gebhart/patrepeval huggingface dataset:
Gated Orthogonal Recurrent Units: On Learning to Forget (2017)

© 2019 Massachusetts Institute of Technology. We present a novel recurrent neural network (RNN)based model that combines the remembering ability of unitary evolution RNNs with the ability of gated RNNs to effectively forget redundant or irrelevant information in its memory. We achieve this by extending restricted orthogonal evolution RNNs with a gating mechanism similar to gated recurrent unit RNNs with a reset gate and an update gate. Our model is able to outperform long short-term memory, gated recurrent units, and vanilla unitary or orthogonal RNNs on several long-term-dependency benchmark tasks. We empirically show that both orthogonal and unitary RNNs lack the ability to forget. This ability plays an important role in RNNs. We provide competitive results along with an analysis of our model on many natural sequential tasks, including question answering, speech spectrum prediction, character-level language modeling, and synthetic tasks that involve long-term dependencies such as algorithmic, denoising, and copying tasks.
Low Dose Computerized Tomography for Detection of Urolithiasis—Its Effectiveness in the Setting of the Urology Clinic (2011)

Low dose computerized tomography may serve as an effective tool in the setting of the urology clinic in patients with urolithiasis. This imaging tool can better assess urolithiasis and associated obstruction than plain abdominal radiographs, but it may be problematic with small stones (less than 2 mm) and evidence of distal ureteral obstruction. Its effectiveness as a long-term followup tool requires further prospective trials.
Introduction (2017)

Computer vision is playing an increasingly vital role in three broad areas of intelligent transportation systems: law enforcement, traffic efficiency, and driver safety. This chapter introduces the reader to key applications in each of these domains, whetting the appetite for deeper exploration in subsequent chapters. A basic computer vision pipeline for roadway transportation systems is presented, which serves as an encompassing framework for the techniques presented in the text. The pipeline comprises the modules of image and video acquisition, data preprocessing, feature extraction, inference, and feedback. Each module is summarized in terms of basic concepts, opportunities, and challenges. In addition, a systemic approach is encouraged that exploits interactions among the modules and optimizes the entire pipeline in a holistic manner.
Feature Dimensionality Reduction for Example-Based Image Super-Resolution (2011)

The Journal of Pattern Recognition Research (JPRR) provides an open access forum for the publication of research articles in areas of pattern recognition, machine learning, artificial intelligence, computational algorithms, and fuzzy learning
Intelligent Adaptation of Hardware Knobs for Improving Performance and Power Consumption (2020)

Current microprocessors include several knobs to modify the hardware behavior in order to improve performance, power, and energy under different workload demands. An impractical and time consuming offline profiling is needed to evaluate the design space to find the optimal knob configuration. Different knobs are typically configured in a decoupled manner to avoid the time-consuming offline profiling process. This can often lead to underperforming configurations and conflicting decisions that jeopardize system power-performance efficiency. Thus, a dynamic management of the different hardware knobs is necessary to find the knob configuration that maximizes system power-performance efficiency without the burden of offline profiling. In this article, we propose libPRISM, an infrastructure that enables the transparent management of multiple hardware knobs in order to adapt the system to the evolving demands of hardware resources in different workloads. libPRISM can minimize execution time, energy-delay product or power consumption by dynamically managing the SMT level, the data prefetcher, and the DVFS hardware knobs. Overall, the proposed solutions increase performance up to 130 percent (16.9 percent on average), reduce energy-delay product up to 80 percent, and reduce power consumption up to 33 percent depending on the target metric compared to the default knob configuration of the system.
A Long‐Lasting Skin Protectant Based on CG‐101, a Deep Eutectic Solvent Comprising Choline and Geranic Acid (2022)

