gebhart/patrepeval huggingface dataset:
Epithelial cell transcriptome of poorly and moderately differentiated prostate cancers (2006)

Proc Amer Assoc Cancer Res, Volume 47, 2006

826 

Introduction: The focus of the current study is to identify prostate cancer (CaP) associated gene expression signatures in specific cell types of the human prostate gland with a goal to define molecular targets/pathways involved in CaP progression. Here we report gene expression features of poorly differentiated (PD) and well differentiated (WD) prostate cancer cells and matched benign prostate epithelial cells. Tumor cell specific gene expression features were defined focusing on genes differentiating PD and WD prostate tumor cells. Such molecular targets have potential to define prognostic markers and biochemical pathways involved in CaP progression. Methods: Laser capture micro-dissected (LCM) epithelial cells from benign and malignant prostate glands of carefully selected CaP patients were analyzed by 80 Affymetrix HG U133 Plus 2.0 GeneChips. As a follow-up of our earlier study, we have further evaluated the expression patterns in paired benign and cancer epithelial cells from two patient groups (20 patients per group), one with “high risk” (HR) CaP (poorly differentiated tumor cells, Gleason score 8-9, PSA recurrence) and the other with “moderate risk” (MR) CaP (well to moderately differentiated tumor cells, Gleason score 6-7, no PSA recurrence). Genes differentially expressed between benign and tumor epithelium of HR and MR groups were analyzed for biochemical pathways/networks. Results: Prostate tumor cell specific expression alterations of genes involved in cancer and inflammatory pathways were highlighted by various bio-informatics approaches. Several genes that were differentially altered in tumor cells of MR groups were part of cell morphology and cell death pathways. Huntington-interacting protein-1 (Hip-1) interactor (Hippi) associating with HR specimens was among genes noted in two independent GeneChip experiments from our group. Hippi has also been implicated in apoptosis pathway. We have further analyzed the expression of Hippi in tumor and benign epithelial cells of 96 CaP patients by QRT-PCR. Hippi significantly discriminated CaP in HR group (up-regulated) from MR group (down-regulated). In addition, statistical analysis revealed a significant correlation of Hippi expression with Gleason sum (ANOVA, p=0.0006) and pathological T stage (T-test, p=0.0243). Conclusion: Our study defines gene expression signatures in benign and malignant prostate tissues that have potential to distinguish CaP with moderate and high risk progression. HIPPI , exhibited similar expression patterns in both GeneChip and QRT-PCR assays. The HIPPI protein interacts with HIP1, that was previously reported to be overexpressed in CaP with poor prognosis. Further evaluations of HR associated gene expression signatures have potential to define functional targets/pathways involved in CaP progression.
Engineering the underlying surface to manipulate the growth of 2D perovskites for highly efficient solar cells (2019)

High efficiency (12.78%) 2D perovskite solar cells are realized by engineering the substrate to manipulate the growth of 2D perovskites.
Wideband arrays using irregular (polyomino) shaped subarrays (2006)

Irregular polyomino-shaped subarrays are shown to provide a practical and effective means for introducing time delay into an array with phase steering. The elimination of quantisation lobes, with resulting peak sidelobes suppressed more than 14 dB below the quantisation lobes of an array of rectangular subarrays, is demonstrated.
Synchronized double-ended fault location algorithm for power distribution systems (2012)

This paper introduces a method for marine system fault location which uses the voltage and current transient information measured at a power supply point and the remote point beyond the fault location to estimate the fault position. The proposed algorithm is demonstrated by computer simulation and also a laboratory experimental test.
USF1 deficiency alleviates inflammation, enhances cholesterol efflux and prevents cholesterol accumulation in macrophages (2018)

Our findings identify USF1 as a novel factor regulating HDL functionality, showing that USF1 inactivation boosts cholesterol efflux, reduces macrophage inflammation and attenuates macrophage cholesterol accumulation, linking improved macrophage cholesterol metabolism and inflammatory pathways to the antiatherogenic function of USF1 deficiency.
Ocular Bioavailability of Ciprofloxacin in Sustained Release Formulations (2001)

