechanical Thinking (2018)

When using photogrammetric method to measure axial forgings, it is impossible to measure the points' coordinates of the same section or spiral line, so the conventional method to evaluate the cylindricity error can't be used. In this paper, a cylindricity error evaluation algorithm based on mechanical thinking is proposed. The measurement points which are near the same shaft parts are divided into a group and projected onto the fitting surface of the bottom of shaft parts. Each group of projected points can do ellipse fitting to obtained the center coordinates. The initial axis equation is obtained through two sets of point coordinates which are the mean value of the coordinates obtained on the bottom surface. Different from grid method and genetic algorithm, the optimal axis equation is obtained by adjusting the axis equation in the corresponding direction based on the mechanical thought and the operation speed is accelerated by changing step length. Experimental results show that this method is equivalent to the traditional measurement method, besides it's simple and efficient without tedious process on measuring the points.
Newborns Develop a Th1-Type Immune Response to Mycobacterium bovis Bacillus Calmette-Guerin Vaccination (1999)

Data obtained in animals indicate that neonatal immune responses are biased toward Th2. This could reduce the efficacy of vaccines against viral and mycobacterial diseases. The ability of human newborns to develop a Th1 immune response upon immunization has not been studied. Since the vaccine Mycobacterium bovis bacillus Calmette-Guérin (BCG) triggers a Th1-type response in adults, we investigated whether it induces a similar response in newborns and whether age at vaccination influences immunogenicity. We found that BCG vaccination at birth induces a memory Th1-type response of similar magnitude to that when given later in life. This study demonstrates that human newborns can be immunized against pathogens controlled by a Th1 immune response.
Generation of synthetic microstructures containing casting defects: a machine learning approach (2023)

This paper presents a new strategy to generate synthetic samples containing casting defects. Four samples of Inconel 100 containing casting defects such as shrinkages and pores have been characterized using X-ray tomography and are used as reference for this application. Shrinkages are known to be tortuous in shape and more detrimental for the mechanical properties of materials, especially metal fatigue, whereas pores can be of two types: broken shrinkage pores with arbitrary shape and gaseous pores of spherical shape. For the generation of synthetic samples, an integrated module of Spatial Point Pattern (SPP) analysis and deep learning techniques such as Generative Adversarial Networks (GANs) and Convolutional Neural Networks (CNNs) are used. The SPP analysis describes the spatial distributions of casting defects in material space, whereas GANs and CNNs generate a defect of arbitrary morphology very close to real defects. SPP analysis reveals the existence of two different void nucleation mechanisms during metal solidification associated to shrinkages and pores. Our deep learning model successfully generates casting defects with defect size ranging from 100 µm to 1.5 mm and of very realistic shapes. The entire synthetic microstructure generation process respects the global defect statistics of reference samples and the generated samples are validated by statistically comparing with real samples.
Comparative Histopathological Analysis of Mitral Valves in Barlow Disease and Fibroelastic Deficiency (2016)

Whether Barlow disease (BD) and fibroelastic deficiency (FED), the main causes of mitral valve prolapse (MVP), should be considered 2 distinct diseases remains unknown. Mitral valves from patients who required surgery for severe mitral regurgitation due to degenerative nonsyndromic MVP were analyzed. Intraoperative diagnosis of BD or FED was based on leaflet redundancy and thickness, number of segments involved, and annular dimension. The removed medial scallop of the posterior leaflet and attached chordae were used for histopathological and immunohistological assessment. Histologically, compared to normal controls (n = 3), BD (n = 14), and FED (n = 9) leaflets demonstrated an altered architecture and increased thickness. Leaflet thickness was greater and chordae thickness lower in BD than FED (P < 0.0001). In BD, increased thickness was owing to spongiosa expansion (proteoglycan accumulation) and intimal thickening on fibrosa and atrialis; in FED, local thickening was predominant on the fibrosa side, with accumulation of proteoglycan-like material around the chordae. Collagen accumulation was observed in FED leaflets and chords and decreased in BD. Fragmented elastin fibers were present in BD and FED; elastin decreased in BD but increased in FED leaflets and around chordae. Activated myofibroblasts accumulate in both diseased leaflets and chords, but more abundantly in FED chordae (P < 0.0001), independently of age, suggesting a role of these cells in chordal rupture. There were more CD34-positive cells in BD leaflets and in FED chordae (P < 0.01). In BD leaflets (but not chordae) proliferative Ki67-positive cells were more abundant (P < 0.01) and matrix metalloproteinase 2 levels were increased (P < 0.01) indicating tissue remodeling. Upregulation of transforming growth factor beta and pERK signaling pathways was evident in both diseases but more prominent in FED leaflets (continued on next page)(P < 0.001), with pERK upregulation in FED chordae (P < 0.0001). Most cellular and signaling markers were negligible in control valves. Quantitative immunohistopathological analyses demonstrated distinct changes between BD and FED valves: predominant matrix degradation in BD and increased profibrotic signaling pathways in FED, indicating that BD and FED are 2 different entities. These results may pave the way for genetic studies of MVP and development of preventive drug therapies.
A programmable focal-plane MIMD image processor chip (2001)