The COVID-19 public health crisis has spotlighted the need to improve global hygiene and sanitization. In addition to causing staggering rates of transmission and fatality, COVID-19 has severely impacted the quality of life and mental health of global citizens. The World Health Organization (WHO) and Centers for Disease Control and Prevention (CDC) encourage hand hygiene as the first defense against the spread of infection, yet frequent handwashing is often impractical. Widely used ethanol-based hand sanitizers provide immediate protection against pathogens on the skin, albeit short-lived, due to their rapid evaporation. Herein, a novel, long-lasting skin protectant formulated with biocompatible ionic liquid/deep eutectic solvents prepared using generally recognized as safe materials - choline and geranic acid (CG-101, 5% w/w) - is described. In vitro studies demonstrated that CG-101 inactivates bacteria and the human coronavirus, hCoV229E, for 4 h after application. Two human clinical studies demonstrate that CG-101 does not cause skin irritation or sensitization, and a single application of CG-101 gel imparts skin protection against microbes for significantly longer than conventional 70% ethanol-based hand sanitizers. These data are the first to indicate that CG-101 may be a better alternative to alcohol-based hand sanitizers for long-term skin protection against infectious diseases.
Guest Editors' Introduction: Digitally Enhanced Wireless Transceivers (2012)

This special issue of IEEE Design & Test of Computers provides an overview of the challenges, current practice, and future research directions of digitally enhanced wireless systems. The author provides an overview of the technical articles and features presented.
Modular General-Purpose Data Filtering for Tracking (2008)

In nearly allmodern tracking systems, signal processing is an important part with state estimation as the fundamental component. To evaluate and to reassess different tracking systems in an affordable way, simulations that are in accordance with reality are largely used. Simulation software that is composed of many different simulating modules, such as high level architecture (HLA) standardized software, is capable of simulating very realistic data and scenarios. A modular and general-purpose state estimation functionality for ﬁltering provides a profound basis for simulating most modern tracking systems, which in this thesis work is precisely what is created and implemented in an HLA-framework. Some of the most widely used estimators, the iterated Schmidt extended Kalman ﬁlter, the scaled unscented Kalman ﬁlter, and the particle ﬁlter, are chosen to form a toolbox of such functionality. An indeed expandable toolbox that offers both unique and general features of each respective ﬁlter is designed and implemented, which can be utilized in not only tracking applications but in any application that is in need of fundamental state estimation. In order to prepare the user to make full use of this toolbox, the ﬁlters’ methods are described thoroughly, some of which are modiﬁed with adjustments that have been discovered in the process. Furthermore, to utilize these ﬁlters easily for the sake of user-friendliness, a linear algebraic shell is created, which has very straight-forward matrix handling and uses BOOST UBLAS as the underlying numerical library. It is used for the implementation of the ﬁlters in C++, which provides a very independent and portable code.
LuXuRies of Lipid Homeostasis: The Unity of Nuclear Hormone Receptors, Transcription Regulation, and Cholesterol Sensing (2002)

Cholesterol homeostasis is maintained by a regulatory network that controls both the acquisition and elimination of cholesterol. Recent studies have elucidated a mechanism by which cholesterol metabolism is transcriptionally regulated by several classes of orphan nuclear receptors. In particular, the liver X receptors, LXRalpha and LXRbeta, appear to serve as key sensors of intracellular sterol levels by regulating the expression of genes that control cholesterol absorption, storage, transport, and elimination. LXRs are also involved in fatty acid metabolism by their ability to increase the expression of sterol regulatory element-binding protein 1c (SREBP-1c). These findings define LXRs as potential therapeutic targets for the treatment of lipid disorders.
Prognostic performance of proteomic testing in advanced non-small cell lung cancer: a systematic literature review and meta-analysis (2020)

Advanced NSCLC patients classified VSGood have significantly longer OS than those classified VSPoor. The summary effect size for OS HRs around 0.4-0.5 indicates that the expected median survival of those with a VSGood classification is approximately 2-2.5 times as long as those with VSPoor. The robust prognostic performance of the VeriStrat test across various lines of therapy and treatment regimens has clinical implications for treatment shared decision-making and potential for novel treatment strategies.
Real-time 3D point cloud segmentation using Growing Neural Gas with Utility (2016)

This paper proposes a real-time feature extraction and segmentation method for a 3D point cloud. First of all, we apply Growing Neural Gas with Utility (GNG-U) to the point cloud for learning a topological structure. However, the standard GNG-U cannot learn the topological structure of 3D space environment and color information simultaneously. To this end, we then modify the GNG-U algorithm by using a weight vector. we propose a surface feature extraction and segmentation method by efficiently utilizing the topological structure. Our segmentation method is based on a region growing method whose similarity value uses the inner value of two normal vectors connected by the topological structure. We show experimental results of the proposed method and discuss the effectiveness of the proposed method.
Adaptor Protein Lnk Negatively Controls the Likelihood of Self-Renewal in Hematopoietic Stem Cells. (2006)

