gebhart/patrepeval huggingface dataset:
HIV Insertions Within and Proximal to Host Cell Genes Are a Common Finding in Tissues Containing High Levels of HIV DNA and Macrophage-Associated p24 Antigen Expression (2003)

HIV integration within host cell genomic DNA is a requisite step of the viral infection cycle. Yet, characteristics of the sites of provirus integration within the host genome remain obscure. The authors present evidence that in diseased tissues showing a high level of HIV DNA and macrophage-associated HIV p24 antigen expression from end stage forms of HIV disease, HIV-1 integration sites were favored within genes and transcriptionally active host cell genomic loci. Using an inverse PCR (IPCR) technique that identified dominant integrated forms of HIV, clonal IPCR products were isolated from AIDS dementia, AIDS lymphoma, and angioimmunoblastic lymphadenopathy tissues. Thirty of 34 disease-associated HIV-1 insertions were identified within annotated and hypothetical genes, an unexpected but highly nonrandom genetic coding region association (p <.026). The 1% sensitivity thresholds used for HIV IPCR suggested some form of selective expansion of cells containing these HIV proviruses. Consistent with this interpretation were the HIV-1 insertion sites identified within introns of genes that encoded for factors associated with signal transduction, apoptosis, and transcription regulation. In addition, HIV-1 proviruses were frequently found proximal to genes that encoded for receptor-associated, signal transduction-associated, transcription-associated, and translation-associated proteins. HIV-1 integration within host cell genomic DNA potentially represents a significant insertional mutagenic event. In certain cases, provirus insertions may mediate the dysregulation of specific gene expression events, providing mechanisms contributing to the pathogenesis associated with certain AIDS-related diseases.
Adipokines: molecular links between obesity and atheroslcerosis (2005)

Atherosclerotic disease remains the leading cause of death in industrialized nations despite major advances in its diagnosis, treatment, and prevention. The increasing epidemic of obesity, insulin resistance, and diabetes will likely add to this burden. Increasingly, it is becoming apparent that adipose tissue is an active endocrine and paracrine organ that releases several bioactive mediators that influence not only body weight homeostasis but also inflammation, coagulation, fibrinolysis, insulin resistance, diabetes, and atherosclerosis. The cellular mechanisms linking obesity and atherosclerosis are complex and have not been fully elucidated. This review summarizes the experimental and clinical evidence on how excess body fat influences cardiovascular health through multiple yet converging pathways. The role of adipose tissue in the development of obesity-linked insulin resistance, metabolic syndrome, and diabetes will be reviewed, including an examination of the molecular links between obesity and atherosclerosis, namely, the effects of fat-derived adipokines. Finally, we will discuss how these new insights may provide us with innovative therapeutic strategies to improve cardiovascular health.
Smart Charging Technologies for Portable Electronic Devices (2012)

In this article we describe our efforts of extending demand-side control concepts to the application in portable electronic devices, such as laptop computers, mobile phones and tablet computers. As these devices feature built-in energy storage (in the form of batteries) and the ability to run complex control routines, they are ideal for the implementation of smart charging concepts. We developed a prototype of a smart laptop charger that controls the charging process depending on the locally measured frequency of the electricity grid. If this technique is incorporated into millions of devices in UK households, this will contribute significantly to the stability of the electricity grid, help to mitigate the power production fluctuations from renewable energy sources and avoid the high cost of building and maintaining conventional power plants as standby reserve.
Regular Expression Pocket Reference (2003)

This handy little book offers programmers a complete overview of the syntax and semantics of regular expressions that are at the heart of every text-processing application. Ideal as a quick reference, Regular Expression Pocket Reference covers the regular expression APIs for Perl 5.8, Ruby (including some upcoming 1.9 features), Java, PHP, .NET and C#, Python, vi, JavaScript, and the PCRE regular expression libraries. This concise and easy-to-use reference puts a very powerful tool for manipulating text and data right at your fingertips. Composed of a mixture of symbols and text, regular exp
Chemistry Is Dead. Long Live Chemistry! (2017)