A novel sustained release delivery system of ciprofloxacin for the eye was developed. The system consists of a viscosity enhancer (carbopol gel or hydroxypropylmethylcellulose solution) plus a penetration enhancer (dodecylmaltoside) to overcome penetration barriers and loss due to wash-out and thus achieve the desired ciprofloxacin ocular absorption. The present studies were designed to assess the ocular penetration and bioavailability of ciprofloxacin in sustained release formulations. In vitro studies in rabbits indicated an approximate 10-fold increase in drug penetration through the rabbit cornea using the penetration enhancer, dodecylmaltoside. In vivo bioavailability studies demonstrate that these formulations provided a long drug duration in the cornea. After administration of a single topical dose of ciprofloxacin (0.3%/30 microL), corneal levels greater than the Minimum Inhibitory Concentration (MIC90) (0.5 microg/g) were observed through eight hours. These sustained release formulations delivered 10-fold more drug into the aqueous humor than the standard solution formulation. Maximum ciprofloxacin concentrations in the aqueous humor (0.5-0.7 microg/mL) were attained between one and two hours after dosing. Using these sustained release formulations, ciprofloxacin can penetrate to the anterior chamber of the eye in concentrations that are inhibitory for most gram-negative and gram-positive organisms. These topical ocular formulations have prophylactic utility for prevention of post-surgical infection, offering greater efficacy and safety than currently available treatments.
Discovery and Structure−Activity Relationship of 3-Methoxy-<i>N</i>-(3-(1-methyl-1<i>H</i>-pyrazol-5-yl)-4-(2-morpholinoethoxy)phenyl)benzamide (APD791): A Highly Selective 5-Hydroxytryptamine<sub>2A</sub> Receptor Inverse Agonist for the Treatment of Arterial Thrombosis (2010)

Serotonin, which is stored in platelets and is released during thrombosis, activates platelets via the 5-HT(2A) receptor. 5-HT(2A) receptor inverse agonists thus represent a potential new class of antithrombotic agents. Our medicinal program began with known compounds that displayed binding affinity for the recombinant 5-HT(2A) receptor, but which had poor activity when tested in human plasma platelet inhibition assays. We herein describe a series of phenyl pyrazole inverse agonists optimized for selectivity, aqueous solubility, antiplatelet activity, low hERG activity, and good pharmacokinetic properties, resulting in the discovery of 10k (APD791). 10k inhibited serotonin-amplified human platelet aggregation with an IC(50) = 8.7 nM and had negligible binding affinity for the closely related 5-HT(2B) and 5-HT(2C) receptors. 10k was orally bioavailable in rats, dogs, and monkeys and had an acceptable safety profile. As a result, 10k was selected further evaluation and advanced into clinical development as a potential treatment for arterial thrombosis.
PREPARATION OF QUICK‐COOKING RICE PRODUCTS USING A CENTRIFUGAL FLUIDIZED BED (1976)

ABSTRACT This paper describes a process utilizing a centrifugal fluidized bed in the critical drying step to produce dry forms of quick‐cooking rice products using a minimum number of treatment steps. The process is very flexible and applicable to all rice varieties and grain sizes (long, medium, short and wild). High heat transfer rates used in the CFB drier result in a 5‐min drying cycle with control of texture and rehydration characteristics.
Water-Soluble, Meso-Substituted Cationic Porphyrins—a Family of Compounds for Cellular Delivery of Oligonucleotides (1999)

The delivery of oligonucleotides to appropriate intracellular compartments is crucial to their development as tools in gene function studies and as therapeutics. Here, we report the characterization of meso-substituted cationic porphyrins as a large class of water-soluble reagents for oligonucleotide delivery. These porphyrins form non-covalent complexes with single-stranded oligonucleotides and deliver these molecules into the nuclei of cell lines in culture. The porphyrins protect oligonucleotides from nuclease degradation, and delivery is unaffected by the presence of serum. Delivery capacity is dependent on the charge ratio and concentration of the oligonucleotide and porphyrin used to form the complex, on the chemical substituents of the oligonucleotide and on the identity of the cationic porphyrin. This class of molecules provides a versatile set of water-soluble delivery reagents that could contribute to the development of oligonucleotide drugs.
Conservative extraction of over-represented extensible motifs (2005)