Abstract Great progresses are promised for the development of stem cell-based regenerative medicine if we can manipulate stem cell self-renewal. Thus, one of the central tasks in stem cell biology is to understand how stem cell fate is determined. Hematopoietic stem cells (HSCs) are the best studied stem cells. Their in vivo self-renewal has been extensively studied, but its in vitro recapitulation remains so difficult. We previously reported that HSCs undergo asymmetrical self-renewal division in culture with stem cell factor (SCF) and thrombopoietin (TPO). Since then, we have sought any condition in which HSCs can symmetrically self-renew. We now report in vitro symmetrical self-renewal division of HSCs in the absence of Lnk. Lnk is an adaptor protein containing praline-rich domain, pleckstrin homology domain, and Src homology domain. Lnk-deficient mice have over 10-fold HSCs due to increased self-renewal capacity. CD34−Kit+Sca-1+Lin− cells were purified from bone marrow of wild-type or Lnk-deficient B6 mice, and were subjected to serum-free single cell cultures in the presence of a variety of cyokines. We found that Lnk-deficient CD34−Kit+Sca-1+Lin− cells are hypersensitive to TPO. Repopulating activity in 40 CD34−Kit+Sca-1+Lin− cells from Lnk-deficient mice increased after 3 day-culture with TPO or with SCF and TPO, but not after 3 day-culture with SCF. In contrast, repopulating activity in 40 CD34−Kit+Sca-1+Lin− cells from wild type mice did not significantly change after 3 day-culture with SCF, TPO, or SCF and TPO. Moreover, paired daughter cell-experiments clearly showed that Lnk-deficient, but not wild-type long-term repopulating cells are able to undergo symmetrical self-renewal division at least once in the presence of SCF and TPO. These data suggest that Lnk acts just like a tuner in the regulation of HSC self-renewal downstream of TPO/Mpl signaling. We further investigated TPO-mediated signal transduction pathways in CD34−Kit+Sca-1+Lin− cells. To this end, we developed a novel assay which allowed us to analyze signal transduction in a very limited number of cells. We detected enhanced up-regulation of STAT5 and Akt pathways, and inversely enhanced down-regulation of p38 MAPK pathway in Lnk-deficient CD34−Kit+Sca-1+Lin− cells, as compared with normal ones. These data suggest that these combinational changes in signal transduction lead to initiation of self-renewal in HSCs. We propose that stem cell self-renewal is determined by a balance of positive and negative signals in multiple signal transduction pathways rather than by any particular self-renewal signals.
Feature-assisted threshold selection for all-zero block detection and its application to video coding optimization in H.264 (2008)

All-zero blocks (AZB) denote blocks with all zero DCT coefficients after quantization. Early determination of AZB can avoid unnecessary DCT/Q/IQ/IDCT computation. Existing techniques in the literature primarily address more efficient thresholds for early determination of AZB. This paper deals with the selection of such thresholds based on low level features including motion activity and texture information. This aspect is then utilized to avoid any: (1) unnecessary quarter accuracy motion estimation, (2) unnecessary multiple reference frame motion estimation, and (3) unnecessary DCT/Q/IQ/IDCT computation. The developed approach has been applied to two different format video sequences CIF and QCIF. The results show that the computational complexity is significantly reduced while the video quality is maintained at a tolerable loss level.
Impact on stent size and indication for stent placement on immediate outcome (1996)

The immediate outcome of 271 procedures involving the intracoronary implantation of 305 stents was determined. Data were analyzed with regard to indication for stenting and stent size. Elective indication was associated with a higher success rate than emergency indication (95.6% vs. 86.6%, P = 0.013) and a lower Q-wave infarction rate (0 vs. 6.4%, P = 0.006). Univariate analysis showed that the odds ratio for procedural success was significantly favored by elective indication (3.37, P = 0.018) but was unrelated to stent size (1.10, P = 0.087). These findings were confirmed on multivariate analysis. The likelihood of Q-wave infarction was lower for elective placement (P = 0.0008) but was not related to size. Requirement for emergency bypass surgery, incidence of subacute closure, and death were not related to indication or to stent size on either univariate or multivariate analysis. Therefore, the immediate outcome of stent placement is related to the indication for stenting, but not to the size of stent implanted. Procedural success is significantly favored by elective indication.
Structure-based design of an osteoclast-selective, nonpeptide Src homology 2 inhibitor with in vivo antiresorptive activity (2000)

