gebhart/patrepeval huggingface dataset:
SHAHED: A MapReduce-based system for querying and visualizing spatio-temporal satellite data (2015)

Remote sensing data collected by satellites are now made publicly available by several space agencies. This data is very useful for scientists pursuing research in several applications including climate change, desertification, and land use change. The benefit of this data comes from its richness as it provides an archived history for over 15 years of satellite observations for natural phenomena such as temperature and vegetation. Unfortunately, the use of such data is very limited due to the huge size of archives (> 500TB) and the limited capabilities of traditional applications. This paper introduces SHAHED; a MapReduce-based system for querying, visualizing, and mining large scale satellite data. SHAHED considers both the spatial and temporal aspects of the data to provide efficient query processing at large scale. The core of SHAHED is composed of four main components. The uncertainty component recovers missing data in the input which comes from cloud coverage and satellite mis-alignment. The indexing component provides a novel multi-resolution quad-tree-based spatio-temporal index structure, which indexes satellite data efficiently with minimal space overhead. The querying component answers selection and aggregate queries in real-time using the constructed index. Finally, the visualization component uses MapReduce programs to generate heat map images and videos for user queries. A set of experiments running on a live system deployed on a cluster of machines show the efficiency of the proposed design. All the features supported by SHAHED are made accessible through an easy to use web interface that hides the complexity of the system and provides a nice user experience.
A 400MHz 10Mbps D-BPSK receiver with a reference-less dynamic phase-to-amplitude demodulation technique (2014)

A 400MHz 10Mbps differential BPSK (D-BPSK) receiver (RX) is presented. This RX adopts a proposed reference-less dynamic phase-to-amplitude demodulation scheme, which converts signal phase transition to distinct amplitude variation. The proposed RX can support a data rate up to 10Mbps. It achieves −63dBm sensitivity at 0.1% BER and draws 1.77mW in 0.18µm CMOS.
Integrated model-based and data-driven fault detection and diagnosis approach for an automotive electric power steering system (2011)

Integrity of electric power steering system is vital to vehicle handling and driving performance. Advances in electric power steering (EPS) system have increased complexity in detecting and isolating faults. In this paper, we propose a hybrid model-based and data-driven approach to fault detection and diagnosis (FDD) in an EPS system. We develop a physics-based model of an EPS system, conduct fault injection experiments to derive fault-sensor measurement dependencies, and investigate various FDD schemes to detect and isolate the faults. Finally, we use an SVM regression technique to estimate the severity of faults.
Connective Tissue‐Associated Proteins in Crevicular Fluid: (1989)

Tests for periodontal disease that are able to detect both ongoing and future loss of clinical attachment would be valuable assets in determining the diagnosis and treatment of periodontal diseases. We hypothesized that connective tissue-associated proteins could be detected in crevicular fluid and would reflect the biochemical activity of the periodontium in health and disease. To test this hypothesis, crevicular fluid samples obtained from patients with various states of periodontal disease were analyzed for the presence of several connective tissue-associated proteins using a dot blot assay. Two such proteins, osteonectin and N-propeptide alpha I type I collagen, were detected in crevicular fluid samples of patients with periodontal disease. Furthermore, the amount of these proteins detected in crevicular fluid appeared to increase with increased probing depth at the sampled site. These studies indicate that measurements of connective tissue-associated proteins in crevicular fluid may prove to be a valuable tool for diagnosing periodontal diseases.
Cognitive multiple access via cooperation: Protocol design and performance analysis (2007)

In this paper, a novel cognitive multiple-access strategy in the presence of a cooperating relay is proposed. Exploiting an important phenomenon in wireless networks, source burstiness, the cognitive relay utilizes the periods of silence of the terminals to enable cooperation. Therefore, no extra channel resources are allocated for cooperation and the system encounters no bandwidth losses. Two protocols are developed to implement the proposed multiple-access strategy. The maximum stable throughput region and the delay performance of the proposed protocols are characterized. The results reveal that the proposed protocols provide significant performance gains over conventional relaying strategies such as selection and incremental relaying, specially at high spectral efficiency regimes. The rationale is that the lossless bandwidth property of the proposed protocols results in a graceful degradation in the maximum stable throughput with increasing the required rate of communication. On the other hand, conventional relaying strategies suffer from catastrophic performance degradation because of their inherent bandwidth inefficiency that results from allocating specific channel resources for cooperation at the relay. The analysis reveals that the throughput region of the proposed strategy is a subset of its maximum stable throughput region, which is different from random access, where both regions are conjectured to be identical.
Single molecule quantitation and sequencing of rare translocations using microfluidic nested digital PCR (2013)