Motivation: The discovery of motifs in biosequences is frequently torn between the rigidity of the model on the one hand and the abundance of candidates on the other. In particular, the variety of motifs described by strings that include 'don't care' (dot) patterns escalates exponentially with the length of the motif, and this gets only worse if a dot is allowed to stretch up to some prescribed maximum length. This circumstance tends to generate daunting computational burdens, and often gives rise to tables that are impossible to visualize and digest. This is unfortunate, as it seems to preclude precisely those massive analyses that have become conceivable with the increasing availability of massive genomic and protein data. Although a part of the problem is endemic, another part of it seems rooted in the various characterizations offered for the notion of a motif, that are typically based either on syntax or on statistics alone. It seems worthwhile to consider alternatives that result from a prudent combination of these two aspects in the model. Results: We introduce and study a notion of extensible motif in a sequence which tightly combines the structure of the motif pattern, as described by its syntactic specification, with the statistical measure of its occurrence count. We show that a combination of appropriate saturation conditions (expressed in terms of minimum number of dots compatible with a given list of occurrences) and the monotonicity of probabilistic scores over regions of constant frequency afford us significant parsimony in the generation and testing of candidate over-represented motifs. The merits of the method are documented by the results obtained in implementation, which specifically targeted protein sequence families. In all cases tested, the motif reported in PROSITE as the most important in terms of functional/structural relevance emerges among the top 30 extensible motifs returned by our algorithm, often right at the top. Of equal importance seems the fact that the sets of all surprising motifs returned in each experiment are extracted faster and come in much more manageable sizes than would be obtained in the absence of saturation constrains. Availability: This software will be available for use with the suite of tools at www.research.ibm.com/bioinformatics
Time-reversal extrapolation for microseismic event localization (2014)

Summary Microseismic event localization is important for microseismic monitoring. Travel-time based and migration based methods are used for microseismic event localization. Traveltime based methods require P- and S- wave first arrival picking before further processing. This type of method does not work well for low quality data because of inaccurate arrival picking. Migration based methods avoid picking first arrivals by backpropagating the recorded field to the source location using the velocity model. Time-reversal extrapolation is a typical migration based method. Traditional time-reversal extrapolation is related to adjoint method. We use a representation theorem based extrapolation method to combine the pressure wavefield with its spatial gradient. We then illustrate the method on synthetic borehole data with a limited aperture.
Histotripsy methods in mechanical disintegration of tissue: Towards clinical applications (2015)

In high intensity focused ultrasound (HIFU) therapy, an ultrasound beam is focused within the body to locally affect the targeted site without damaging intervening tissues. The most common HIFU regime is thermal ablation. Recently there has been increasing interest in generating purely mechanical lesions in tissue (histotripsy). This paper provides an overview of several studies on the development of histotripsy methods toward clinical applications. Two histotripsy approaches and examples of their applications are presented. In one approach, sequences of high-amplitude, short (microsecond-long), focused ultrasound pulses periodically produce dense, energetic bubble clouds that mechanically disintegrate tissue. In an alternative approach, longer (millisecond-long) pulses with shock fronts generate boiling bubbles and the interaction of shock fronts with the resulting vapour cavity causes tissue disintegration. Recent preclinical studies on histotripsy are reviewed for treating benign prostatic hyperplasia (BPH), liver and kidney tumours, kidney stone fragmentation, enhancing anti-tumour immune response, and tissue decellularisation for regenerative medicine applications. Potential clinical advantages of the histotripsy methods are discussed. Histotripsy methods can be used to mechanically ablate a wide variety of tissues, whilst selectivity sparing structures such as large vessels. Both ultrasound and MR imaging can be used for targeting and monitoring the treatment in real time. Although the two approaches utilise different mechanisms for tissue disintegration, both have many of the same advantages and offer a promising alternative method of non-invasive surgery.
Systems Design Approach to Low-Cost Coinage Materials (2018)