Targeted disruption of the pp60(src) (Src) gene has implicated this tyrosine kinase in osteoclast-mediated bone resorption and as a therapeutic target for the treatment of osteoporosis and other bone-related diseases. Herein we describe the discovery of a nonpeptide inhibitor (AP22408) of Src that demonstrates in vivo antiresorptive activity. Based on a cocrystal structure of the noncatalytic Src homology 2 (SH2) domain of Src complexed with citrate [in the phosphotyrosine (pTyr) binding pocket], we designed 3',4'-diphosphonophenylalanine (Dpp) as a pTyr mimic. In addition to its design to bind Src SH2, the Dpp moiety exhibits bone-targeting properties that confer osteoclast selectivity, hence minimizing possible undesired effects on other cells that have Src-dependent activities. The chemical structure AP22408 also illustrates a bicyclic template to replace the post-pTyr sequence of cognate Src SH2 phosphopeptides such as Ac-pTyr-Glu-Glu-Ile (1). An x-ray structure of AP22408 complexed with Lck (S164C) SH2 confirmed molecular interactions of both the Dpp and bicyclic template of AP22408 as predicted from molecular modeling. Relative to the cognate phosphopeptide, AP22408 exhibits significantly increased Src SH2 binding affinity (IC(50) = 0.30 microM for AP22408 and 5.5 microM for 1). Furthermore, AP22408 inhibits rabbit osteoclast-mediated resorption of dentine in a cellular assay, exhibits bone-targeting properties based on a hydroxyapatite adsorption assay, and demonstrates in vivo antiresorptive activity in a parathyroid hormone-induced rat model.
Practical Signal-Dependent Noise Parameter Estimation From a Single Noisy Image (2014)

The additive white Gaussian noise is widely assumed in many image processing algorithms. However, in the real world, the noise from actual cameras is better modeled as signal-dependent noise (SDN). In this paper, we focus on the SDN model and propose an algorithm to automatically estimate its parameters from a single noisy image. The proposed algorithm identifies the noise level function of signal-dependent noise assuming the generalized signal-dependent noise model and is also applicable to the Poisson-Gaussian noise model. The accuracy is achieved by improved estimation of local mean and local noise variance from the selected low-rank patches. We evaluate the proposed algorithm with both synthetic and real noisy images. Experiments demonstrate that the proposed estimation algorithm outperforms the state-of-the-art methods.
RbAp48 Regulates Cytoskeletal Organization and Morphology by Increasing K-Ras Activity and Signaling through Mitogen-Activated Protein Kinase (2007)

RbAp48 is a WD-40 protein that plays an important role in chromatin metabolism and regulates Ras signaling. Here, we report that RbAp48 is involved in the regulation of cytoskeletal organization, a novel function. First, we show that transfection of RbAp48 into Hs-578T breast cancer cells (Hs-RbAp48-hi) leads to cell size reduction, a rounded cell shape, decreased cellular protrusions, and a higher nuclear/cytoplasmic ratio. Furthermore, we observed cytoskeletal F-actin organization disruption with loss of actin stress fibers and formation of membranous F-actin rings in Hs-RbAp48-hi cells. These morphologic changes were partially reversed by RbAp48 knockdown. Interestingly, mitogen-activated protein kinase (MAPK) was activated in Hs-RbAp48-hi cells, and this activity was also partly reversed by RbAp48 down-regulation. Furthermore, pharmacologic inhibition of MAPK led to the reappearance of organized actin fibers and focal contacts, suggesting MAPK as the effector pathway. Moreover, we show an increase in total Ras activity in Hs-RbAp48-hi cells with K-Ras-GTP becoming the dominant isoform. This reverted to baseline activity levels on RbAp48 small interfering RNA transfection, thus suggesting a direct role for RbAp48 in Ras regulation. Finally, we tested the model in transformed 3T3-K-Ras-G12V fibroblasts. As expected, RbAp48 knockdown in 3T3-K-Ras-hi fibroblasts resulted in reappearance of an organized cytoskeleton and shutdown of K-Ras activity. In conclusion, our data support a model whereby RbAp48 regulates cellular morphology and cytoskeletal organization by increasing K-Ras activity and signaling through MAPK.
Enrichment of Presenilin 1 Peptides in Neuronal Large Dense‐Core and Somatodendritic Clathrin‐Coated Vesicles (1998)

