gebhart/patrepeval huggingface dataset:
Su1294 Computed Tomography Enterography Versus Magnetic Resonance Enterography for Assessment of Disease Activity and Complications in Small Bowel Crohn's Disease: A Meta-Analysis of Head-to-Head Comparative Studies (2014)

Introduction. Infliximab has led to new therapeutic goals in Crohn's disease (CD) such as complete mucosal healing and improvement of quality of life. The current standard for assessing mucosal healing is endoscopy. However, frequent assessments are costly and uncomfortable to the patient. Non-invasive, accurate surrogate serum markers would therefore be welcomed to aid clinicians in predicting mucosal healing.Methods. In a retrospective study, 119 CD patients who started infliximab and who underwent serial endoscopies (before and during infliximab) were included. Serum samples were available at the time of endoscopy and levels of markers were correlated with the degree of healing (not healed, marked improvement or complete healing). Thirty-five biomarkers were measured in 181 serum samples with the use of CEER, a proprietary highly sensitive protein micro-array, or homogenous mobility shift assays (Prometheus Laboratories Inc., San Diego, CA). These markers included growth and repair factors, pro -and anti-inflammatory markers and the IBD SGI serology panel. Infliximab and antibodies to infliximab were also measured. Clinical information regarding age at sampling, gender, age at diagnosis, location of disease, anal involvement and previous surgery was included. For statistical analysis SPSS and R were used. Results. From the 119 CD patients, 64 CD patients showed complete healing with no relapse, whereas 55 CD patients never showed mucosal healing. Univariate analyses indicated that age and 12 serum markers (HGF, BTC, TWEAK, CRP, ICAM, SAA, VCAM, IL-2, IL-8, IFN-γ, IL-6 and IL-10) were significantly associated with mucosal healing (p 11.44 CU/ml, TWEAK>20.62 CU/ml and VCAM<4200 μg/ml) which resulted in a significant and gradual increased prediction of mucosal healing (Figure 1, linear-by-linear p<0.001). Conclusion. We have identified 1 clinical parameter and 4 serum markers as independent predictors of mucosal healing. All serum markers play a role in the pathogenic mechanisms of CD. HGF has a central role in angiogenesis and tissue regeneration, BTC is a member of the EGF family of growth factors, TWEAK is a cytokine that has overlapping signaling functions with TNF and VCAM is a cell-adhesion molecule. The combined biomarker panel could facilitate prediction of mucosal healing in the future.
Potent and Orally Efficacious Bisthiazole-Based Histone Deacetylase Inhibitors (2014)

Inspired by the thiazole-thiazoline cap group in natural product largazole, a series of structurally simplified bisthiazole-based histone deacetylase inhibitors were prepared and evaluated. Compound 8f was evaluated in vivo in an experimental autoimmune encephalomyelitis (EAE) model and found to be orally efficacious in ameliorating clinical symptoms of EAE mice.
Deep neural network using trainable activation functions (2016)

This paper proposes trainable activation functions for deep neural network (DNN). A DNN is a feed-forward neural network composed of more than one hidden nonlinear layer. It is characterized by a set of weight matrices, bias vectors, and a nonlinear activation function. In model parameter training, weight matrices and bias vectors are updated using an error back-propagation algorithm but activation functions is not. It is just fixed empirically. Many rectifier-type nonlinear functions have been proposed as activation functions, but the best nonlinear functions for any given task domain remain unknown. In order to address the issue, we propose a trainable activation function. In the proposed approach, conventional nonlinear activation functions were approximated for a Taylor series, and the coefficients were retrained simultaneously with other parameters. The effectiveness of the proposed approach was evaluated for MNIST handwritten digit recognition domain.
Nature: A rich source for developing multifunctional agents. tumor‐imaging and photodynamic therapy (2006)

The purpose of this review is to call attention in the use of chlorophyll-a and bacteriochlorophyll-a to develop more than 600 photosensitizers (lambda (max) 660 nm-800 nm) during the last 15 years (1990-2005) at the Photodynamic Therapy Center, Roswell Park Cancer Institute, Buffalo. This article mainly includes the chemistry, preclinical results, and brief clinical data of some of the most effective photosensitizers. The utility of the tumor-avid photosensitizers in developing multimodality agents (imaging and therapy) is also presented.
Diff-Index: Differentiated Index in Distributed Log-Structured Data Stores (2014)