Cancers are heterogeneous and genetically unstable. New methods are needed that provide the sensitivity and specificity to query single cells at the genetic loci that drive cancer progression, thereby enabling researchers to study the progression of individual tumors. Here, we report the development and application of a bead-based hemi-nested microfluidic droplet digital PCR (dPCR) technology to achieve 'quantitative' measurement and single-molecule sequencing of somatically acquired carcinogenic translocations at extremely low levels (<10(-6)) in healthy subjects. We use this technique in our healthy study population to determine the overall concentration of the t(14;18) translocation, which is strongly associated with follicular lymphoma. The nested dPCR approach improves the detection limit to 1×10(-7) or lower while maintaining the analysis efficiency and specificity. Further, the bead-based dPCR enabled us to isolate and quantify the relative amounts of the various clonal forms of t(14;18) translocation in these subjects, and the single-molecule sensitivity and resolution of dPCR led to the discovery of new clonal forms of t(14;18) that were otherwise masked by the conventional quantitative PCR measurements. In this manner, we created a quantitative map for this carcinogenic mutation in this healthy population and identified the positions on chromosomes 14 and 18 where the vast majority of these t(14;18) events occur.
Bert-Pair-Networks for Sentiment Classification (2020)

BERT has demonstrated excellent performance in natural language processing due to the training on large amounts of text corpus in an unsupervised way. However, this model is trained to predict the next sentence, and thus it is good at dealing with sentence pair tasks but may not be sufficiently good for other tasks. In our paper, we introduce a novel representation framework BERT-pair-Networks (p-BERTs) for sentiment classification, where p-BERTs involve adopting BERT to encode sentences for sentiment classification as a classic task of single sentence classification, using the auxiliary sentence, and a feature extraction layer on the top. Results on three datasets show that our method achieves considerably improved performance.
E-business innovation and customs renovation for secure supply chain management (2003)

Information technologies (ITs) and supply chain management (SCM) are increasingly considered as indispensable tools of competitiveness especially for companies facing excessive global competition, although these companies have not necessarily succeeded in taking full advantage of such cutting-edge technologies and management systems. Their use, especially of international SCMs, is limited to a small number of purchaser-suppliers groups that are formed primarily by transnational corporations (TNCs). The factors impeding a proliferation of SCMs at a global scale include the difficulties that companies face in establishing flexible electronic data interchange (EDI) systems with their business partners, the high costs involved in building seamless and real-time information sharing systems where long-term business partnerships do not exist, and uncertainty on and high costs involved in international trade such as trade finance and customs procedures. In addition, the terrorist attacks on September 11, 2001 in New York magnified national security concerns, which seem to have a negative effect on global SCMs. On the other hand, new technological innovations in web services and tracking/tracing are emerging from the efforts to overcome these hurdles. This paper examines the late efforts on e-commerce, customs modernization, and trade facilitation, in response to the recent dynamic progress in information and web technologies. In the first chapter, we study some cases of SCMs emphasizing the importance of the state of the art information systems as an important instrument of trade facilitation. The second chapter reviews the recent efforts by the international community for trade facilitation, as well as new technologies and services based on eXtensible Mark-up Language (XML) and radio frequency identification (RFID) that have a great potential to change the online business environment dramatically. The third chapter consists of case studies on renovations of customs and trade information systems in Asia, Europe and North America while the fourth chapter reviews the present situations and efforts in Latin America. Based on these chapters, policy implications will be derived in the last chapter.
PolyLarva : technology agnostic runtime verification (2013)

With numerous specialised technologies available to industry, it is become increasingly frequent for computer systems to be composed of heterogeneous components, built over, and using different technologies and languages. While this enables developers to use the appropriate technologies for specific contexts, it becomes more challenging to ensure the correctness of the overall system. In this paper we propose a framework to enable extensible technology agnostic runtime verification and we present an extension of polyLarva, a runtime-verification tool able to handle the monitoring of heterogeneous-component system. The approach is then applied to a case study with C and Java components.
<i>In vitro</i> Antitumor Activity, Intracellular Accumulation, and DNA Adduct Formation of <i>cis</i>‐[((1<i>R</i>, 2<i>R</i>)‐1,2‐Cyclohexanediamine‐<i>N, N'</i>)bis(myristato)] Platinum (II) Suspended in Lipiodol (2000)