Chemistry, once king of fluorescence microscopy, was usurped by the field of fluorescent proteins. The increased demands of modern microscopy techniques on the "photon budget" require better and brighter fluorophores, causing a renewed interest in synthetic dyes. Here, we review the recent advances in biochemistry, protein engineering, and organic synthesis that have allowed a triumphant return of chemical fluorophores to modern biological imaging.
Vitamin E reduces liver stiffness in nonalcoholic fatty liver disease (2015)

One year of vitamin E treatment improved noninvasive fibrosis scores and liver stiffness in NAFLD patients. The responses were similar between different PNPLA3 genotypes.
Epigenetics, DNA Organization, and Inflammatory Bowel Disease (2018)

Inflammatory bowel diseases (IBDs) are chronic inflammatory disorders affecting the gastrointestinal tract. The incidence of IBD is increasing, with more cases occurring in developed countries. Multiple factors such as genetics, environmental changes, gut microbiota, and immune abnormalities have been associated with development of IBD. In recent years, it has become increasingly apparent that epigenetic modifications of chromatin and the manner in which chromatin is organized in the nucleus are additionally important elements that can influence responses induced by the factors described above, and may therefore contribute to the onset and pathogenesis of IBD. Epigenetics and chromatin organization regulate diverse functions that include maintenance of homeostasis in the intestinal epithelium, the development and differentiation of immune cells, and modulation of responses generated by the immune system to defend against potential pathogens. Furthermore, changes in epigenetic chromatin marks and in chromatin organization have now been linked to differential gene expression in IBD patient cells. Although direct evidence for a role of histone modifications in IBD is currently very limited, in this review, we summarize the links between various epigenetic modifications, the proteins that catalyze or recognize these modifications, and the development or progression of IBD in human and experimental IBD. We also discuss how epigenetics influence the organization of DNA contacts to regulate gene expression and the implications this may have for diagnosing and treating IBD.
Cloud Testing- Issues, Challenges, Needs and Practice (2011)

Cloud computing not only changes the way of obtaining computing resources (such as computers, infrastructures, data storage, and application services), but also changes the way of managing and delivering computing services, technologies, and solutions. Cloud computing leads an opportunity in offering testing as a service (TaaS) for SaaS and clouds. Meanwhile, it causes new issues, challenges and needs in software testing, particular in testing clouds and cloud-based applications. This paper provides a comprehensive tutorial on cloud testing and cloud-based application testing. It answers the common questions raised by engineers and managers, and it provides clear concepts, discusses the special objectives, features, requirements, and needs in cloud testing. It offers a clear comparative view between web-based software testing and cloud-based application testing. In addition, it examines the major issues, challenges, and needs in testing cloud-based software applications. Furthermore, it also summarizes and compares different commercial products and solutions supporting cloud testing as services.
Short-Term Traffic Prediction Based on DeepCluster in Large-Scale Road Networks (2019)

Short-term traffic prediction (STTP) is one of the most critical capabilities in Intelligent Transportation Systems (ITS), which can be used to support driving decisions, alleviate traffic congestion and improve transportation efficiency. However, STTP of large-scale road networks remains challenging due to the difficulties of effectively modeling the diverse traffic patterns by high-dimensional time series. Therefore, this paper proposes a framework that involves a deep clustering method for STTP in large-scale road networks. The deep clustering method is employed to supervise the representation learning in a visualized way from the large unlabeled dataset. More specifically, to fully exploit the traffic periodicity, the raw series is first divided into a number of sub-series for triplet generation. The convolutional neural networks (CNNs) with triplet loss are utilized to extract the features of shape by transforming the series into visual images. The shape-based representations are then used to cluster road segments into groups. Thereafter, a model sharing strategy is further proposed to build recurrent NNs-based predictions through group-based models (GBMs). GBM is built for a type of traffic patterns, instead of one road segment exclusively or all road segments uniformly. Our framework can not only significantly reduce the number of prediction models, but also improve their generalization by virtue of being trained on more diverse examples. Furthermore, the proposed framework over a selected road network in Beijing is evaluated. Experiment results show that the deep clustering method can effectively cluster the road segments and GBM can achieve comparable prediction accuracy against the IBM with less number of prediction models.
Delay-Line-Based Analog-to-Digital Converters (2009)