Log-Structured-Merge (LSM) Tree gains much attention recently because of its superior performance in write-intensive workloads. LSM Tree uses an append-only structure in memory to achieve low write latency; at memory capacity, in-memory data are flushed to other storage media (e.g. disk). Consequently, read access is slower comparing to write. These specific features of LSM, including no in-place update and asymmetric read/write performance raise unique challenges in index maintenance for LSM. The structural difference between LSM and B-Tree also prevents mature B-Tree based approaches from being directly applied. To address the issues of index maintenance for LSM, we propose Diff-Index to support a spectrum of index maintenance schemes to suit different objectives in index consistency and performance. The schemes consist of sync-full, sync-insert, async-simple and async-session. Experiments on our HBase implementation quantitatively demonstrate that Diff-Index offers various performance/consistency balance and satisfactory scalability while avoiding global coordination. Syncinsert and async-simple can reduce 60%-80% of the overall index update latency when compared to the baseline syncfull ; async-simple can achieve superior index update performance with an acceptable inconsistency. Diff-Index exploits LSM features such as versioning and the flush-compact process to achieve goals of concurrency control and failure ∗Work done while author was at IBM Almaden Research Center. †Work done while author was an intern at IBM T. J. Watson Research Center. (c) 2014, Copyright is with the authors. Published in Proc. EDBT on OpenProceedings.org. Distribution of this paper is permitted under the terms of the Creative Commons license CC-by-nc-nd 4.0. recovery with low complexity and overhead. Diff-Index is included in IBM InfoSphere BigInsights, an IBM big data offering.
Insecticidal Activity of EG 4961, a Novel Strain of Bacillus Thuringiensis Toxic to Larvae and Adults of Southern Corn Rootworm (Coleoptera: Chrysomelidae) and Colorado Potato Beetle (Coleoptera: Chrysomelidae) (1993)

Journal Article Insecticidal Activity of EG 4961, a Novel Strain of Bacillus Thuringiensis Toxic to Larvae and Adults of Southern Corn Rootworm (Coleoptera: Chrysomelidae) and Colorado Potato Beetle (Coleoptera: Chrysomelidae) Get access Timothy B. Johnson, Timothy B. Johnson Ecogen Inc., 2005 W. Cabot Blvd., Langhorne, PA 19047 Search for other works by this author on: Oxford Academic PubMed Google Scholar Annette C. Slaney, Annette C. Slaney Ecogen Inc., 2005 W. Cabot Blvd., Langhorne, PA 19047 Search for other works by this author on: Oxford Academic PubMed Google Scholar William P. Donovan, William P. Donovan Ecogen Inc., 2005 W. Cabot Blvd., Langhorne, PA 19047 Search for other works by this author on: Oxford Academic PubMed Google Scholar Mark J. Rupar Mark J. Rupar Ecogen Inc., 2005 W. Cabot Blvd., Langhorne, PA 19047 Search for other works by this author on: Oxford Academic PubMed Google Scholar Journal of Economic Entomology, Volume 86, Issue 2, 1 April 1993, Pages 330–333, https://doi.org/10.1093/jee/86.2.330 Published: 01 April 1993 Article history Received: 06 January 1992 Accepted: 22 October 1992 Published: 01 April 1993
Modeling, Simulation and Comparison of Models for Wormhole Formation During Matrix Stimulation of Carbonates (2002)

Abstract A new averaged/continuum model is presented for simulation of wormhole formation during matrix stimulation of carbonates. The model presented here differs from existing literature models in three fundamental aspects. First, we show that the dissolution process creates a Darcy velocity field with non-zero divergence. Second, we use two concentration variables to account for the local gradients at the pore level caused by the coupling between the flow, species diffusion and chemical reaction. Third, we account for both the asymptotic/diffusive and convective contributions to the local mass transfer coefficient between the fluid and solid. We argue that models that do not account for these effects do not retain the qualitative features of the reactive dissolution process and hence cannot be predictive. The averaged model developed here accounts for pore level physics by coupling the local pore scale phenomena to the macroscopic variables (Darcy velocity, pressure and reactant cup-mixing concentration) through the structure-property relationships (permeability-porosity, average pore size-porosity and interfacial area-porosity), and the dependence of the fluid-solid mass transfer coefficient and fluid phase dispersion coefficient on the evolving pore scale variables (average pore size and local Reynolds and Schmidt numbers). A preliminary analysis of the model is presented and the influence of various factors on flow channeling is examined using the new model. The model predictions are compared with the available laboratory data.
Very low bit rate video coding using morphological segmentation and contour/texture motion compensation (2002)