Presenilin 1 is an integral membrane protein specifically cleaved to yield an N-terminal and a C-terminal fragment, both membrane-associated. More than 40 presenilin 1 mutations have been linked to early-onset familial Alzheimer disease, although the mechanism by which these mutations induce the Alzheimer disease neuropathology is not clear. Presenilin 1 is expressed predominantly in neurons, suggesting that the familial Alzheimer disease mutants may compromise or change the neuronal function (s) of the wild-type protein. To elucidate the function of this protein, we studied its expression in neuronal vesicular systems using as models the chromaffin granules of the neuroendocrine chromaffin cells and the major categories of brain neuronal vesicles, including the small clear-core synaptic vesicles, the large dense-core vesicles, and the somatodendritic and nerve terminal clathrin-coated vesicles. Both the N- and C-terminal presenilin 1 proteolytic fragments were greatly enriched in chromaffin granule and neuronal large dense-core vesicle membranes, indicating that these fragments are targeted to these vesicles and may regulate the large dense-core vesicle-mediated secretion of neuropeptides and neurotransmitters at synaptic sites. The presenilin 1 fragments were also enriched in the somatodendritic clathrin-coated vesicle membranes, suggesting that they are targeted to the somatodendritic membrane, where they may regulate constitutive secretion and endocytosis. In contrast, these fragments were not enriched in the small clear-core synaptic vesicle or in the nerve terminal clathrin-coated vesicle membranes. Taken together, our data indicate that presenilin 1 proteolytic fragments are targeted to specific populations of neuronal vesicles where they may regulate vesicular function. Although full-length presenilin 1 was present in crude homogenates, it was not detected in any of the vesicles studied, indicating that, unlike the presenilin fragments, full-length protein may not have a vesicular function.
Can Ground Truth Label Propagation from Video help Semantic Segmentation? (2016)

For state-of-the-art semantic segmentation task, training convolutional neural networks (CNNs) requires dense pixelwise ground truth (GT) labeling, which is expensive and involves extensive human effort. In this work, we study the possibility of using auxiliary ground truth, so-called \textit{pseudo ground truth} (PGT) to improve the performance. The PGT is obtained by propagating the labels of a GT frame to its subsequent frames in the video using a simple CRF-based, cue integration framework. Our main contribution is to demonstrate the use of noisy PGT along with GT to improve the performance of a CNN. We perform a systematic analysis to find the right kind of PGT that needs to be added along with the GT for training a CNN. In this regard, we explore three aspects of PGT which influence the learning of a CNN: i) the PGT labeling has to be of good quality; ii) the PGT images have to be different compared to the GT images; iii) the PGT has to be trusted differently than GT. We conclude that PGT which is diverse from GT images and has good quality of labeling can indeed help improve the performance of a CNN. Also, when PGT is multiple folds larger than GT, weighing down the trust on PGT helps in improving the accuracy. Finally, We show that using PGT along with GT, the performance of Fully Convolutional Network (FCN) on Camvid data is increased by $2.7\%$ on IoU accuracy. We believe such an approach can be used to train CNNs for semantic video segmentation where sequentially labeled image frames are needed. To this end, we provide recommendations for using PGT strategically for semantic segmentation and hence bypass the need for extensive human efforts in labeling.
Adsorption Chemistry of Sulfur Dioxide in Hydrated Na–Y Zeolite (2004)

Exceptional resistance to sulfur poisoning of the Na–Y zeolite arises from the localization of adsorbed sulfur dioxide on the zeolite in the presence of water. The work shows that Rietveld refinement of guest molecules is a powerful method to determine positions and states of different molecules co-adsorbed on a zeolite (see picture; H2SO3 in yellow (S) and large red spheres (O); zeolite framework in small red (O) and gray (Si or Al) spheres; large gray sphere is the Na cation).