We will introduce a design of analog-to-digital converters (ADCs) based on digital delay lines. Instead of voltage comparators, they convert the input voltage into a digital code by delay lines and are mainly built on digital blocks. This makes it compatible with process scaling. Two structures are proposed, and tradeoffs in the design are discussed. The effects of jitter and mismatch are also studied. We will present two 4 bit, 1 GS/s prototypes in 0.13 mum and 65 nm CMOS processes, which show a small area (0.015 mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> ) and small power consumption (<2.4 mW).
Mitigation Techniques for High Power and Long Duration Interference in DVB-T/H Systems (2007)

This paper describes different techniques for mitigation of high power and long duration interference in terrestrial digital video broadcasting (DVB-T/H) systems. The interference is assumed to distort the DVB-T/H signal severely so that on average one fourth of the DVB-T/H symbol is lost. We investigate the use of long enough time interleaver in combination with simple soft bits scaling. Additional mitigation of the interference effects is also achieved using the pilots carried by the DVB-T/H signal. The mitigation schemes are evaluated in the case where the interference occurs in additive white Gaussian noise (AWGN) and static frequency selective channels.
Anticipating events of in-hospital cardiac arrest (2004)

Most in-hospital cardiac arrests are preceded by events that often go overlooked and whose correct interpretation could be associated with a reduced mortality rate.
User specific cell clustering to improve mobility robustness in 5G ultra-dense cellular networks (2018)

One of the key challenges in very dense cellular network deployments is keeping mobility robustness. Connection dropping and throughput degradation appear significantly when considering vehicle to infrastructure communications. In order to cope with this problem, this paper proposes the use of User Specific and Adaptive Cell Clustering. Each device is served by a different set of cooperative cells that depends on its mobility state. That is to say, the network customizes the cell cluster size separately for each user. This is accomplished by dual connectivity and splitting the data and control planes. The methodology for evaluation is system level simulations considering a realistic mobility model in which user's velocity varies based on the traffic load. Results show network performance enhancements in terms of mobility and throughput. Thus, this technique is an interesting mobility management option in such ultra-dense deployments.
Investigation of the component of Propionibacterium acnes (Corynebacterium parvum) responsible for macrophage activation (1980)

Mouse peritoneal macrophages, activated with Propionibacterium acnes (Corynebacterium parvum) in vivo, exhibited altered morphological characteristics, increased acid phosphatase activity, and release of [EH]thymidine-labeled DNA from tumor cells in vitro. Comparison with macrophages from mice injected with a control organism, P. jensenii, showed that the morphological changes, but not acid phosphatase, correlated with the development of tumoricidal activity. Investigation of the microbial component responsible for this activity indicated it was heat stable and refractory to extraction by methanol-chloroform, dilute acid, butanol, or a serial combination of extraction procedures. When the cells were disrupted by mechanical breakage, no activity could be found in the cell wall, soluble cytoplasm, or particulate cytoplasm. These results suggest that intact organisms are required for macrophage activation, and they may resolve conflicting reports on the nature of the immunostimulating activity of P. acnes.
Automated georegistration of motion imagery (2011)

Georegistration is the assignment of 3-D coordinates to the pixels of an image. It is necessary for aligning imagery with map data, fusing images from different sensors, and geolocating moving objects. Georegistration requires recovery of the exterior camera orientation or pose - that is, position and attitude - for every image in the motion imagery sequence, and often the recovery of the intrinsic camera parameters of focal length, sensor pixel aspect ratio, and radial distortion. We have developed a real- time, automated solution to this problem. It is based on the registration of actual images to predicted images from a high-resolution digital elevation model (DEM). Beginning from an initial camera estimate for the first image, the algorithm iterates on the process of forming a predicted image, registering it to the actual image, and then refining the camera estimate based on the registration results. The resulting camera model forms the initial camera estimate of the next image. In this way, the camera model of each image is recovered as well as the platform motion, and the resulting camera models are used with the DEM to stabilize and georegister the motion imagery. The algorithm works with a wide variety of DEMs, including high-resolution LIDAR and low-resolution USGS DEMs. Implemented on a dual quad-core PC, the software georegisters one gigapixel of imagery per second. Results are presented for wide area motion imagery, full motion video, and thermal infrared video, along with applications to surveillance and border security.
Insights into the ion-exchange properties of Zn(<scp>ii</scp>)-incorporated MOR zeolites for the capture of multivalent cations (2019)