SM-11355, cis-[((1R,2R)-1,2-cyclohexanediamine-N,N')bis(myristato)] platinum (II), is a lipophilic platinum complex under clinical development that targets primary hepatocellular carcinoma using Lipiodol as a carrier. SM-11355 was compared with cisplatin (CDDP) using an in vitro evaluation system capable of examining the release characteristics and the cytotoxicity of drugs suspended in Lipiodol. SM-11355 suspended in Lipiodol (SM-11355/Lipiodol) and CDDP suspended in Lipiodol (CDDP/Lipiodol) showed cytotoxic activity against rat ascites hepatoma AH-109A cells in a dose-dependent manner. Their IC50 values following 7-day exposure were 22.3 and 0.40 microg/ml, respectively. Following the subsequent 7-day exposure, from day 7 to day 14 after preparation of the suspension, SM-11355/Lipiodol showed an almost equivalent activity, but CDDP/Lipiodol did not show any activity at all. SM-11355/Lipiodol showed a sustained release into the culture medium over the course of a 14-day exposure. Following the exposure to CDDP/Lipiodol, the platinum concentration in the medium was at its maximum on the first day and remained constant thereafter. Intracellular platinum uptake and formation of platinum-DNA adducts were dependent on the release characteristics of each drug suspension. For SM-11355/Lipiodol, the drug release, intracellular drug uptake, and formation of platinum-DNA adducts over the course of the subsequent 7-day exposure were similar to those observed during the first 7 days. DPC, one of the compounds released from SM-11355/Lipiodol, was taken up by cells and showed formation of platinum-DNA adducts. Thus, this study suggests that SM-11355/Lipiodol may release active platinum compound(s) that bind to nuclear DNA and mediate the cytotoxic activity of SM-11355/Lipiodol.
Identification of novel GLI1 target genes and regulatory circuits in human cancer cells (2018)

Hedgehog (HH) signaling is involved in many physiological processes, and pathway deregulation can result in a wide range of malignancies. Glioma-associated oncogene 1 (GLI1) is a transcription factor and a terminal effector of the HH cascade. Despite its crucial role in tumorigenesis, our understanding of the GLI1 cellular targets is quite limited. In this study, we identified multiple new GLI1 target genes using a combination of different genomic surveys and then subjected them to in-depth validation in human cancer cell lines. We were able to validate >90% of the new targets, which were enriched in functions involved in neurogenesis and regulation of transcription, in at least one type of follow-up experiment. Strikingly, we found that RNA editing of GLI1 can modulate effects on the targets. Furthermore, one of the top targets, FOXS1, a gene encoding a transcription factor previously implicated in nervous system development, was shown to act in a negative feedback loop limiting the cellular effects of GLI1 in medulloblastoma and rhabdomyosarcoma cells. Moreover, FOXS1 is both highly expressed and positively correlated with GLI1 in medulloblastoma samples of the Sonic HH subgroup, further arguing for the existence of FOXS1/GLI1 interplay in human tumors. Consistently, high FOXS1 expression predicts longer relapse-free survival in breast cancer. Overall, our findings open multiple new avenues in HH signaling pathway research and have potential for translational implications.
Dipeptidylpeptidase 4 as a Marker of Activated Fibroblasts and a Potential Target for the Treatment of Fibrosis in Systemic Sclerosis (2019)

DPP-4 characterizes a population of activated fibroblasts and shows that DPP-4 regulates TGFβ-induced fibroblast activation in the fibrotic skin of SSc patients. Inhibition of DPP4 exerts potent antifibrotic effects when administered in well-tolerated doses. As DPP4 inhibitors are already in clinical use for diabetes, these results may have direct translational implications for the treatment of fibrosis in patients with SSc.
RD-Optimized 3D Planar Model Reconstruction & Encoding for Video Compression (2018)

Conventional video coding approaches follow a hybrid motion prediction / residual transform coding paradigm, which limits the discovery of redundancy to individual pairs of video frames. On the other hand, computer vision techniques like structure-from-motion (SfM) have long exploited redundancy across a large group of frames to estimate a rigid 3D object structure. In this paper, leveraging on previous SfM techniques, we construct a rate-distortion (RD) optimized 3D planar model from a target spatial region in a frame group as a unified signal predictor for these frames. The prediction accuracy of the model is optimally traded off with the cost of coding such representation as side information (SI). Specifically, we approximate a roughly flat spatial region in the video as a 2D plane in 3D space, and project pixels from the frame group to a 2D grid on the plane with appropriate density. The boundary of the irregularly shaped pixel body on the plane is first coded using arithmetic edge coding (AEC), and then the body is encapsulated into a tight-fitting rectangular region, which is encoded as an intra-frame using HEVC. The pixels inside the rectangle but outside the pixel body-called don't care region (DCR)-are filled optimally by minimizing an l <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">1</inf> -norm of the transform coefficients using linear programming. Experimental results show that the RD-optimized planar model improves coding performance over native HEVC implementation.
The amino acid sequence of a trypsin inhibitor from the seeds of <i>Momordica charantia</i> Linn. Cucurbitaceae (1988)