A systems approach within an Integrated Computational Materials Engineering framework was used to design three new low-cost seamless replacement coinage alloys to reduce the raw material of the current US coinage alloys. Maintaining compatibility with current coinage materials required matching the currently used alloy properties of yield strength, work-hardening behavior, electrical conductivity, color, corrosion resistance and wear resistance. In addition, the design alloys were required to use current production processes. CALPHAD-based models for electrical conductivity and color were developed to integrate into the system design. Three prototype alloys were designed, produced and characterized. The design process highlighted the trade-off between minimizing the raw material costs and achieving the desired color properties. Characterization of the three prototype alloys showed good agreement with the design goals.
Study of the Noise-Reduction Problem in the Karhunen–LoÈve Expansion Domain (2009)

<para xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> Noise reduction, which aims at estimating a clean speech from a noisy observation, has long been an active research area. The standard approach to this problem is to obtain the clean speech estimate by linearly filtering the noisy signal. The core issue, then, becomes how to design an optimal linear filter that can significantly suppress noise without introducing perceptually noticeable speech distortion. Traditionally, the optimal noise-reduction filters are formulated in either the time or the frequency domains. This paper studies the problem in the Karhunen–LoÈve expansion domain. We develop two classes of optimal filters. The first class achieves a frame of speech estimate by filtering the corresponding frame of the noisy speech. We will show that many existing methods such as the widely used Wiener filter and subspace technique are closely related to this category. The second class obtains noise reduction by filtering not only the current frame, but also a number of previous consecutive frames of the noisy speech. We will discuss how to design the optimal noise-reduction filters in each class and demonstrate, through both theoretical analysis and experiments, the properties of the deduced optimal filters. </para>
The SVT-AV1 encoder: overview, features and speed-quality tradeoffs (2020)

The Scalable Video Technology AV1 (SVT-AV1) encoder is an open-source software AV1 encoder that is architected to yield excellent quality-speed-latency tradeoffs on CPU platforms for a wide range of video coding applications. The SVTAV1 encoder is based on the SVT architecture, which supports multi-dimensional parallelism, multi-pass partitioning decision, multi-stage/multi-class mode decision, and multi-level spatiotemporal prediction and residual coding algorithms. Given a latency constraint, the SVT-AV1 encoder maximizes the CPU utilization on multicore CPUs, through picturebased parallelism for high-latency video applications, and through segment-based parallelism for low-latency video applications. The picture-level/segment-level parallelism allows the SVT-AV1 encoder to produce identical bit streams, irrespective of whether single- or multi-threaded encoding is performed. In mode decision, the SVT-AV1 encoder yields many speed-quality tradeoffs with high granularity, mainly through multi-pass processing of each superblock and multistage/ multi-class processing of each block, and through the different levels of the prediction/coding features. The resulting speed-quality tradeoffs of SVT-AV1 are compared, in Video-On-Demand (VOD) use-cases, to those of libaom (another open-source AV1 encoder), and to those of the latest x264 (AVC), x265 (HEVC) and libvpx (VP9) open source encoders.
Analysis of white blood cell dynamics in nailfold capillaries (2015)

Based on video data acquired with low-cost, portable microscopy equipment, we introduce a semi-automatic method to count visual gaps in the blood flow as a proxy for white blood cells (WBC) passing through nailfold capillaries. Following minimal user interaction and a pre-processing stage, our method consists in the spatio-temporal segmentation and analysis of capillary profiles. Besides the mere count information, it also estimates the speed associated with every WBC event. The accuracy of our algorithm is validated through the analysis of two capillaries acquired from one healthy subject. Results are compared with manual counts from four human raters and confronted with related physiological data reported in literature.
Demonstration of augmented-reality optical narrowcasting (2018)