Understanding the properties of zeolites for cation exchange is important because the ion-exchange performance largely determines their suitability in applications such as catalysis and adsorptive separation. We synthesized a Zn(ii)-incorporated mordenite-framework aluminosilicate zeolite (Zn,Al-MOR), in which both Zn and Al are substituted in the framework, and studied its ion-exchange behavior for multivalent cations. For comparison, the original aluminosilicate mordenite (Al-MOR) was also synthesized with a composition adjusted to ensure that its charge density was similar to that of Zn,Al-MOR. While the incorporation of Zn(ii) led to a slower kinetic process, the selectivities and the exchange capacities toward multivalent cations (especially divalent cations) were significantly improved. Herein, we discussed the mechanism responsible for improving the ion-exchange performance in the presence of Zn(ii) and found that the incorporation of Zn(ii) led to a significant improvement in the ion-exchange temperature dependence of the MOR, which led to the ability to enhance ion-exchange capacity through temperature control during actual application. It was also revealed that the presence of Zn(ii) significantly improves selectivity and spontaneity toward the exchange of multivalent cations, Ni2+. Moreover, XRD and nitrogen-adsorption/desorption analyses revealed that the structures of the materials are maintained during the ion exchange, which is indicative of superior structural stability and tolerance to ion exchange.
The kinetochore is part of the metaphase chromosome scaffold. (1984)

We used antisera from patients with the CREST syndrome of scleroderma (calcinosis, Raynaud's phenomenon, esophageal dysmotility, sclerodactyly, telangiectasia) to show that an antigenic component of the kinetochore present in metaphase chromosomes is also present in nonhistone chromosome scaffolds isolated following extensive digestion of the DNA and extraction of the bulk of chromosomal protein. All sera from 12 scleroderma CREST patients previously shown by immunofluorescence microscopy to have circulating antikinetochore antibodies recognise a protein of Mr 77,000 (CREST-77) in an immunoblotting assay. 9 of the 12 sera also recognise an antigen of Mr 110,000 (CREST-110). These proteins are present in isolated chromosomes and nonhistone scaffolds derived from them by two different procedures. Sera of five scleroderma CREST patients who are antikinetochore negative (by immunofluorescence) bind to neither protein in immunoblots. These data suggest that CREST-77 (and possibly CREST-110) is a component of the human kinetochore, and that the kinetochore is an integral part of the mitotic chromosome scaffolding.
Switching Mature Retinal Ganglion Cells to a Robust Growth State<i>In Vivo</i>: Gene Expression and Synergy with RhoA Inactivation (2004)

The inability of mature CNS neurons to regenerate injured axons has been attributed to a loss of inherent growth potential of cells and to inhibitory signals associated with myelin and the glial scar. The present study investigated two complementary issues: (1) whether mature CNS neurons can be stimulated to alter their gene expression profile and switch into a strong growth state; and (2) whether inactivating RhoA, a convergence point for multiple inhibitory signals, is sufficient to produce strong regeneration even without activating the growth state of neurons. In the mature rat, retinal ganglion cells (RGCs) normally fail to regenerate axons through the injured optic nerve but can be stimulated to do so by activating macrophages in the eye (e.g., by lens injury). To investigate underlying changes in gene expression, we retrogradely labeled RGCs with a fluorescent dye, performed optic nerve surgery with or without lens injury, and 4 d later, dissociated retinas, isolated RGCs by fluorescence-activated cell sorting, and examined their profiles of gene expression using microarrays. To investigate the effects of inactivating RhoA, we transfected RGCs with adeno-associated viruses carrying a gene for C3 ribosyltransferase. Our results show that, with appropriate stimulation, mature CNS neurons can undergo dramatic changes in gene expression comparable with those seen in regenerating neurons of the PNS, and that RhoA inactivation by itself results in moderate regeneration, and strongly potentiates axon regeneration through the mature optic nerve when the growth state of neurons is activated.
Combining open vocabulary recognition and word confusion networks (2008)