A trypsin inhibitor (MCI‐3) was isolated from the seeds of Momordica charantia Linn. Cucurbitaceae in three steps involving the affinity chromatography, CM‐Sephadex chromatography and HPLC. It is composed of 62 amino acid residues: Asp 3 Thr. 5 Ser 4 Glu 5 Pro 4 Gly 7 Ala 8 Val 9 Ile 4 Leu 1 Lys 3 Arg 8 Trp 1 ; contained no cysteine; and its M r was 7443. The amino acid sequence showed significant homology with ‘potato inhibitor I family’ inhibitors.
Performance Analysis of Direct Gold Wire Bonding on Superconducting <inline-formula><tex-math notation="LaTeX">$\mbox{YBa}_{2}\mbox{Cu}_{3}\mbox{O}_{7\mbox{-}x}$</tex-math></inline-formula> Thin Films and Devices (2015)

The performance analysis of direct gold (Au) wire bonding on YBa <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> Cu <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> O <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">7-x</sub> (YBCO) thin films was performed. In a number of applications, YBCO thin films and devices are wire bonded on chip carriers or printed circuit boards for further electronic connections via the metallization of the contact pads of YBCO thin films. Although metallization for contact wiring is generally performed by thermal evaporation or sputtering at room temperature, the surface of a film is generally exposed to high temperatures by evaporated material or sputtering plasma. Moreover, an additional lithographic process (i.e, the application of a photoresist, baking, developing, and dry or wet etching) is necessary after the metal layer deposition in order to define contact pads. Since the superconducting properties of YBCO thin films and Josephson junctions are very sensitive to temperature and a humid environment, the metallization and additional lithographic processes during the fabrication cause significant degradation in the performance of the devices. In order to eliminate these additional steps, we performed a direct wire bonding process on YBCO thin films. Films of various thicknesses were deposited onto (100) SrTiO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> (STO) substrates by direct-current magnetron sputtering, and 20-μm-wide meander-type microbridges were patterned. The contact pads of the devices were wire bonded onto chip carriers by a thermosonic wedge bonder without using any metallization layer. The reliability and performance analyses of the bonds were performed under several aggressive thermal cycling conditions from liquid nitrogen (LN, 77 K) up to 450 K. The superconducting properties of the samples were then analyzed by means of resistance-temperature (R-T) and current-voltage (I-V ) measurements. A resistance model was developed for the bonding layout, and a specific contact resistivity was derived as ~3 × 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-6</sup> Ω · cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> .
Mycobacterium avium in a shower linked to pulmonary disease (2008)

Mycobacterium avium was isolated from hot and cold water samples and from sediment (biofilm) collected from the showerhead in the home of a woman with M. avium pulmonary disease lacking known M. avium risk factors. IS1245/IS1311 DNA fingerprinting demonstrated that M. avium isolates from the hot and cold water and showerhead sediment demonstrated a clonal relationship with the patient's M. avium isolate. The data provide evidence that showers may serve as sources of infection by waterborne M. avium.
Er:YAG laser skin resurfacing using repetitive long‐pulse exposure and cryogen spray cooling: II. Theoretical analysis (2001)

When applied in combination with repetitive Er:YAG laser exposure, CSC strongly affects the amount of heat available for dermal coagulation. As a result, CSC may not provide spatially selective epidermal protection in Er:YAG laser skin resurfacing.
Phase-coherent link from optical to microwave frequencies by means of the broadband continuum from a 1-GHz Ti:sapphire femtosecond oscillator (2002)

An optical clockwork is created with a compact 1-GHz repetition-rate laser and three nonlinear crystals. The broadband continuum output of the laser covers sufficient bandwidth to provide direct access to its carrier-envelope offset frequency without the use of a microstructure fiber. We phase lock the femtosecond comb to a Ca optical standard and monitor the stability of the repetition rate, f(r) , at 1 GHz. We demonstrate that the short-term stability of the microwave output of the optical clock is at least as good as that of a high-performance hydrogen maser.
From Innate Immunity to de-Novo Designed Antimicrobial Peptides (2002)

Antimicrobial peptides are a large group of gene-encoded, net positively charged polypeptides, produced by living organisms of all types including human and plants. They are mobilized shortly after infection as part of the innate immunity of these species and act rapidly to neutralize a broad range of microbes. Nowadays, thousands of native and de-novo designed antimicrobial peptides are available. They vary considerably in length, composition, charge and secondary structure. Despite these variations most antimicrobial peptides use a similar target, which is the bacterial phospholipid membrane. Many of them use a common general mechanism, the carpet mechanism, in which they accumulate on the bacterial membrane up to a threshold concentration, and then effect membrane permeation/disintegration. However, the structure of the permeation pathway may vary for different peptides and may include channel aggregates, toroidal pores or channels. Target specificity is determined by the negatively charged bacterial membrane, the net positive charge of the peptide, its hydrophobicity, oligomeric state in solution and in the membrane, and the stability of its secondary structure. A novel group of non hemolytic antimicrobial peptides were derived from diastereomers (containing D- and L-amino acids) of lytic peptides based on parameters required by the carpet mechanism. Because these disastereomers exhibit several advantages over their all-L amino acid counterparts, they have a potential to be developed for therapeutic use both in vitro and in vivo.