This paper describes a segmentation-based coding algorithm for very low bit rate. The algorithm involves a segmentation relying on a time recursive morphological segmentation technique. It extracts both large and contrasted regions. Then, a simple region-based motion estimation is performed. Finally, the sequence is coded by contour-texture motion compensation. The proposed method leads to very low bit rates while being able to represent the meaningful regions of the scene. Moreover, it makes no assumption about the scene content and can be used for any sequence.
<i>Pseudomonas syringae</i> Hrp type III secretion system and effector proteins (2000)

Pseudomonas syringae is a member of an important group of Gram-negative bacterial pathogens of plants and animals that depend on a type III secretion system to inject virulence effector proteins into host cells. In P. syringae, hrp/hrc genes encode the Hrp (type III secretion) system, and avirulence (avr) and Hrp-dependent outer protein (hop) genes encode effector proteins. The hrp/hrc genes of P. syringae pv syringae 61, P. syringae pv syringae B728a, and P. syringae pv tomato DC3000 are flanked by an exchangeable effector locus and a conserved effector locus in a tripartite mosaic Hrp pathogenicity island (Pai) that is linked to a tRNA(Leu) gene found also in Pseudomonas aeruginosa but without linkage to Hrp system genes. Cosmid pHIR11 carries a portion of the strain 61 Hrp pathogenicity island that is sufficient to direct Escherichia coli and Pseudomonas fluorescens to inject HopPsyA into tobacco cells, thereby eliciting a hypersensitive response normally triggered only by plant pathogens. Large deletions in strain DC3000 revealed that the conserved effector locus is essential for pathogenicity but the exchangeable effector locus has only a minor role in growth in tomato. P. syringae secretes HopPsyA and AvrPto in culture in a Hrp-dependent manner at pH and temperature conditions associated with pathogenesis. AvrPto is also secreted by Yersinia enterocolitica. The secretion of AvrPto depends on the first 15 codons, which are also sufficient to direct the secretion of an Npt reporter from Y. enterocolitica, indicating that a universal targeting signal is recognized by the type III secretion systems of both plant and animal pathogens.
Terabit/sec-class board-level optical interconnects through polymer waveguides using 24-channel bidirectional transceiver modules (2011)

We report here on the design, fabrication and characterization of an integrated optical data bus designed for terabit/sec-class module-to-module on-board data transfer using integrated optical transceivers. The parallel optical transceiver is based on a through-silicon-via (TSV) silicon carrier as the platform for integration of 24-channel VCSEL and photodiode arrays with CMOS ICs. The Si carrier also includes optical vias (holes) for optical access to conventional surface-emitting 850-nm optoelectronic (OE) devices. The 48-channel transceiver is flip-chip soldered to an organic carrier forming the transceiver Optomodule. The optical printed circuit board (o-PCB) is a typical FR4 board with a polymer waveguide layer added on top. A 48-channel flex-waveguide is fabricated separately and attached to the FR4 board. Turning mirrors are fabricated into the waveguides and a lens array is attached to facilitate optical coupling. An assembly procedure has been developed to surface mount the Optomodule to the o-PCB using a ball grid array (BGA) process which provides both electrical and optical interconnections. Efficient optical coupling is achieved using a dual-lens optical system, with one lens array incorporated into the Optomodule and a second on the o-PCB. Fully functional Optomodules with 24 transmitter + 24 receiver channels were characterized with transmitters operating up to 20 Gb/s and receivers up to 15 Gb/s. Finally, two Optomodules were assembled onto an o-PCB and a full optical link demonstrated, achieving >; 20 bidirectional links at 10 Gb/s. At 15 Gb/s, error-free operation was demonstrated for 15 channels in each direction, realizing a record o-PCB link with a 225 Gb/s bidirectional aggregate data rate.
RF-Interrogated End-State Chip-Scale Atomic Clock (2007)