A limitation of most speech recognizers is that they only recognize words from a fixed vocabulary. In this paper, we explore a technique for addressing this deficiency using automatically derived units made up of letters and phones. We show how these units can be used for letter-to-phone conversion and open-vocabulary recognition. We further show how these units can be merged to form novel words while maintaining a word lattice structure. This allows creation of a word confusion network containing both in- and out-of-vocabulary (OOV) words. Experiments show these open vocabulary confusion networks improve recognition accuracy. They also allow open vocabulary recognition to be used in concert with a convenient confusion network result representation.
사회 수업 전문성 신장을 위한 대학-학교간 협력 프로그램 개발: C교육대학교와 S초등학교 사례를 중심으로 (2010)

교사의 전문성 신장과 관련된 최근의 연구들은 교사의 전문성 신장에 있어, 공동체적 접근(학습공동체), 협력, 반성에 대한 중요성을 언급하고 있다. 그러나 실제로 이를 기반으로 한 전문성 신장 프로그램은 개발되어 있지 않다. 이에 C교육대학교와 S초등학교의 사례를 중심으로 사회 수업 전문성 신장을 위한 대학-학교간의 협력 프로그램을 개발하였다. 프로그램의 개발 과정은 크게 3단계로 이루어졌다. 첫째, 협력 학교를 선정하고 둘째, 구성원을 대상으로 협력에 대한 인식을 조사하고 셋째, 전문성 신장 프로그램의 기준 및 요소 검토의 과정을 거쳐 프로그램의 형식적(운영 형태 및 방식) 조건과 내용적(주요 활동) 조건을 도출하였다. 도출된 사회 수업 전문성 신장 프로그램은 동료교사와 교과전문가가 포함된 학습공동체로 수평적 관계에서의 의사결정을 원칙으로 하고, 공동으로 수업을 설계, 실천하고, 실천에 대한 반성을 통해 수업에 대한 관점을 점검하는 것을 주 내용으로 한다.
Correction of spatial distortion, gain nonuniformity and efficiency variation in detectors for positron emission mammography (2002)

Each of two detectors used in our positron emission mammography (PEM) system consists of four 36 mm/spl times/36 mm/spl times/20 mm bismuth germanate (BGO) crystal detector blocks coupled to a crossed-wire anode position-sensitive photomultiplier tube (PS-PMT). To facilitate high spatial-resolution imaging, the crystal blocks have been pixellated into small elements on two opposite faces. In total, there are 71/spl times/71 elements on each detector. In order to improve the quality of images obtained using this system, we have identified three required aspects of detector calibration. First, in order to correct for spatial distortion inherent in the detectors, an accurate method for crystal element identification has been developed. This algorithm successfully identifies 59/spl times/49 crystal elements, and these results are used to generate a distortion Look-Up-Table (LUT). Second, corrections for a marked spatial variation of detector gain are required in order to facilitate accurate energy discrimination. This variation is quantitated by generating energy spectra specific to each of the identified crystal elements, and recording the relative gain of each element in an energy LUT. Finally, by using a third LUT containing the relative efficiencies of crystal elements, the flood-image nonuniformity has been reduced from 50% to 13%.
LabelRankT: Incremental Community Detection in Dynamic Networks via Label Propagation (2013)

An increasingly important challenge in network analysis is efficient detection and tracking of communities in dynamic networks for which changes arrive as a stream. There is a need for algorithms that can incrementally update and monitor communities whose evolution generates huge realtime data streams, such as the Internet or on-line social networks. In this paper, we propose LabelRankT, an online distributed algorithm for detection of communities in large-scale dynamic networks through stabilized label propagation. Results of tests on real-world networks demonstrate that LabelRankT has much lower computational costs than other algorithms. It also improves the quality of the detected communities compared to dynamic detection methods and matches the quality achieved by static detection approaches. Unlike most of other algorithms which apply only to binary networks, LabelRankT works on weighted and directed networks, which provides a flexible and promising solution for real-world applications.