An 80/spl times/78 pixels vision chip for focal-plane image processing is presented. The chip employs a Multiple-Instruction-Multiple-Data (MIMD) architecture to provide five spatially processed images in parallel. The size, configuration, and coefficients of the spatial kernels are programmable. The chip's architecture allows the photoreceptor cells to be small and parked densely by performing all computations on the read-out, away from the array. The processing core uses digitally programmed current-mode analog computation. Operating at 9.6 K frames/s in 800-lux ambient light, the chip consumes 4 mW from a 2.5-V power supply. Performing 11/spl times/11 spatial convolutions, an equivalent computation (5.5 bit scale-accumulate) rate of 12.4 GOPS/mW is achieved using 22 mm/sup 2/ in a 1.2-/spl mu/m CMOS process. The application of the chip to line-segment orientation detection is also presented.
The flagella of enteropathogenicEscherichia colimediate adherence to epithelial cells (2002)

Enteropathogenic Escherichia coli (EPEC) utilizes a type III protein secretion system to target effector molecules into the host cell leading to effacement of the intestinal mucosa. This secretion apparatus shares many structural features of the flagellar type III export system involved in flagella assembly and motility. We report here that fliC insertional mutants constructed in two wild-type EPEC strains were markedly impaired in adherence and microcolony formation on cultured cells. An E. coli K-12 strain harbouring the EPEC H6 fliC gene on a plasmid showed discrete adhering clusters on HeLa cells, albeit to less extent than the wild-type EPEC strain. Flagella purified from EPEC bound to cultured epithelial cells and antiflagella antibodies blocked adherence of several EPEC serotypes. We determined that eukaryotic cells in culture stimulate expression of flagella by motile and non-motile EPEC. Isogenic strains mutated in perA (a transcriptional activator), bfpA (a type IV pilin), luxS (a quorum-sensing autoinducer gene) and in the type III secretion genes were reduced for motility in Dulbecco's modified Eagle medium (DMEM) motility agar and produced none or few flagella when associated with epithelial cells. Growth of these mutants in preconditioned tissue culture medium restored motility and their ability to produce flagella, suggesting the influence of a signal provided by mammalian cells that triggers flagella production. This study shows for the first time that the flagella of EPEC are directly involved in the adherence of these bacteria and supports the existence of a molecular relationship between the two existing type III secretion pathways of EPEC, the EPEC adherence factor (EAF) plasmid-encoded regulator, quorum sensing and epithelial cells.
A Comparison of the Results of Total Hip and Knee Arthroplasty Performed on a Teaching Service or a Private Practice Service (2007)

Teaching and active participation from residents and fellows during total hip and total knee arthroplasty did not have a detrimental effect on the early clinical results, except for a longer surgical time.
Missing sensor value estimation method for participatory sensing environment (2014)

Participatory sensing produces incomplete sensor data. Thus, we have to fill in the gaps of any missing values in the sensor data in order to provide sensor-based services. We propose a method to estimate a missing value of incomplete sensor data. It accurately estimates a missing value by repeating two processes: selecting sensors locally correlated with the sensor that includes the missing value and then updating the training sensor dataset that consist of data from the selected sensors available for multiple regression. This procedure effectively helps to find more suitable neighbor records of a query record from the training sensor dataset and to refine the regression model using the records. It overcomes three problems that other estimation methods have: a decrease in the amount of available training sensor dataset due to missing values, the difficulty in finding similar records of a query due to the “curse of dimensionality,” and the complexity in formalizing the estimation model due to “overfitting.” The main feature of our method is the way it repeatedly prunes inessential sensors while exploiting the anti-monotone property in which the training sensor dataset R' that consist of the sensors V' ⊂ V is larger than the data R that consist of V. Empirical evaluations done using public datasets in which we appended missing values show that our method increases the training sensor dataset for estimation and improves estimation accuracy through repeated sensor selections. Furthermore, we confirmed through a field trial and a life-log enrichment trial, that our method was effective for estimating missing sensor values in a participatory sensing environment.
Efficient Energy-Optimal Routing for Electric Vehicles (2011)

Traditionally routing has focused on finding shortest paths in networks with positive, static edge costs representing the distance between two nodes. Energy-optimal routing for electric vehicles creates novel algorithmic challenges, as simply understanding edge costs as energy values and applying standard algorithms does not work. First, edge costs can be negative due to recuperation, excluding Dijkstra-like algorithms. Second, edge costs may depend on parameters such as vehicle weight only known at query time, ruling out existing preprocessing techniques. Third, considering battery capacity limitations implies that the cost of a path is no longer just the sum of its edge costs. This paper shows how these challenges can be met within the framework of A* search. We show how the specific domain gives rise to a consistent heuristic function yielding an O(n2) routing algorithm. Moreover, we show how battery constraints can be treated by dynamically adapting edge costs and hence can be handled in the same way as parameters given at query time, without increasing run-time complexity. Experimental results with real road networks and vehicle data demonstrate the advantages of our solution.