A chip-scale atomic clock implemented with end-state physics has been fabricated and characterized. Batch-fabricated components were specifically designed and developed to enable integration within a small form-factor package. The full physics package, implemented with CW VCSEL optical pump, direct end-state hyperfine RF and Zeeman interrogation for magnetic field stabilization, was demonstrated within a 4 cm3 volume, consuming 25 mW of power, and exhibiting an Allan deviation stability. In addition, end-state signal contrast exceeded 40% from millimeter-scale vapor cells with buffer-gas pressures exceeding 2.5 atmospheres, demonstrating the route to submillimeter vapor-cells within high-performance CSACs for high shock/vibration environments.
Convolutive blind source separation based on multiple decorrelation (2002)

Acoustic signals recorded simultaneously in a reverberant environment can be described as sums of differently convolved sources. The task of source separation is to identify the multiple channels and possibly to invert those in order to obtain estimates of the underlying sources. We tackle the problem by explicitly exploiting the nonstationarity of the acoustic sources. Changing cross-correlations at multiple times give a sufficient set of constraints for the unknown channels. A least squares optimization allows us to estimate a forward model, identifying thus the multipath channel. In the same manner we can find an FIR backward model, which generates well separated model sources. Under certain conditions we obtain up to 14 dB signal enhancement in a real room environment.
Active common mode cancellation (2018)

This paper introduces a new way of implementing an Active Common Mode Cancellation filter for removal of common mode signals, generated by inverter dv/dt, in order to reduce conducted emission and bearing currents. it can be applied to all fast switching power applications. This paper focuses on the application case of drive trains for electric or hybrid electric vehicles but the concept is not limited to.
Chemically resistant and thermally stable quantum dots prepared by shell encapsulation with cross-linkable block copolymer ligands (2020)

Abstract Endowing quantum dots (QDs) with robustness and durability have been one of the most important issues in this field, since the major limitations of QDs in practical applications are their thermal and oxidative instabilities. In this work, we propose a facile and effective passivation method to enhance the photochemical stability of QDs using polymeric double shell structures from thiol-terminated poly(methyl methacrylate- b -glycidyl methacrylate) (P(MMA- b -GMA)-SH) block copolymer ligands. To generate a densely cross-linked network, the cross-linking reaction of GMA epoxides in the PGMA block was conducted using a Lewis acid catalyst under an ambient environment to avoid affecting the photophysical properties of the pristine QDs. This provides QDs encapsulated with robust double layers consisting of highly transparent PMMA outer-shell and oxidation-protective cross-linked inner shell. Consequently, the resulting QDs exhibited exceptional tolerance to heat and oxidants when dispersed in organic solvents or QD-nanocomposite films, as demonstrated under various harsh conditions with respect to temperature and oxidant species. The present approach not only provides simple yet effective chemical means to enhance the thermochemical stability of QDs, but also offers a promising platform for the hybridization of QDs with polymeric materials for developing robust light-emitting or light-harvesting devices.
Case History of Using Integrated Reservoir Modeling Workflow for Tight Gas Reservoirs (2013)

Abstract As the demand for energy increases, more and more low-permeability reservoirs are being developed with the help of advancements in hydraulic fracturing and horizontal drilling technologies. Integrated reservoir modeling studies become increasingly important to understand and improve reservoir management of such reservoirs for optimum depletion planning. This paper presents the approach used for applying an integrated reservoir modeling workflow to the tight gas sands of the Cotton Valley reservoir. The main objective of the study is to understand well performance for horizontal infill wells with multiple hydraulic fractures. In order to accurately simulate gas flow in hydraulically fractured wells (HFW) in full-field or regional models of unconventional gas reservoirs with many HFW, it is critical to appropriately represent these wells in the simulation models. Various methods have been used in the industry to numerically simulate hydraulic fractures in large reservoir models. In this paper, we will also review these methods and show that almost all the methods require calibration with fine grid models in which the hydraulic fracture is explicitly gridded. For homogeneous models calibration is relatively easy, but it is almost impossible for heterogeneous models. Therefore, we used local grid refinement (LGR) as the solution for modeling hydraulically fractured wells in coarse grid simulation. Our approach is different than other LGR approaches presented in the literature in that we only refine the coarse gridblocks that contain the fractures and wells. Finally, since it is very time consuming to generate LGRs manually for models with many wells a software tool was developed to generate LGR gridding automatically for HFW for commercial simulators.
Generation of Induced Pluripotent Stem Cells from Urine (2011)