We introduce a new communications technology, which we refer to as augmented-reality optical narrowcasting. This technology has the potential to significantly enhance smartphone consumer communications by enabling information exchange between multiple transmitters and multiple receivers using free-space optical data transmission. A practical communication range of 400 meters in broad daylight is achievable with miniaturized optics transmitting HD video. An augmented-reality-style user interface, wherein visual representations of available information sources are overlaid on a live display of video imagery allows users to conveniently manage transmissions from multiple parties. The new technology is envisioned to be installed in smartphones and other mobile devices and in vehicles, opening new vistas for commerce and social interaction. We will demonstrate key features of the technology using custom optical communications hardware and software developed especially for this purpose.
Re-structuring, Re-labeling, and Re-aligning for Syntax-Based Machine Translation (2010)

This article shows that the structure of bilingual material from standard parsing and alignment tools is not optimal for training syntax-based statistical machine translation (SMT) systems. We present three modifications to the MT training data to improve the accuracy of a state-of-the-art syntax MT system: re-structuring changes the syntactic structure of training parse trees to enable reuse of substructures; re-labeling alters bracket labels to enrich rule application context; and re-aligning unifies word alignment across sentences to remove bad word alignments and refine good ones. Better structures, labels, and word alignments are learned by the EM algorithm. We show that each individual technique leads to improvement as measured by BLEU, and we also show that the greatest improvement is achieved by combining them. We report an overall 1.48 BLEU improvement on the NIST08 evaluation set over a strong baseline in Chinese/English translation.
Word-level confidence estimation for machine translation using phrase-based translation models (2005)

Confidence measures for machine translation is a method for labeling each word in an automatically generated translation as correct or incorrect. In this paper, we will present a new approach to confidence estimation which has the advantage that it does not rely on system output such as N-best lists or word graphs as many other confidence measures do. It is, thus, applicable to any kind of machine translation system.Experimental evaluation has been performed on translation of technical manuals in three different language pairs. Results will be presented for different machine translation systems to show that the new approach is independent of the underlying machine translation system which generated the translations. To the best of our knowledge, the performance of the new confidence measure is better than that of any existing confidence measure.
Abstract 1461: Wnt2 Plays a Key Role in Cardiac Development Via a Non-Canonical Pathway (2008)

Embryonic stem (ES) cells are a promising source of cardiomyocytes, but their clinical application has been hindered by the lack of selective differentiation methods. Although several signals are involved in heart development, the precise signals that mediate cardiomyocyte differentiation remain undetermined. Wnt family has a potent effect on the various organ development. To address this issue, we investigated the expression of wnt genes in the embryonic heart. Then we applied these findings to establish an efficient protocol to induce cardiomyocytes in vitro . (1) We analyzed TOP-EGFP mice to clarify whether canonical wnt signal pathway is important in the developing heart. TOP-EGFP mice are transgenic mice in which the EGFP gene is located under the β-catenin binding site so that the EGFP protein expresses when the canonical pathway is activated. They did not reveal any GFP in early stage heart, indicating that the canonical pathway is not involved. (2) Expression of non-canonical wnt was screened. Whole mount in situ hybridization of wnt2 and nkx2.5 (positive control) was performed at mouse embryo. Wnt2 was strongly expressed in the the heart-forming area in stages from E7.5 to E9.0. (3) We applied this embryonic wnt2 expression pattern to ES cell differentiation. Using siRNA we knocked-down wnt2 protein in various phases, which inhibited formation of beating EB, and decreased cardiac muscle genes only during the primitive stage (day 2– 4). Also adding wnt2 protein to embryonic cells in the appropriate phase led to a marked induction of cardiac specific genes. But wnt2 did not affect the mesodermal gene expression, Brachyury T and Mesp1, suggesting that Wnt2 does not affect the primitive development of the mesodermal progenitor cells. However, Wnt2 critically promotes cardiac specification after mesodermal induction and increases the eventual cardiac musculature. Wnt2 was strongly expressed in the heart-forming region. We applied this finding to develop an effective protocol for obtaining cardiomyocytes from mouse ES cells by adding wnt2 protein and also to inhibit generation of cardiomyocytes by inhibition of wnt2 signaling. We concluded that wnt2 plays a key role in cardiac development via a non-canonical pathway.