Forced expression of selected transcription factors can transform somatic cells into embryonic stem cell (ESC)-like cells, termed induced pluripotent stem cells (iPSCs). There is no consensus regarding the preferred tissue from which to harvest donor cells for reprogramming into iPSCs, and some donor cell types may be more prone than others to accumulation of epigenetic imprints and somatic cell mutations. Here, we present a simple, reproducible, noninvasive method for generating human iPSCs from renal tubular cells present in urine. This procedure eliminates many problems associated with other protocols, and the resulting iPSCs display an excellent ability to differentiate. These data suggest that urine may be a preferred source for generating iPSCs.
Generation of longer cDNA fragments from serial analysis of gene expression tags for gene identification (2000)

We have developed a technique called the generation of longer cDNA fragments from serial analysis of gene expression (SAGE) tags for gene identification (GLGI), to convert SAGE tags of 10 bases into their corresponding 3' cDNA fragments covering hundred bases. A primer containing the 10-base SAGE tag is used as the sense primer, and a single base anchored oligo(dT) primer is used as an antisense primer in PCR, together with Pfu DNA polymerase. By using this approach, a cDNA fragment extending from the SAGE tag toward the 3' end of the corresponding sequence can be generated. Application of the GLGI technique can solve two critical issues in applying the SAGE technique: one is that a longer fragment corresponding to a SAGE tag, which has no match in databases, can be generated for further studies; the other is that the specific fragment corresponding to a SAGE tag can be identified from multiple sequences that match the same SAGE tag. The development of the GLGI method provides several potential applications. First, it provides a strategy for even wider application of the SAGE technique for quantitative analysis of global gene expression. Second, a combined application of SAGE/GLGI can be used to complete the catalogue of the expressed genes in human and in other eukaryotic species. Third, it can be used to identify the 3' cDNA sequence from any exon within a gene. It can also be used to confirm the reality of exons predicted by bioinformatic tools in genomic sequences. Fourth, a combined application of SAGE/GLGI can be applied to define the 3' boundary of expressed genes in the genomic sequences in human and in other eukaryotic genomes.
Triboelectric nanogenerators as flexible power sources (2017)

Abstract The triboelectric nanogenerator (TENG) as a new power-generation technology was reported by Wang and co-workers in 2012. Because of its great potential for scavenging mechanical energy from living environment and sustainably driving portable devices, many researchers have developed various methods to improve output performances of TENG. In this paper, we review the progress in TENG made as flexible power sources by integrating flexible materials and stretching structures, especially for the applications of flexible electronics. For optimizing performances of TENG, the structural designs, material selections, and hybrid energy cells are presented. The reported TENG as flexible power sources has the potential applications in lighting up light emitting diodes (LEDs), powering sensors, and monitoring biomechanical motions.
Towards predictor, quantizer and entropy coder optimality in scalable video coding (2012)

A novel coding paradigm is proposed to jointly optimize the prediction, quantization, and entropy coding modules, thereby approaching optimality in scalable video coding. It departs from conventional video coding schemes that consider prediction, transformation, quantization, and entropy coding, as largely separate sequential functional components. The method draws inspiration from an early estimation-theoretic approach, developed by our group for enhancement layer prediction, which efficiently combines all the information available to the enhancement layer coder, to produce the optimal prediction. The framework is significantly expanded here to also incorporate optimization of entropy-constrained quantization and arithmetic coding, while fully accounting for hitherto ignored relevant factors, inherent to predictive scalable coding, including information from the base layer quantization operation, and from the enhancement layer motion compensated reference. Experimental evidence is provided for substantial coding gains over conventional scalable video coding.